EP1165792A2

EP1165792A2 - Plant centromeres

Info

Publication number: EP1165792A2
Application number: EP00916559A
Authority: EP
Inventors: Daphne Preuss; Gregory Copenhaver; Kevin Keith
Original assignee: University of Chicago
Current assignee: University of Chicago
Priority date: 1999-03-18
Filing date: 2000-03-17
Publication date: 2002-01-02
Also published as: WO2000055325A3; JP2004512806A; WO2000055325A2; BR0009119A; CA2904855A1; WO2000055325A9; JP2011125354A; CA2362897A1

Abstract

The present invention provides for the identification and cloning of functional plant centromeres in Arabidopsis. This will permit construction of stably inherited minichromosomes which can serve as vectors for the construction of transgenic plant and animal cells. In addition, information on the structure and function of these regions will prove valuable in isolating additional centrometric and centromere related genetic elements and polypeptides from other species.

Description

PLANT CHROMOSOME COMPOSITIONS AND METHODS

BACKGROUND OF THE INVENTION

This application claims the priority of U S Piowsional Application Sei No 60/125.219 filed March 18, 1999 U S Provisional Application Ser No 60/127 409 filed April 1. 1999. U S Provisional Application Ser No 60/134,770. filed May 18 1999, U S Provisional Application Ser No 60/153.584 filed September 13, 1999 U S Provisional Application Ser No 60/154 603 filed September 17 1999 and U S

Provisional Application Ser No — / . filed December 16, 1999 each of which disclosures is specifically incorporated herein by reference in its entirety

The government owns rights in the invention pursuant to U S Department of Agriculture Grant No 96-35304-3491 National Science Foundation Grant No 9872641 and Grant No DOEDE-FG05-920R22072 from the Consortium for Plant Biotechnology

I. Field of the Invention

The present invention relates generally to the field of molecular biology More particularly it concerns plant chromosome compositions and methods for using the same

II. Description of Related Art Two general approaches are used for introduction of new genetic information

(' transformation") into cells One approach is to introduce the new genetic information as part of another DNA molecule, referred to as a vector which can be maintained as an independent unit (an episome) apart from the chromosomal DNA molecule(s) Episomal vectors contain all the necessary DNA sequence elements required for DNA replication and maintenance of the vector within the cell Many episomal vectors are available for use in bacterial cells (for example see Maniatis et al 1982) Howevei only a few episomal vectors that function in higher eukaryotic cells have been developed The available higher eukaryotic episomal vectors are based on naturally occurring viruses and most function only in mammalian cells (Willard 1997) In higher plant systems the only known double-stranded DNA viruses that replicate through a double-stranded intermediate upon which an episomal vector could be based is the gemini virus, although the gemini virus is limited to an approximately 800 bp insert Although an episomal plant vector based on the Cauliflower Mosaic Vnus has been developed, its capacity to carry new genetic information also is limited (Bπsson et al , 1984).

The other general method of genetic transformation involves integration of introduced DNA sequences into the recipient cell's chromosomes, permitting the new information to be replicated and partitioned to the cell's progeny as a part of the natural chromosomes The most common form of integrative transformation is called "transfection" and is frequently used in mammalian cell culture systems Transfection involves introduction of relatively large quantities of deproteinized DNA into cells The introduced DNA usually is broken and joined together in various combinations before it is integrated at random sites into the cell's chromosome (see. for example Wigler er ^/., 1977) Common problems with this procedure are the rearrangement of introduced DNA sequences and unpredictable levels of expression due to the location of the transgene in the genome or so called "position effect variation^"' (Shingo et al , 1986). Further, unlike episomal DNA. integrated DNA cannot normally be precisely removed A more refined form of integrative transformation can be achieved by exploiting naturally occurring viruses that integrate into the host's chromosomes as part of their life cycle. such as retroviruses (see Cepko et al . 1984) In mouse, homologous integration has recently become common, although it is significantly moie difficult to use in plants (Lam et al 1996)

The most common genetic transformation method used in higher plants is based on the transfer of bacterial DNA into plant chromosomes that occurs during infection by the phytopathogenic soil bacterium Agrobactermm (see Nester et al , 1984) By substituting genes of interest for the naturally transferred bacterial sequences (called T-DNA). investigators have been able to introduce new DNA into plant cells However, even this more "refined" integrative transformation system is limited in three major ways First. DNA sequences introduced into plant cells using the Agrobactermm T-DNA system are frequently rearranged (see Jones et l., 1987). Second, the expression of the introduced DNA sequences varies between individual transformants (see Jones et l., 1985). This variability is presumably caused by rearranged sequences and the influence of surrounding sequences in the plant chromosome (i.e., position effects), as well as methylation of the transgene. A third drawback of the Agrobacterium T-DNA system is the reliance on a "gene addition" mechanism: the new genetic information is added to the genome (i.e., all the genetic information a cell possesses) but does not replace information already present in the genome.

One attractive alternative to commonly used methods of transformation is the use of an artificial chromosome. Artificial chromosomes are man-made linear or circular DNA molecules constructed from cis-acting DNA sequence elements that are responsible for the proper replication and partitioning of natural chromosomes (see Murray et al., 1983). Desired elements include: ( 1 ) Autonomous Replication Sequences (ARS) (these have properties of replication origins, which are the sites for initiation of DNA replication), (2) Centromeres (site of kinetochore assembly and responsible for proper distribution of replicated chromosomes at mitosis or meiosis), and (3) Telomeres (specialized DNA structures at the ends of linear chromosomes that function to stabilize the ends and facilitate the complete replication of the extreme termini of the DNA molecule).

At present, the essential chromosomal elements for construction of artificial chromosomes have been precisely characterized only from lower eukaryotic species. ARSs have been isolated from unicellular fungi, including Saccharomyces cerevisiae (brewer's yeast) and Schizosaccharomyces pombe (see Stinchcomb et al., 1979 and Hsiao et al., 1979). An ARS behaves like a replication origin allowing DNA molecules that contain the ARS to be replicated as an episome after introduction into the cell nuclei of these fungi. Plasmids containing these sequences replicate, but in the absence of a centromere they are partitioned randomly into daughter cells. Artificial chromosomes have been constructed in yeast using the thiee cloned essential chromosomal elements Murray et al 1983. disclose a cloning system based on the in vitro constiuction of linear DNA molecules that can be transformed into yeast where they are maintained as artificial chromosomes These yeast artificial chromosomes (YACs) contain cloned genes, origins of replication centromeres and telomeres and are segregated in daughter cells with high fidelity when the YAC is at least 100 kB in length Smaller CEN containing vectors may be stably segregated, however, when in circular form

None of the essential components identified in unicellular organisms, however, function in higher eukaryotic systems For example, a yeast CEN sequence will not confer stable inheritance upon vectors transformed into higher eukaryotes While such DNA fragments can be readily introduced they do not stably exist as episomes in the host cell This has seriously hampered efforts to produce artificial chromosomes in higher organisms

In one case, a plant artificial chromosome was discussed (Richards et al U S Patent No 5.270.201 ) However, this vector was based on plant telomeres. as a functional plant centromere was not disclosed While telomeres are important in maintaining the stability of chromosomal termini they do not encode the information needed to ensure stable inheritance of an artificial chromosome It is well documented that centromere function is crucial for stable chromosomal inheritance in almost all eukaryotic organisms (reviewed in Nicklas 1988) For example, broken chromosomes that lack a centromere (acentric chromosomes) are rapidly lost from cell lines while fragments that have a centromere are faithfully segregated The centromere accomplishes this by attaching via centromere binding proteins to the spindle fibers during mitosis and meiosis, thus ensuring proper gene segregation during cell divisions

In contrast to the detailed studies done in -S ιsιae and S pombe. little is known about the molecular structure of functional centromenc DNA of hisher eukaryotes Ultrastructural studies indicate that higher eukaryotic kinetochores which are specialized complexes of proteins that form on the chromosome during late prophase, are large structures (mammalian kinetochoie plates aie approximately 0 3 μm in diameter) which possess multiple microtubule attachment sites (reviewed in Rieder 1982) It is therefore possible that the centromeπc DNA regions of these organisms will be correspondingly large although the minimal amount of DNA necessary for centromere function may be much smaller

While the above studies have been useful in elucidating the structure and function of centromeres, they have failed to provide a cloned centromere from a higher eukaryotic organism The extensive literature indicating both the necessity of centromeres for stable inheritance of chromosomes and the non-functionality of yeast centromeres in higher organisms demonstrate that cloning of a functional centromere from a higher eukaryote is a necessary first step in the production of artificial chromosomes suitable for use in higher plants and animals The production of artificial chromosomes with centromeres which function in higher eukaryotes would overcome many of the problems associated with the prior art and represent a significant breakthrough in biotechnology research

SUMMARY OF THE INVENTION

In one aspect of the invention a method is provided for the identification of plant centromeres In one embodiment of the invention the method may comprise tetrad analysis Briefly, tetrad analysis measures the recombination frequency between genetic makers and a centromere by analyzing all four products of individual meiosis A particular advantage arises from the cμiat tet (qi t 1) mutation in Arabidopsis, which causes the four products of pollen mother cell meiosis in Ai abidop i to remain attached The cμiaitet mutation may also find use in accordance with the invention in species other than Aiahidopsis For example, several naturally occurring plant species are also known to release pollen clusters including water lilies cattails heath (Eπcaceae and Epaci idceae) evening primrose (Onaeiaceae) sundew s (Dioseiaceae) orchids (Orchidaceae) and acacias (Mimosaceae) (Preuss 1994: Smyth 1994). None of these species however, has been developed into an experimental systems thus severely limiting their use for genetic analysis Howev er, it is contemplated by the inventors that a cμiai tct mutation could be introduced into a host plant to enable the use of tetrad analysis in potentially any species When used to pollinate a flower, one tetrad can result in the formation of four seeds, and the plants from these seeds can be analyzed genetically. With unordered tetrads, however, such as those produced by Arabidopsis, genetic mapping using tetrad analysis requires that two markers be scored simultaneously.

In another aspect, the invention provides a recombinant DNA construct comprising a plant centromere The recombinant DNA construct may additionally comprise any other desired sequences, for example, a telomere. including a plant telomere such as an Arabidopsis thaliana telomere. or alternatively, a yeast or any other type of telomere One may also desire to include an autonomous replicating sequence (ARS), such as a plant ARS, including an Arabidopsis thaliana ARS. Still further, one may wish to include a structural gene on the construct, or multiple genes (for example, two. three, four. five. six. seven, eight, nine, ten. fifteen, twenty, twenty-five, fifty, one hundred, two hundred, five hundred, one thousand) up to and including the maximum number of structural genes (roughly 5000) which can physically be placed on the recombinant DNA construct Examples of structural genes one may wish to use include a selectable or screenable marker gene, an antibiotic resistance gene, a herbicide resistance gene, a nitrogen fixation gene, a plant pathogen defense gene, a plant stre.ss-induced gene, a toxin gene, a receptor gene, a ligand gene, a hormone gene, an enzyme gene, an interleukin gene, a clotting factor gene, a cytokine gene, an antibody gene, a growth factor gene and a seed storage gene In one embodiment of the invention, the construct is capable of expressing the structural gene, for example, in a prokaryote oi eukaryote, including a lower eukaryote. or a higher eukaryote such as a plant

In yet another aspect, the invention provides a recombinant DNA construct comprising a plant centromere and which is a plasmid The plasmid may contain any desired sequences, such as an origin of replication, including an origin of replication functions in bacteria, such as E. coli and Agrobactermm, or in plants or yeast, for example, such as S cerevisiae The plasmid may also comprises a selection marker, which may function in bacteria, including E. coli and Agrobactermm. as well as a selection marker that functions in plants or yeast, such as 5 cerevisiae.

In still yet another aspect, the invention provides a recombinant DNA construct comprising a plant centromere and which is capable of being maintained as a chromosome, wherein the chromosome is transmitted in dividing cells. The plant centromere may be from any plant.

In still yet another aspect, the invention provides a plant centromere which is further defined as an Arabidopsis thaliana centromere. In yet another embodiment of the invention, the plant centromere is an Arabidopsis thaliana chromosome 1 centromere. and may still further be defined as flanked by the genetic markers T22C23-T7 and T3P8-SP6, or still further as flanked by the genetic markers T22C23-T7 and T5D18, T22C23-T7 and T3L4, T5D18 and T3P8-SP6, T5D 18 and T3L4, and T3L4 and T3P8-SP6. In yet another embodiment of the invention, the plant centromere comprises an Arabidopsis thaliana chromosome 2 centromere The chromosome 2 centromere may comprise, for example, from about 100 to about 61 1.000. about 500 to about 61 1.000, about 1.000 to about 61 1.000, about 10.000 to about 61 1.000. about 20.000 to about 61 1.000. about 40.000 to about 61 1.000, about 80.000 to about 61 1.000, about 150.000 to about 61 1 ,000. or about 300,000 to about 61 1.000 contiguous nucleotides of the nucleic acid sequence of SEQ ID NO:209. including comprising the nucleic acid sequence of SEQ ID NO:209 The centromere may also be defined as comprising from about 100 to about 50,959. about 500 to about 50.959, about 1.000 to about 50.959, about 5,000 to about 50.959. about 10.000 to about 50.959. 20.000 to about 50.959. about 30.000 to about 50.959. or about 40,000 to about 50.959 contiguous nucleotides of the nucleic acid sequence of SEQ ID NO:210. and may comprise the nucleic acid sequence of SEQ ID NO:210. The centromere may comprise sequences from both SEQ ID NOS.209 and 210. including the aforementioned fragments, or the entirety of SEQ ID NOS 209 and 210 In particular embodimemnts. the inventors contemplate a 3' fragment of SEQ ID NO 209 can be fused to a 5' fragment of SEQ ID NO 210. optionally including one or more 180 bp repeat sequence disposed therebetween

In still yet another aspect, the invention provides an Arabidopsis thaliana chromosome 3 centromere In one embodiment of the invention, the centromere may be further defined as flanked by the genetic markers T9G9-SP6 and T5M 14-SP6. and still further defined as flanked by a pair of genetic markeis selected from the group consisting of T9G9-SP6 and TI4H20. T9G9-SP6 and T7K14. T9G9-SP6 and T21P20. T14H20 and T7K14, T14H20 and T21P20, T 14H20 and T5M 14-SP6. T7K14 and T5M 14-SP6. T7K14 and T21P20. and T21P20 and T5M14-SP6

In still yet another aspect, the invention provides an Arabidopsis thaliana chromosome 4 centromere In certain embodiments of the invention, the centromere may comprise from about 100 to about 1.082.000. about 500 to about 1.082,000. about 1.000 to about 1.082,000. about 5,000 to about 1.082.000. about 10.000 to about 1.082.000. about 50,000 to about 1 ,082.000. about 100.000 to about 1,082,000, about 200.000 to about 1.082.000, about 400.000 to about 1.082,000, or about 800,000 to about 1 ,082,000 contiguous nucleotides of the nucleic acid sequence of SEQ ID NO 21 1. including comprising the nucleic acid sequence of SEQ ID NO 21 1 The centromere may also be defined as comprising from about 100 to about 163.317. about 500 to about 163.317. about 1.000 to about 163,317. about 5.000 to about 163.317, about 10,000 to about 163,317, about 30.000 to about 163.317, about 50.000 to about 163.3 17. about 80.000 to about 163.317, or about 120.000 to about 163.317 contiguous nucleotides of the nucleic acid sequence of SEQ ID N0.212. and may be defined as comprising the nucleic acid sequence of SEQ ID N0.212. The centromere may comprise sequences from both SEQ ID NOS 21 1 and 212. including the aforementioned fragments, or the entirety of SEQ ID NOS 21 1 and 212 In particular embodimemnts. the inventors contemplate a 3^' fragment of SEQ ID NO:21 1 can be fused to a 5' fragment of SEQ ID NO:212. optionally including one or more 180 bp repeat sequence disposed therebetween.

In yet another embodiment, there is provided a Arabidopsis thaliana chromosome 1 , 3 or 5 centromere selected from the nucleic acid sequence given by SEQ ID NO: 184. SEQ ID NO: 185. SEQ ID NO: 186. SEQ ID NO: 187, SEQ ID NO: 188. SEQ ID NO: 189. SEQ ID NO: 190. SEQ ID NO: 191. SEQ ID NO- 192. SEQ ID NO: 193. SEQ ID NO.194. SEQ ID NO: 195. SEQ ID NO: 196. SEQ ID NO: 197. SEQ ID NO: 198. SEQ ID NO: 199. SEQ ID NO:200. SEQ ID NO:201. SEQ ID NO:202. SEQ ID NO:203. SEQ ID NO:204, SEQ ID NO:205, SEQ ID NO:206. SEQ ID NO:207, SEQ ID NO:208. or fragments thereof. In one embodiment, the construct comprises at least 100 base pairs, up to an including the full length, of one of the preceding sequences. In addition, the construct may include 1 or more 180 base pair repeats.

In still yet another aspect, the invention provides an Arabidopsis thaliana chromosome 5 centromere. The centromere may be further defined as flanked by the genetic markers F13K20-T7 and CUE 1. and still further defined as flanked by a pair of genetic markers selected from the group consisting of F13K20-T7 and T 18M4. F13K20-T7 and T18F2. F13K20-T7 and T24I20, T18M4 and T18F2. T18M4 and T24I20. T18M4 and CUE1. T 18F2 and T24I20. T 18F2 and CUE 1. and T24I20 and CUE1.

In still yet another aspect, the invention provides a recombinant DNA construct comprising a plant centromere, and further defined as comprising n copies of a repeated nucleotide sequence, wherein n is at least 2 Potentially any number of repeat copies capable of physically being placed on the recombinant construct could be included on the construct, including about 5. 10. 15. 20. 30. 50. 75. 100. 150. 200. 300. 400. 500. 750. 1.000. 1.500. 2,000. 3.000. 5.000. 7.500. 10.000. 20.000. 30.000. 40.000. 50.000. 60.000. 70.000. 80.000. 90,000 and about 100.000. including all ranges in-between such copy numbers In one embodiment the repeated nucleotide sequence may be isolatable from the nucleic acid sequence given by SEQ ID NO: 184, SEQ ID NO: 185. SEQ ID NO: 186. SEQ ID NO: 187. SEQ ID NO: 188. SEQ ID NO: 189. SEQ ID NO: 190. SEQ ID NO: 191. SEQ ID NO: 192. SEQ ID NO: 193. SEQ ID NO: 194. SEQ ID NO: 195. SEQ ID NO: 196. SEQ ID NO: 197. SEQ ID NO: 198. SEQ ID NO: 199. SEQ ID NO:200. SEQ ID NO:201. SEQ ID NO:202. SEQ ID NO:203. SEQ ID NO:204. SEQ ID NO:205, SEQ ID NO:206, SEQ ID NO:207. SEQ ID NO:208. SEQ ID NO:209, SEQ ID NO:210. SEQ ID NO:21 1 or SEQ ID NO:212. Examples of such sequences that could be used are given in FIGs. 23A-23D. The length of the repeat used may vary, but will preferably range from about 20 bp to about 250 bp, from about 50 bp to about 225 bp, from about 75 bp to about 210 bp. from about 100 bp to about 205 bp, from about 125 bp to about 200 bp. from about 150 bp to about 195 bp. from about 160 bp to about 190 and from about 170 bp to about 185 bp including about 180 bp.

In conjunction with SEQ ID NOS:209. 210. 21 1 and 212. the repeats may be included as part of centromeric structures. The number of repeats may vary and include 1. 2, 3. 4. 5. 6. 7. 8. 9. 10, 1 1. 12. 13, 14, 15. 16, 17. 18, 19. 20. 21. 22. 23. 24. 25, 30. 35. 40. 45. 50. 60. 70. 80. 90. 100. 125, 150. 175. 200. 300. 400. 500 or more.

In still yet another aspect, the invention provides a minichromosome vector comprising a plant centromere and a telomere sequence. Any additional desired sequences may be added to the minichromosome. such as an autonomous replicating sequence, a second telomere sequence and a structural gene. One or more of the foregoing sequences may be added . up to the maximum number of such sequences that can physically be placed on the minichromosome. The minichromosome may comprise any of the centromere compositions disclosed herein. In one embodiment of the invention, the minichromosome may comprise a nucleic acid sequence selected from the group consisting of SEQ ID NO: 1. SEQ ID NO:2, SEQ ID NO:3. SEQ ID NO:4. SEQ ID

NO:5. SEQ ID NO:6. SEQ ID NO:7. SEQ ID NO:8. SEQ ID NO:9. SEQ ID NO: 10. SEQ

ID NO: l l . SEQ ID NO: 12. SEQ ID NO: 13. SEQ ID NO: 14. SEQ TD NO: 15. SEQ ID NO: 16. SEQ ID NO: 17. SEQ ID NO: 18. SEQ ID NO: 19. SEQ ID NO:20. and SEQ ID NO.21 The minichromosome also may contain "negative^" selectable markers which confer susceptibility to an antibiotic, herbicide 01 other agent, thereby allowing tor selection against plants, plant cells or cells of any othei organism of interest containing a minichromosome The minichromosome also mav include genes which control the copy number of the minichromosome within a cell One or more structural genes also may be included in the minichromosome Specifically contemplated as being useful will be as many structural genes as may be inserted into the minichromosome while still maintaining a functional vector. This may include one. two. three, four, five. six. seven, eight, nine or more structural genes

In still yet another aspect, the invention prov ides a recombinant DNA construct comprising a plant centromere. The cell may be of any type, including a prokaryotic cell or eukaryotic cell Where the cell is a eukaryotic cell, the cell may be. foi example, a yeast cell or a higher eukaryotic cell, such as plant cell The plant cell may be from a dicotyledonous plant, such as tobacco, tomato, potato, soybean, canola. sunflower, alfalfa. cotton and Arabidopsis. or may be a monocotyledonous plant cell, such as wheat, maize, rye. rice, turfgrass. oat. barley, sorghum, millet, and sugarcane In one embodiment of the invention, the plant centromere is an Arabidopsis thaliana centromere, and the cell may be an Arabidopsis thaliana cell. The recombinant DNA construct may comprise additional sequences, such as a telomere. an autonomous replicating sequence (ARS). a structural gene, or a selectable or screenable marker gene, including as many of such sequences as may physically be placed on said recombinant DNA construct. In one embodiment of the invention, the cell is further defined as capable of expressing said

.structural gene In another embodiment of the invention, a plant is provided comprising the aforementioned cells

In still yet another aspect, the invention provides a method of preparing a transgenic plant cell compnsmg contacting a starting plant cell with a recombinant DNA construct comprising a plant centromere, whereby said starting plant cell is transformed with said recombinant DNA construct The recombinant DNA construct may comprise any desired sequences such as manv structuial genes as can physically be placed on said lecombinant DNA construct In particular embodiments the centromere is an Aiabidopsis thaliana centiomeie. and the plant cell may be an Aiabidopsis thaliana cell

In still yet another aspect, the invention provides a tiansgenic plant comprising a minichromosome vectoi , wherein the v ector comprises a plant centromere and a telomere sequence The minichromosome vector may further comprise an autonomous replicating sequence, second telomere sequence, or a structural gene, such as an antibiotic resistance gene, a herbicide resistance gene, a nitrogen fixation gene, a plant pathogen defense gene. a plant stress-induced gene, a toxin gene, a receptor gene, a ligand gene, a seed stoiage gene a hormone gene, an enzyme gene, an interleukin gene a clotting factor gene, a cytokine gene, an antibody gene, and a growth factor gene As many of such sequences may be included as can physically be placed on the minichromosome The minichromosome vector may further comprise a nucleic acid sequence selected from the group consisting of SEQ ID NO 1 , SEQ ID NO 2, SEQ ID NO 3, SEQ ID NO 4, SEQ ID NO 5 SEQ ID NO 6. SEQ ID NO 7. SEQ ID NO 8 SEQ ID NO 9. SEQ ID NO 10 SEQ ID NO 1 1. SEQ ID NO 12, SEQ ID NO 13. SEQ ID NO 14. SEQ ID NO 15. SEQ ID NO 16. SEQ ID NO 17. SEQ ID NO 18 SEQ ID NO 19 SEQ ID NO 20 and SEQ ID NO 21 The transgenic plant may be any type of plant such as a dicotyledonous plant for example, tobacco, tomato, potato pea, carrot, cauliflower, broccoli, soybean canola sunflower, alfalta cotton and Aiabidopsis or may be a monocotyledonous plant such as wheat maize, rye. rice turfgrass, oat barlev- sorghum, millet, and sugarcane

In still yet another aspect, the invention provides a method of producing a minichromosome vector comprising (a) obtaining a first vector and a second vector wherein said first vector oi said second vector comprises a selectable or screenable marker, an origin of replication a telomere, and a plant centromere and wherein said first vector and said second vector comprises a site for site-specific recombination and (b) contacting said first v ector with said second v ectoi to allow site-specific recombination to occur between said site for site-specific recombination on said first vector and said site for site-specific recombination on said second vector to create a minichromosome vector comprising said selectable or screenable marker, said origin of replication, said telomere and said plant centromere. The contacting may be done in vitro or /; vivo, including wherein the contacting is carried out in a prokaryotic cell such as an Agrobcicterium or E. coli cell, or in a lower eukaryotic cell, such as a yeast cell. The contacting may still further be carried out in a higher eukaryotic cell, such as a plant cell, including an Arabidopsis thaliana cell. The contacting may be done in the presence of potentially any recombinase. including Cre, Flp, Gin, Pin, Sre, pinD, Int-B 13. and R. The first vector or second vector may comprise border sequences for Agrobacterium-mediated transformation. In one embodiment of the invention, the plant centromere is an Arabidopsis thaliana centromere. The telomere may be a plant telomere. Any plant selectable or screenable marker could be used, including GFP. GUS, BAR, PAT, HPT or NPTII.

In still yet another aspect, a method is provided of screening a candidate centromere sequence for plant centromere activity, said method comprising the steps of: (a) obtaining an isolated nucleic acid sequence comprising a candidate centromere sequence: (b) integratively transforming plant cells with said isolated nucleic acid: and (c) screening for centromere activity of said candidate centromere sequence. In the method, the screening may comprise ob.serving a phenotypic effect present in the integratively transformed plant cells or plants comprising the plant cells, wherein the phenotypic effect is absent in a control plant cell not integratively transformed with said isolated nucleic acid sequence, or a plant comprising said control plant cell. Types of phenotypic effects that could be screened for include reduced viability, reduced efficiency of said transforming, genetic instability in the integratively transformed nucleic acid, aberrant plant sectors, increased ploidy, aneuploidy, and increased integrative transformation in distal or centromeric chromosome regions. The isolated nucleic acid sequence may comprise a bacterial artificial chromosome, which may be further defined as a binary bacterial artificial chromosome. The integratively transforming may comprise use of any type of transformation, such as Agrohacterimn- edinted transformation. In one embodiment of the invention, the control plant cell has been integratively transformed with a nucleic acid sequence other than a candidate centromere sequence

In still yet another aspect, the invention provides a iecombinant DNA construct comprising an Arabidopsis polyubiquitin 1 1 promoter, wherein the promotei comprises from about 25 to about 2.000 contiguous nucleotides of the nucleic acid sequence of SEQ ID NO 180 In further embodiments of the invention, the promoter may comprise from about 75 to about 2.000, from about 125 to about 2.000. from about 200 to about 2.000. from about 400 to about 2,000. from about 800 to about 2.000, from about 1 ,000 to about 2.000, or from about 1 ,500 to about 200 contiguous nucleotides of the nucleic acid sequence of SEQ ID NO 180, or may comprise the nucleic acid sequence of SEQ ID NO.180. The promoter containing construct may comprise any additional desired sequences, for example, that of an enhancer, a telomere sequence, a plant centromere sequence, an ARS, or a structural gene, including an antibiotic resistance gene, a herbicide resistance gene, a nitrogen fixation gene, a plant pathogen defense gene, a plant stress-induced gene, a toxin gene, a receptor gene, a ligand gene, a seed storage gene, a hormone gene, an enzyme gene, an interleukin gene, a clotting factor gene, a cytokine gene, an antibody gene, and a growth factor gene In one embodiment of the invention, the promoter may be operably linked to the 5^' end of the structuial gene

In still yet another aspect, the invention provides a recombinant DNA construct comprising an Aiabidopsis 40S πbosomal protein S 16 promoter, wherein said promoter comprises from about 25 to about 2.000 contiguous nucleotides of the nucleic acid sequence of SEQ ID NO 182 In particular embodiments of the invention, the promotei may comprise from about 75 to about 2.000. from about 125 to about 2.000. from about 200 to about 2.000. from about 400 to about 2.000. from about 800 to about 2,000. from about 1 ,000 to about 2.000 or from about 1500 to about 2.000 contiguous nucleotides of the nucleic acid sequence of SEQ ID NO 182. or may comprise the nucleic acid sequence of SEQ ID NO 182 The promoter containing construct may comprise any additional desiied sequences, for example, that of an enhancer, a telomere sequence, a plant

3- centromeie sequence, an ARS. or a structural gene, including an antibiotic resistance gene, a herbicide resistance gene, a nitrogen fixation gene, a plant pathogen defense gene, a plant stress-induced gene, a toxin gene, a receptoi gene, a ligand gene, a seed storage gene, a hormone gene, an enzyme gene, an interleukin gene, a clotting factoi gene, a cytokine gene, an antibody gene, and a growth factor gene In one embodiment of the invention, the promoter may be operably linked to the 5^' end of the structural gene.

In still yet another aspect, the invention provides a recombinant DNA construct comprising an Arabidopsis polyubiquitin 1 1 3^' regulatory sequence including the terminator sequence, wherein the 3^' regulatory sequence comprises from about 25 to about 2001 contiguous nucleotides of the nucleic acid sequence of SEQ ID NO: 181. In one embodiment of the invention, the 3^' regulatory sequence may be further defined as comprising from about 75 to about 2001. from about 125 to about 2001 , from about 200 to about 2001. from about 400 to about 2001. from about 800 to about 2001 , or from about 1,000 to about 2001 contiguous nucleotides of the nucleic acid sequence of SEQ ID NO' 181 , and may comprise the nucleic acid sequence of SEQ ID NO: 181 The recombinant sequence may further comprise any other sequence, for example, an enhancer, a telomere sequence, a plant centromere sequence, an ARS, and a structural gene, including an antibiotic resistance gene, a herbicide resistance gene, a nitrogen fixation gene, a plant pathogen defense gene, a plant stress-induced gene, a toxin gene, a receptor gene, a ligand gene, a seed storage gene, a hormone gene, an enzyme gene, an interleukin gene, a clotting factor gene, a cytokine gene, an antibody gene, and a growth factor gene. In one embodiment of the invention, the terminator may be operably linked to the 3' end of the structural gene.

In still yet another aspect, the invention provides a recombinant DNA construct comprising an Arabidopsis 40S πbosomal protein S 16 3^' regulatory sequence including the terminator sequence, wherein the 3' regulatory sequence comprises from about 25 to about 2.000 contiguous nucleotides of the nucleic acid sequence of SEQ ID NO. 183. In particular embodiments of the invention, the 3^' regulatory sequence may comprise from about 75 to about 2.000, from about 125 to about 2,000. from about 200 to about 2.000, from about 400 to about 2,000. from about 800 to about 2,000, or from about 1.000 to about 2.000 contiguous nucleotides of the nucleic acid sequence of SEQ ID NO: 183. and may comprise the nucleic acid sequence of SEQ ID NO: 183. The recombinant sequence may further comprise any other sequence, for example, an enhancer, a telomere sequence, a plant centromere sequence, an ARS, and a structural gene, including an antibiotic- resistance gene, a herbicide resistance gene, a nitrogen fixation gene, a plant pathogen defense gene, a plant stress-induced gene, a toxin gene, a receptor gene, a ligand gene, a seed storage gene, a hormone gene, an enzyme gene, an interleukin gene, a clotting factor gene, a cytokine gene, an antibody gene, and a growth factor gene. In one embodiment of the invention, the terminator may be operably linked to the 3' end of the structural gene.

In still yet another aspect, the invention provides methods for expressing foreign genes in plants, plant cells or cells of any other organism of interest. The foreign genes may be from any organism, including plants, animals and bacteria. It is further contemplated that minichromosomes could be used to simultaneously transfer multiple foreign genes to a plant comprising entire biochemical or regulatory pathways. In yet another embodiment of the invention, it is contemplated that the minichromosomes can be used as DNA cloning vectors. Such a vector could be used in plant and animal sequencing projects. The current invention may be of particular use in the cloning of sequences which are "unclonable^" in yeast and bacteria, but which may be easier to clone in a plant based system.

In still yet another aspect of the invention, it is contemplated that the minichromosomes disclosed herein may be used to clone functional segments of DNA such as origins of DNA replication, telomeres, telomere associated genes, nuclear matrix attachment regions (MARs), scaffold attachment regions (SARs), boundary elements, enhancers, silencers, promoters, recombinational hot-spots and centromeres. This embodiment may be carried out by cloning DNA into a defective minichromosome which is deficient for one or more type of functional elements. Sequences which complement such deficient elements would cause the minichromosome to be stably inherited A selectable or screenable marker on the minichromosome could then be used to select foi viable minichromosome containing cells which contain cloned functional elements of the type that weie non-functional in the defective minichromosome

In still yet another aspect of the invention, the sequences disclosed herein may be used for the isolation of centromeπc sequences from plants other than Arabidopsis Such techniques may employ, for example, hybridization or sequence-based analysis In one embodiment of the invention, the centromere may be isolated from agriculturally important species such as. for example, vegetable crops, including artichokes, kohlrabi, arugula, leeks, asparagus, lettuce (e g , head, leaf, romaine). bok choy. malanga. broccoli, melons (e.g . muskmelon. watermelon, crenshaw, honeydew. cantaloupe), brussels sprouts, cabbage, cardoni carrots, napa. cauliflower, okra. onions, celery, parsley, chick peas, parsnips, chicory. Chinese cabbage, peppers, collards. potatoes, cucumber plants (marrows, cucumbers), pumpkins, cucurbits, radishes, dry bulb onions, rutabaga, eggplant, salsify, escarole. shallots, endive, garlic, spinach, green onions, squash, greens, beet (sugar beet and fodder beet), sweet potatoes, swiss chard, horseradish, tomatoes, kale, turnips, and spices Alterantively, centromeres could be isolated from fruit and vine crops such as apples, apricots, cherries, nectarines, peaches, pears, plums, prunes, quince almonds, chestnuts, filberts, pecans, pistachios walnuts, citrus, blueberries, boysenberπes. cranberries, currants, loganberries, raspberries, strawberries, blackberries, grapes, avocados, bananas kiwi, persimmons pomegranate, pineapple, tropical fruits. pomes, melon, mango, papaya, and lychee

In still yet another aspect of the invention, centromeres could be isolated in accordance with the invention from field crop plants, such as evening primrose, meadow foam, corn (field, sweet popcorn), hops. jo|oba. peanuts rice, safflower small grains (barley, oats. rye. wheat, etc ). sorghum, tobacco, kapok, leguminous plants (beans, lentils, peas, soybeans), oil plants (rape, mustard, poppy, olives, sunfloweis. coconut. castor oil plants, cocoa beans, groundnuts), fibre plants (cotton flax. hemp. |ute). lauraceae (cinnamon, camphor), or plants such as coffee, sugarcane, tea. and natural rubber plants. Still other examples of plants from which centromeres could be isolated include bedding plants such as flowers, cactus, succulents and ornamental plants, as well as trees such as forest (broad-leaved trees and evergreens, such as conifers), fruit. ornamental, and nut-bearing trees, as well as shrubs and other nursery stock.

In still yet another aspect of the invention, the minichromosome vectors described herein may be used to perform efficient gene replacement studies. At present, gene replacement has been detected on only a few occasions in plant systems and has only been detected at low frequency in mammalian tissue culture systems (see Thomas et al., 1986; Smithies et al., 1985) The reason for this is the high frequency of illegitimate nonhomologous recombination events relative to the frequency of homologous recombination events (the latter are responsible for gene replacement) Artificial chromosomes may participate in homologous recombination preferentially. Since the artificial chromosomes remain intact upon delivery, no recombinogenic broken ends will be generated to serve as substrates for the extremely efficient illegitimate recombination machinery. Thus, the artificial chromosome vectors disclosed by the present invention will be maintained in the nucleus through meiosis and available to participate in homology-dependent meiotic recombination In addition, because in principle, artificial chromosomes of any length could be constructed using the teaching of the present invention, the vectors could be used to introduce extremely long stretches of DNA from the same or any other organism into cells. Specifically contemplated inserts include those from about several base pans to one hundred megabase pans, including about 1 kb, 25 kB. 50 kB, 100 kB, 125 kB, 150 kB. 200 kB. 300 kB. 400 kB. 500 kB. 600 kB, 700 kB. 800 B. 900 kB. 1 MB. 1.25 Mb. 1.5 Mb. 2 Mb, 3 Mb. 5 Mb, 10 Mb. 25 Mb. 50 Mb and 100 Mb

In still yet another aspect, the present invention provides methods for the construction of minichromosome vectors for the genetic transformation of plant cells. uses of the vectors, and organisms transformed by them. Standard reference works setting forth the general principles of recombinant DNA technology include Lewin 1985 Other works describe methods and products of genetic engineering See, e g Maniatis et al 1982 Watson et al 1983 Setlow et al 1979 and Dillon et al 1985

In still yet another aspect the inv ention provides a method of preparing a transgenic cell In one embodiment of the invention the method comprises the steps of a ) obtaining a nucleic acid molecule comprising Aiabidopsis thaliana centromere DNA having the following characteristics 1 ) mapping to a location on an Arabidopsis thaliana chromosome defined by a pair of genetic markers selected from the group consisting of mι342 and T27K 12 mι310 and g4133, atpox and ATA mι233 and mι l67, and F13K20- t7 and CUE1 , and 2 ) sorts DNA to the spindle poles in meiosis 1 in a pattern indicating the disjunction of homologous chromosomes b) preparing a recombinant construct comprising said nucleic acid molecule and c) transforming a recipient cell with said recombinant construct

The cell may be, for example a lower eukaryotic cell including a yeast cell, or may be a higher eukaryotic cell Where the cell is a higher eukaryotic cell, the cell may be an animal or plant cell In one embodiment of the invention, the cell is not an Arabidopsis thaliana cell In another embodiment of the invention, the Arabidopsis thaliana centromere is defined by the marker pair mι342 and T27K12 which may be further defined by the genetic marker pair T22C23-t7 and T3P8-sp6, and / or is defined by the marker pair mι310 and g4133 which may be fuithei defined by the genetic marker pair F5J 15-sp6 and T15D9 and / or is defined by the marker pair atpox and ATA which may be further defined by the genetic marker pair T9G9-sp6 and T5M 14-sp6. and / or is defined by the marker pair mι233 and mi 167 which may be further defined by the genetic marker pair T24H24 30k3 and F13H 14-t7 and / or is defined by the genetic marker pair F13K20-t7 and CUE 1 which may be further defined by a genetic marker pair selected from the group consisting of F13K20-T7 and T18M4 F13K20-T7 and T18F2 F13K20-T7 and T24I20 T 18M4 and T 18F2 T18M4 and T24I20 T 18M4 and CUE1 T 18F2 and T24I20 T 18F2 and CUE l and T24I20 and CUE 1 In one embodiment of the invention, the transforming may comprise use of a method selected from the group consisting of Agrobacteriiim- ediated transformation, protoplast transfoimation. electroporation. or particle bombardment The recombinant construct may comprise desired elements, including a telomere. such as an Arabidopsis thaliana or yeast telomere. The recombinant construct may also comprise an autonomous replicating sequence (ARS). for example, an Arabidopsis thaliana ARS The recombinant construct may also comprise a prokaryotic or eukaryotic selectable or screenable marker gene. Also desired to include with a recombinant construct may be one or more structural genes Exemplary structural genes include a gene selected from the group consisting of an antibiotic resistance gene, a herbicide resistance gene, a nitrogen fixation gene, a plant pathogen defense gene, a plant stress-induced gene, a toxin gene, a seed storage gene, a hormone gene, an enzyme gene, an interleukin gene, a clotting factor gene, a cytokine gene, an antibody gene, and a growth factor gene. The method may further comprise the step of regenerating a transgenic plant from said cell

In still yet another aspect, the invention provides a method of identifying a nucleic acid molecule capable of conferring centromere activity comprising the steps of: a) obtaining a nucleic acid molecule comprising Arabidopsis thaliana centromere DNA. wherein the Arabidopsis thaliana centromere is defined by a pair of genetic markers selected from the group consisting of mι342 and T27K 12. mι310 and g4133, atpox and ATA. mι233 and mι l67. and F13K20-t7 and T17M l l-sp6. b) preparing a recombinant construct that comprises the nucleic acid molecule, and c) determining the ability of the recombinant construct to demonstrate a stable inheritance pattern In the method, the ability to demonstrate a stable inheritance pattern may be determined by preparing a recombinant cell that comprises the recombinant construct. In another embodiment of the invention, the Arabidopsis thaliana centromere is defined by the marker pair mι342 and T27K12. which may be further defined by the genetic marker pair T22C23-t7 and T3P8-sp6. and / or is defined by the marker pair mι310 and g4133, which may be further defined by the genetic marker pair F5J 15-sp6 and T 15D9. and / or is defined by the marker pair atpox and ATA. which may be further defined by the genetic marker pair T9G9-sp6 and T5M 14-sp6. and / or is defined by the markei pair mι233 and mi 167, which may be further defined by the genetic marker pan T24H24 30k3 and F13H !4-t7. and / or is defined by the genetic marker pair F13K20-t7 and CUE1. which may be further defined bv a genetic marker pair selected from the group consisting of F13K20-T7 and T18M4. F13K20-T7 and T18F2, F13K20-T7 and T24I20. T18M4 and T18F2. T18M4 and T24I20, T 18M4 and CUE1 , T18F2 and T24I20, T18F2 and CUE 1. and T24I20 and CUEl .

In one embodiment of the invention, the recombinant construct is not chromosomally integrated Said obtaining may comprise obtaining a BAC or YAC clone comprising said Arabidopsis thaliana centromere DNA The DNA may be obtained by a method that includes the use of pulsed-field gel electrophoresis. and may be obtained by a method that includes positional cloning. In another embodiment of the invention, the positional cloning may comprise identifying a contiguous set of clones comprising said Arabidopsis thaliana centromere DNA. wherein said set of clones is flanked by a pair of genetic markers selected from the group consisting of mι342 and T27K12. mι310 and g4133. atpox and ATA. mι233 and mi 167. and F13K20-t7 and T17M 1 l-sp6

The contiguous set of clones may span the Arabidopsis thaliana centromeie The recombinant construct may comprise a selectable or screenable marker and said step of determining may comprise determining a phenotype conferred by the selectable oi screenable marker The determining may comprise, for example, determining the ability of the recombinant construct to demonstrate a stable inheritance pattern in mitosis and / or meiosis. In still another embodiment, the invention provides a transgenic cell prepared by a method provided by the invention Also provided by the invention aie a transgenic plant, plant parts and tissue cultures comprising the transgenic cell In anothei embodiment of the invention, the Aiabidopsis thaliana centromere is defined by the marker pair mι342 and T27K12. which may be further defined by the genetic maiker pair T22C23-t7 and T3P8-sp6. and / or is defined by the marker pair mι310 and g4133. which

-09- may be further defined by the genetic marker pair F5J 15-sp6 and T15D9: and / or is defined by the marker pair atpox and ATA. which may be further defined by the genetic marker pair T9G9-sp6 and T5M 14-sp6: and / or is defined by the marker pair mi233 and mi 167. which may be further defined by the genetic marker pair T24H24.30k3 and F13H 14-t7: and / or is defined by the genetic marker pair F13K20-t7 and CUE 1. which may be further defined by a genetic marker pair selected from the group consisting of F13K20-T7 and T18M4, F13K20-T7 and T 18F2. F13K20-T7 and T24I20, T18M4 and T18F2, T18M4 and T24I20, T18M4 and CUE 1 , T18F2 and T24I20. T18F2 and CUE1, and T24I20 and CUEl .

In still yet another aspect of the invention, a centromere used in accordance with the invention is not from Arabidopsis, for example, from Arabidopsis thaliana. Similarly, a plant or plant cell comprising a centromere composition in accordance with the invention, may also be from a plant other than Arabidopsis.

BRIEF DESCRIPTION OF THE DRAWINGS

The following drawings form part of the present specification and are included to further demonstrate certain aspects of the present invention. The invention may be better understood by reference to one or more of these drawings in combination with the detailed description of specific embodiments presented herein. The file of this patent contains at least one drawing executed in color. Copies of this patent with color drawing(s) will be provided by the Patent and Trademark Office upon request and payment of the necessary fee.

FIG. 1. Centromere mapping with unordered tetrads: A cross of two parents (AABB x aabb). in which "A" is on the centromere of one chromosome, and "B" is linked to the centromere of a second chromosome. At meiosis, the A and B chromosomes assort independently, resulting in equivalent numbers of parental ditype (PD) and nonparental ditype (NPD) tetrads (recombinant progeny are shown in gray). Tetratype tetrads (TT) result only from a crossover between "B^" and the centromere.

FIG. 2. Low resolution map location of Arabidopsis centromeres. Trisomic mapping was used to determine the map position of centromeres on four of the five Arabidopsis chromosomes (Koornneef, 1983: Sears et al.. 1970). For chromosome 4. useful trisomic strains were not obtained. With the methods of Koornneef and Sears et al, 1983. (which rely on low-resolution deletion mapping) the centromere on chromosome 1 was found to lie between the two visible markers, ttl and chl, that are separated by 5 cM. Centromere positions on the other chromosomes are mapped to a lower resolution.

FIG. 3. Physical maps of the genetically-defined Arabidopsis centromeres. Each centromeric region is drawn to scale; physical sizes are derived from DNA sequencing (chromosomes II and IV) or from estimates based on BAC fingerprinting (Marra er /., 1999; Mozo et al, 1999) (chromosomes I, III. and V). Indicated for each chromosome are positions of markers (above), the number of tetratype / total tetrads at those markers (below), the boundaries of the centromere (thick black bars), and the name of contigs derived from fingerprint analysis (Marra et al, 1999; Mozo et al, 1999). For each contig, more than two genetic markers, developed from the database of BAC-end sequences (http://www.tigr.org/tdb/at/abe bac_end_search.html) were scored. PCR primers corresponding to these sequences were used to identify size or restriction site polymorphisms in the Columbia and Landsberg ecotypes (Bell and Ecker, 1994: Konieczny and Ausubel. 1993); primer sequences are available (http://genome-wwvv.stanford.edu/Arabidopsis/aboutcaps.html). Tetratype tetrads resulting from treatments that stimulate crossing over (boxes); positions of markers in centimorgans (cM) shared with the recombinant inbred (RI) map (ovals) (http://nasc.nott.ac.uk/new_ri_map.html: Somerville and Somerville, 1999); and sequences bordering gaps in the physical map that correspond to 180 bp repeats (open circles) (Round et al . 1997). 5S rDNA (black circles) or 160 bp repeats (gray cucles) uie indicated (Copenhaver et al , 1999)

FIG. 4. Exemplary list of seed stock used foi tetiad analysis in Aiabidopsis thaliana The individual strains are identified by the strain number (column B) The tetrad member number (column A) indicates the tetrad souice (i e . T l indicates seeds from tetrad number 1 , and the numbers - 1. -2, -3 or -4 indicate individual membeis of the tetrad) The strains listed have been deposited with the Aiabidopsis Biological Resources Centei (ABRC) at Ohio State University undei the name of Daphne Preuss

FIG. 5. Marker information for centromere mapping DNA polymorphisms used to localize the centromeres are indicated by chromosome (Column 1 ) The name of each marker is shown in Column 2 the name of the markers used by Copenhaver et al 1999 to position centromeres is given in Column 3 and marker type is indicated in Column 4 CAPS (Co-dominant Amplified Polymorphic Sites) are markers that can be amplified with PCR and detected by digesting with the appropriate restriction enzyme (also indicated in Column 3) SSLPs (Simple Sequence Length Polymorphisms) detect polymorphisms by amplifying different length PCR products Column 5 notes if the marker is available on public web sites (e http //genome-www Stanford edu/ Arabidopsis) For those markers that are not available on public web sites the sequences of the foiwaid and reverse primers used to amplify the marker aie listed in columns 6 and 7 respectively

FIG. 6. Scoring PCR-based markers for tetrad analysis The genotype of the progeny from one pollen tetrad (T2 > was determined tor two genetic markers (S0392 and nga76) Analysis of the four progeny plants (T2- 1 through T2-4) using PCR and gel electrophoresis allows the genotype of the plant to be deteimined. and the genotype of the pollen parent to be interred FIG. 7A-7N. Exemplary Minichromosome vectors: The vectors shown in FIG. 7A, FIG. 7B, FIG. 7E, FIG. 7F, FIG. 71 and FIG. 7J have an E. coli origin of replication which can be high copy number, low copy number or single copy. In FIGS. 7A-7N. the vectors include a multiple cloning site which can contain recognition sequences for conventional restriction endonucleases with 4-8 bp specificity as well as recognition sequences for very rare cutting enzymes such as, for example. I-Ppo I. I-Cue I, PI-Tli, PI-Psp I, Not I, and PI See I. In FIG. 7A-7N, the centromere is flanked by Lox sites which can act as targets for the site specific recombinase Cre. FIG. 7A. Shows an E. coli plant circular shuttle vector with a plant ARS. FIG. 7B. Shows a plant circular vector without a plant ARS. The vector relies on a plant origin of replication function found in other plant DNA sequences such as selectable or screenable markers. FIG. 7C. Shows a yeast-plant circular shuttle vector with a plant ARS. The yeast ARS is included twice, once on either side of multiple cloning site to ensure that large inserts are stable. FIG. 7D. Shows a yeast-plant circular shuttle vector without a plant ARS. The vector relies on a plant origin of replication function found in other plant DNA sequences such as selectable markers. The yeast ARS is included twice, once on either side of the multiple cloning site to ensure that large inserts are stable. FIG. 7E. Shows an E. coli-Agrobacteriitm-plani circular shuttle vector with a plant ARS. Vir functions for T-DNA transfer would be provided in trans by a using the appropriate Agrobαcterium strain. FIG. 7F. Shows an E. coli-Agrohαcteriitm-planl circular shuttle vector without a plant ARS. The vector relies on a plant origin of replication function found in other plant DNA sequences such as selectable markers. Vir functions for T-DNA transfer would be provided in trans by a using the appropriate Agrobαcterium strain. FIG. 7G. Shows a linear plant vector with a plant ARS. The linear vector could be assembled in vitro and then transferred into the plant by, for example, mechanical means such as micro projectile bombardment, electroporation, or PEG-mediated transformation. FIG. 7H. Shows a linear plant vector without a plant ARS. The linear vector could be assembled in vitro and then transferred into the plant by, for example, mechanical means such as micro projectile bombardment, electroporation. or PEG-mediated transformation. FIGs. 7I-7N. The figures are identical to FIGs. 7A-7F, respectively, with the exception that they do not contain plant telomeres These vectors will remain circular once delivered into the plant cell and therefore do not require telomeres to stabilize their ends

FIG. 8. Sequence teatuies at CEN2 (A) and CEN 4 (B) Central bars depict annotated genomic sequence of indicated BAC clones, black, genetically-defined centromeres, white regions flanking the centromeres Sequences corresponding to genes and repetitive features, filled boxes (above and below the bars, respectively), are defined as in FIG 12A-T, predicted nonmobile genes, red genes carried by mobile elements, black, nonmobile pseudogenes, pink, pseudogenes carried by mobile elements, gray. retroelements, yellow, transposons, green, previously defined centromenc repeats, dark blue 180 bp repeats, pale blue Chromosome-specific centromere features include a large mitochondπal DNA insertion (orange CEN2). and a novel array of tandem repeats (purple, CEN4) Gaps in the physical maps (//). unannotated regions (hatched boxes), and expressed genes (filled circles) are shown

FIG. 9. Method for converting a BAC clone (or any other bacterial clone) into a minichromosome A portion of the conversion vector will integrate into the BAC clone (or other bacterial clone of interest) either through non-homologous recombination (transposable element mediated) or by the action of a site specific recombinase system such as Cre-Lox or FLP-FRT

FIG. 10. Method for analysis of diccntπc chromosomes in Aiabidopsis BiBAC vectors containing centromeie fragments (- 100 kb) are integrated into the Aiabidopsis genome using A robactermm-medialed transformation procedures and studied for adverse affects due to formation of dicentπc chromosomes 1) BiBACs containing centromere fragments are identified using standard protocols 2) Plant transformation 3) Analysis of detects in growth and development of plants containing dicentπc chromosomes FIG. 11A-G. Method for converting a BAC clone (or any other bacterial clone) into a minichromosome. The necessary selectable markers and origins of replication for propagation of genetic material in E. coli. Agrohacterium and Arabidopsis as well as the necessary genetic loci for Agrohacterium mediated transformation into Arabidopsis are cloned into a conversion vector. Using Cre/loxP recombination, the conversion vectors are recombined into BACs containing centromere fragments to form minichromosomes.

FIG. 12A-T. Properties of centromeric regions on chromosomes II and IV. (Top) Drawing of genetically-defined centromeres (gray shading, CEN2, left: CEN4, right), adjacent pericentromeric DNA. and a distal segment of each chromosome, scaled in Mb as determined by DNA sequencing (gaps in the grey shading correspond to gaps in the physical maps). Positions in cM on the RI map (http://nasc.nott.ac.uk/new_ri_map.html) and physical distances in Mb, beginning at the northern telomere and at the centromeric gap, are shown. (Bottom) The density of each feature (FIGs. 12A-12T) is plotted relative to the position on the chromosome in Mb. (FIG. 12A, 12K) cM positions for markers on the RI map (solid squares) and a curve representing the genomic average of 1 cM/221 kb (dashed line). A single crossover within CEN4 in the RI mapping population (http://nasc.nott.ac.uk/new_ri_map.html: Somerville and Somerville, 1999) may reflect a difference between male meiotic recombination monitored here and recombination in female meiosis. (FIGs. 12B-12E and FIGs. 12L-120) The % of DNA occupied by repetitive elements was calculated for a 100 kb window whh a sliding interval of 10 kb. (FIGs. 12B, 12L) 180 bp repeats: (FIGs. 12C. 12M) sequences with similarity to retroelements, including del, Tal , Tal l , copia, Athila, LINE, Ty3, TSCL, 106B (Athila-like), Tat l . LTRs and Cinful: (FIGs. 12D, 12N) sequences with similarity to transposons, including Tagl, En/Spm. Ac/Ds, Tam l MuDR, Limpet. MITES and Mariner: (FIGs. 12E, 120) previously described centromeric repeats including 163 A. 164A, 164B. 278A, 1 1 B7RE, mι l 67. pAT27, 160-. 180- and 500-bp repeats, and telomeric sequences (Murata et al. 1997: Heslop-Harrison et al, 1999 Brandes et fl/., 1997; Franz et al. 1998: Wright et al, 1996; Konieczny et al, 1991 Pelissier et a/.. 1995: Voytas and Ausubel. 1988: Chye et f//., 1997: Tsay et <://., 1993 Richards et al. 1991 ; Simoens et al. 1988; Thompson et al, 1996: Pelissier et al, 1996 Franz et al, 1998: Pelissier et al, 1995; Voytas and Ausubel. 1988; Thompson et al, 1996). (FIGs. 12F, 12P) % adenosine + thymidine was calculated for a 50 kb window with a sliding interval of 25 kb (FIGs. 12G-12J, 12Q-12T). The number of predicted genes or pseudogenes was plotted over a window of 100 kb with a sliding interval of 10 kb. (FIGs. 12G, 121, 12Q, 12S> predicted genes (FIGs. 12G, 12Q) and pseudogenes (FIGs. 121, 12S) typically not found on mobile DNA elements: (FIGs. 12H, 12J, 12R, 12T) predicted genes (FIGs. 12H, 12R) and pseudogenes (FIGs. 12,1, 12T) often carried on mobile DNA, including reverse transcriptase, transposase. and retroviral polyproteins. Dashed lines indicate regions in which sequencing or annotation is in progress, annotation was obtained from GenBank records

(http://www.ncbi.nlm.nih.gov/Entrez/nucleotide.html), from the AGAD database (http://www.tigr.org/tdb/at/agad .), and by BLAST comparisons to the database of repetitive Arabidopsis sequences (http://nucleus.cshl.org/protarab/AtRepBase.htm); though updates to annotation records may change individual entries, the overall structure of the region will not be significantly altered.

FIG. 13. Methods for converting a BAC clone containing centromere DNA into a minichromosome for introduction into plant cells. The specific elements described are provided for exemplary purposes and are not limiting. A) diagram of the BAC clone, noting the position of the centromere DNA (red), a site-specific recombination site (for example, lox P). and the F origin of replication. B) Conversion vector containing selectable and color markers (for example. 35S-Bar, nptll, LAT52-GUS. Scarecrow- GFP), telomeres, a site-specific recombination site (for example, lox P), antibiotic resistance markers (for example, amp or spc/str). Agrohacterium T-DNA borders (Agro Left and Right) and origin of replication (RiA4). C) The product of site specific recombination with the Cre recombinase at the lox P sites yields a circular product with centromeric DNA and markers flanked by telomeres. D) Minichromosome immediately after transformation into plants: subsequently, the left and right borders will likely be removed bv the plant cell and additional telomeric sequence added by the plant telomerase

FIG. 14A-B. Conservation of centromere DNA BAC clones (bars) used to sequence CEN2 (FIG. 14A) and CEN4 (FIG. 14B) are indicated, arrows denote the boundaries of the genetically-defined centromeres PCR primer pans yielding products from only Columbia (filled circles) or from both Landsberg and Columbia (open circles). BACs encoding DNA with homology to the mitochondπal genome (gray bars), 180 bp repeats (gray boxes), unsequenced DNA (dashed lines), and gaps in the physical map (double slashes) are shown

FIG. 15A-B. Primers used to analyze conservation of centromere sequences in the A thaliana Columbia and Landsberg ecotvpes FIG. 15A: Primers used for amplification of chromosome 2 sequences FIG. 15B: Primers used for amplification of chromosome 4 sequences

FIG. 16. Sequences common to CEN2 and CEN4 Genetically-defined centromeres (bold lines), sequenced (thin lines), and unannotated (dashed lines) BAC clones are displayed as in FIG 14A, B Repeats AtCCS l (A thaliana centromere conserved sequence) and AtCCS2 (closed and open circles, respectively), AtCCS3 (triangles), and AtCCS4-7 (4-7. respectively) are indicated (GenBank Accession numbers AF204874 to AF204880). and were identified using BLAST 2 0 (http //blast wustl edu)

FIG. 17. Sequenced BAC clones from centromere 2 The sequenced BAC clones are indicated by the horizontal lines near the top of the figure (see for example T14A4) The red box denotes the boundaries of centromere 2. and for the BAC clones that comprise the centromere. GenBank Accession numbers are given in the lower right panel The contiguous sequences within the red box aie given by SEQ ID NO 209 and SEQ ID NO 210 Horizontal lines below the sequenced clones indicate additional BAC clones. sequenced end points of these BACs are indicated with a closed circle Clones with one or more endpoints that aie undetermined are indicated by led text

FIG. 18. Sequenced BAC clones from centiomere 4 The sequenced BAC clones from centromeie 4 are indicated by the horizontal lines near the top of the figure (see for example T24M8) The red box denotes the boundaries of centromere 4 and for the BAC clones that comprise the centromere GenBank Accession numbers are given in the lower right panel The contiguous sequences w ithin the red box are given by SEQ ID NO 21 1 and SEQ ID NO 212 Horizontal lines below the sequenced clones indicate additional BAC clones, sequenced end points of these BACs are indicated with a closed circle Clones with one or more endpoints that are undetermined are indicated by red text

FIG. 19. Sequence tiling path of centromeres 1 3 and 5 The boundaries of these centromeres was determined as described in Copenhaver et al ( 1999) Contig numbers refer to the fingerprint contigs assembled by Marra et al ( 1999) Some of these clones have been sequenced and accession numbers are provided (see attached list) In other cases sequencing will be finished bv the Aiabidopsis genome project

FIG. 20. Position of DNA from centiomere 2 earned in BiBAC vectors Clones were placed on the physical map by fingerprint and PCR analysis and comparison with the sequenced BAC clones

FIG. 21. Exemplary methods tor adding selectable oi screenable markers to BiBAC clones The desired marker is flanked by transposon borders and incubated with the BiBAC in the presence of transposase Subsequently the BiBAC is introduced into plants Often these BiBACs may integrate into natural chromosome, creating a dicentπc chromosome which may have altered stability and mav cause chromosome breakage resulting in novel chromosome fiagments FIG. 22. Assay of chromosome stability The stability of natural chromosomes, constructed minichromosome. or dicentπc chromosomes can be assessed by monitoring the assoitment of coloi maikers thiough cell div ision The markei s are linked to the centromere in modified BAC or BiBAC vectors and introduced into plants Regulation of the marker gene by an appropriate promoter determines which tissues will be assayed For example, root-specific promotei s, such as SCARECROW make it possible to monitor assortment in files of root cells, post-meiotic pollen-specific promoters such as LAT52 allow monitoring of assortment through meiosis, and general promoters such as the 35S Cauliflower mosaic virus promoter make it possible to monitor assortment in many other plant tissues Qualitative assays assess the general pattern of stability and measure the size of sectors corresponding to marker loss, while quantitative assays require knowledge of cell lineage and allow the number of chromosome loss events to be calculated during mitosis and meiosis

FIG. 23A-D. Sequence alignments for 180 bp repeats from centromeres 1 -4 The left hand column indicates the BAC source of the repeat copy and an arbitrarily assigned number given to the sequence For example, the designation fl 2g6-l indicates a repeat copy from BAC number f 12g6 and arbitrarily given a repeat number of 1 The nucleic acid sequences of the BACs containing the repeat copies, designated fl 2g6, f5al 3, t25fl5. t l2j2, tl4c8, t6c20. f21ι2. and f6h8 are given by SEQ ID NO 184. SEQ ID NO 191. SEQ ID NO 189, SEQ ID NO 205. SEQ ID NO 206. SEQ ID NO 186 SEQ ID NO 208 and SEQ ID NO 207. respectively FIG. 23A Alignment of 180 bp repeats from centromere 1 FIG. 23B Alignment of 180 bp repeats from centromere 2 FIG. 23C Alignment of 180 bp repeats from centromere 3 FIG. 23D Alignment of 180 bp repeats from centromere 4

DETAILED DESCRIPTION OF THE INVENTION

The inventors have overcome the deficiencies in the prior art by providing, for the first time, the nucleic acid sequence of a plant chromosome The significance of this achievement relative to the prior art is exemplified by the general lack of detailed information in the art regarding the centromeres of multicellular organisms in geneial To date, the most extensiv e and reliable charactenzation of centromere sequences has come from studies of low er eukaryotes such as S. cerevisiae and S. pombe. wheie the ability to analyze centromere functions has provided a clear picture of the desired DNA sequences The S. cere\ ιsιae centromere consists of three essential regions, CDEI. CDEII, and CDEIII, totaling only 125 bp, or approximately 0.006 to 0.06% of each yeast chromosome (Carbon et al, 1990; Bloom 1993). 5. pombe centromeres are between 40 and 100 kB in length and consist of repetitive elements that comprise 1 to 3% of each chromosome (Baum et al, 1994). Subsequent studies, using tetrad analysis to follow the segregation of artificial chromosomes, demonstrated that less than 1/5 of the naturally occurring S. pombe centromere is sufficient for centromere function (Baum et al , 1994)

In contrast, the centromeres of mammals and other higher eukaryotes are poorly defined Although DNA fragments that hybridize to centromeric regions in higher eukaryotes have been identified, little is known regarding the functionality of these sequences (see Tyler-Smith et al, 1993) In many cases centromere repeats correlate with centromere location, with probes to the repeats mapping both cytologically and genetically to centromere regions Many of these sequences are tandemly-repeated satellite elements and dispersed repeated sequences in arrays ranging from 300 kB to 5000 kB in length (Willard 1990) To date, only one of these repeats, a 171 bp element known as the alphoid satellite, has been shown by in situ hybridization to be present at each human centromere (Tyler-Smith et al , 1993) Whether repeats themselves repiesent functional centromeres remains controversial, as othei genomic DNA is requned to confer inheritance upon a region of DNA (Willard. 1997). Alternatively, the positions of some higher eukaryotic centromeres have been estimated by analyzing the segregation of chromosome fragments. This approach is imprecise, however, because a limited set of fragments can be obtained, and because normal centromere function is influenced by surrounding chromosomal sequences (for example, see Koornneef. 1983: FIG 2) A more precise method for mapping centromeres that can be used in intact chromosomes is tetrad analysis (Mortimer et al. 1981 ). which provides a functional definition of a centromere in its nativ e chromosomal context. At present, the only centromeres that have been mapped in this manner are from lower eukaryotes. including the yeasts Saccharomyces cerevisiae, Schizosaccharoimces pombe, and Kluyveromyces lactis (Carbon et al, 1990; Hegemann et al , 1993) In these systems, accurate mapping of the centromeres made it possible to clone centromeric DNA. using a chromosome walking strategy (Clarke et al, 1980). Subsequently, artificial chromosome assays were used to define more precisely the centromere sequences (Hegemann et al. 1993. Baum t fl/., 1994).

Attempts to develop a reliable centromeric assay in mammals have yielded ambiguous results For example. Hadlaczky et al . ( 1991 ) identified a 14 kB human fragment that can. at low frequency, result in de o centromere formation in a mouse cell line. In situ hybridization studies, however, hav e shown that this fragment is absent from naturally occurring centromeres, calling into question the reliability of this approach for testing centromere function (Tyler-Smith et al . 1993) Similarly, transfection of alphoid satellites into cell lines results in the formation of new chromosomes, yet these chromosomes also contain host sequences that could contribute centromere activity (Haaf et c// , 1992; Willard. 1997). Further, the novel chiomosomes can have alphoid DNA spread throughout their length yet have only a single centromeric constriction, indicating that a block of alphoid DNA alone may be insufficient for centromere function (Tyler-Smith et al. 1993)

Although plant centromeres can be visualized easily in condensed chromosomes, they have not been characterized as extensively as centromeres from yeast or mammals Genetic characterization has relied on segregation analysis of chromosome fragments, and in particular on analysis of trisomic strains that carry a genetically marked, telocentπc fragment (for example, see Koornneef 1983. FIG 2 ) In addition, repetitive elements have been identified that are either genetically (Richards et al 1991 ) or physically (Alfenito et al , 1993. Maluszynska et al 1991 ) linked to a centromere In no case howe er, has the functional significance of these sequences been tested

Cytology in Aiabidopsis thaliana has served to coi relate centromere structuie with repeat sequences A fluorescent dye DAPI. allows visualization of centromeric chromatin domains in metaphase chromosomes A fluorescence //; situ hv bndization (FISH) probe based on 180 bp pALl repeat sequences colocahzed with the DAPI signature near the centromeres of all five Aiabidopsis chromosomes (Maluszynska et al , 1991 , Martinez-Zapater et al , 1986) Although a functional role for pALl has been proposed, more recent studies have failed to detect this sequence near the centromeres in species closely related to Aiabidopsis thaliana (Maluszynska et al 1993) These results are particularly troubling because one of the species tested, A pumila, is thought to be an amphidiploid. derived from a cross between A thaliana and another close relative (Maluszynska et al , 1991 , Price et al 1995) Another repetitiv e sequence pAtT12 has been genetically mapped to w ithin 5 cM of the centiomere on chromosome 1 and to the central region of chromosome 5 (Richards et al 1991). although its presence on other chromosomes has not been established Like pALl . a role for pAtT12 in centromere function remains to be demonstrated

Due to the fact that kinetochores constitute a necessary link between centromeric

DNA and the spindle apparatus the proteins that are associated with these structures recently have been the focus of intense investigation (Bloom 1993 Earnshaw 1991 ) Human autoantibodies that bind specifically in the vicinity of the centromere have facilitated the cloning of centromere-associated proteins (CENPs, Rattner 1991 ) and at least one of these proteins belongs to the kinesin superfamily of microtubule-based motors (Yen 1991 ) Yeast centromere-binding proteins also have been identified both through genetic and biochemical studies (Bloom 1993. Lechner et al 1991 )

The centromeres of Arabidopsis thaliana have been mapped using trisomic strains where the segregation of chromosome fragments (Koornneef 1983 ) oi whole chromosomes (Sears et al 1970) w as used to localize four of the centromeres to within 5 12 17 and 38 cM respectively (FIG 2) These positions have not been refined by moie iecent studies because the method is limited the difficulty of obtaining v iable trisomic strains (Koornneef 1983) These factors introduce significant error into the calculated position of the centromere and in Aiabidopsis where 1 cM coriesponds roughly to 200 kB (Koornneef 1987 Hwang et al 1991 ), this method did not map any of the centromeres with sufficient precision to make chromosome walking stiategies practical Mapping of the Arabidopsis genome was also discussed by (Hauge et al , 1991)

I. Tetrad Analysis

With tetrad analysis the recombination frequency between genetic markeis and a centromere can be measured directlv (FIG 1 ) This method requires analysis ol all foui products of individual meiosis and it has not been applied previously to multicellular eukaryotes because their meiotic products typically are dissociated Identification of the quaitet mutation makes tetrad analysis possible for the first time in a higher eukaryotic system (Preuss et al 1994) The quartet (qi t 1) mutation causes the four products of pollen mother cell meiosis in Aiabidopsis to remain attached When used to pollinate a flower one tetrad can result in the formation of four seeds and the plants from these seeds can be analyzed genetically

With unordered tetrads such as those pioduced by S ceievtsiae or Aiabidopsis genetic mapping using tetrad analysis requires that two markers be scored simultaneously (Whitehouse 1950) Tetrads fall into different classes depending on whether the markers are in a parental (nonrecombinant) or nonparental (recombinant) configuration (FIG 1 ) A tetrad with only nonrecombinant members is referred to as a parental ditype (PD) one with only recombinant members as a nonpaiental ditype (NPD) and a tetrad w ith two recombinant and two nonrecombinant members as a tetratype (TT) (Perkins 1953) If two genetic loci are on different chromosomes and thus assort independently, the equencv, of tetratype (crossover products) versus paiental oi nonparental assortment ditype (noncrossover products) depends on the frequency of crossover between each of the two loci and their respective centromeres.

Tetratype tetrads arise only when a crossover has occurred between a marker in question and its centromere. Thus, to identify genes that are closely linked to the centromere, markers are examined in a pair-wise fashion until the TT frequency approaches zero. The genetic distance (in centimorgans, cM) between the markers and their respective centromeres is defined by the function [( 1/2)TT]/100 (Mortimer et al, 1981 ). Because positional information obtained by tetrad analysis is a representation of physical distance between two points, as one approaches the centromere the chance of a recombination event declines.

Tetrad analysis has been used to genetically track centromeres in yeasts and other fungi in which products of a single meioses can be collected. The budding yeast Saccharomyces cerevisiae lacks mitotic condensation and thus cytogenetics (Hegemann et al, 1993), yet due to tetrad analysis, has served as the vehicle of discovery for centromere function. Meiosis is followed by the generation of four spores held within an ascus and these can be directly assayed for gene segregation.

The recessive qrtl mutation makes it possible to perform tetrad analysis in

Arabidopsis by causing the four products of meiosis to remain attached (Preuss et al, 1994; and Smythe 1994: both incorporated herein by reference). As previously shown, within each tetrad, genetic loci segregate in a 2:2 ratio (FIG. 6). Individual tetrads can be manipulated onto flowers with a fine brush (at a rate of 20 tetrads per hour), and in 30% of such crosses, four viable seeds can be obtained (Preuss et <;/., 1994).

Mapping centromeres with high precision requires a dense genetic map. and although the current Arabidopsis map contains many visible markers, it would be laborious to cross each into the qrti background. Alternatively, hundreds of DNA polymoφhi ms can be introduced simultaneously by crossing two different strains, both containing the qrtl mutation. A dense RFLP map (Chang et al, 1988) and PCR-based maps (Konieczny et al , 1993. Bell et al. 1994) hav e been generated in Arabidopsis from crosses of the Landsberg and Columbia strains (Arabidopsis map and genetic marker data is available from the internet at http://genome-vvww.stanford.edu/Arabidopsis and http://cbil.humgen.upenn.edu/atgc/sslp_info/sslp.html). These strains differ by 1 % at the DNA sequence level and have cohnear genetic maps (Chang et al, 1988; Koornneef. 1987).

Centromere mapping with tetrad analysis requires simultaneous analysis of two markers, one of which must be centromere-linked (FIG. 1 ) To identify these centromere-linked markers, markers distributed across all 5 chromosomes were scored and compared in a pairwise fashion.

Initially, genetic markers that can be scored by PCR analysis were tested

(Konieczny et al, 1993; Bell et al, 1994). Such markers are now sufficiently dense to map any locus an as additional PCR-detectable polymoφhisms are identified they are incoφorated into the analyses. In addition, as described in FIG. 5. new CAPS and SSLP markers useful for mapping the centromere can be readily identified.

A collection of Arabidopsis tetrad sets was prepared by the inventors for use in tetrad analysis. To date, progeny plants from > 1.000 isolated tetrad seed sets have been germinated and leaf tissue collected and stored from each of the tetrad piogeny plants The leaf tissue from individual plants was used to make DNA for PCR based marker analysis. The plants also were allowed to self-fertilize and the seed they produced was collected. From each of these individual seed sets, seedlings can be germinated and their tissues utilized for making genomic DNA Tissue pooled from multiple seedlings is useful for making Southern genomic DNA blots for the analysis of restriction fragment length polymoφhisms (RFLPs). An exemplary list of the seed stock of informative individuals used for tetrad analysis is gi en in FIG 4 II. Mapping Strategy

Previous DNA fingeφπnt and hybridization analysis of two bacterial artificial chromosome (BAC) libranes had led to the assembly of physical maps coveting neai ly all single-copy portions of the Arabidopsis genome (Marra et al , 1999) However, the presence of repetitive DNA near the Arabidopsis centromeres, including 180 bp repeats, retroelements. and middle repetitive sequences complicated efforts to anchor centromenc BAC contigs to particular chromosomes (Murata et c;/ , 1997; Heslop-Harπson et al, 1999. Brandes et «/., 1997; Franz et al, 1998. Wright et al , 1996; Komecznyet al . 1991 ; Pehssier et α/., 1995, Voytas and Ausubel. 1988, Chye t al, 1997: T say et al , 1993. Richards et al , 1991 : Simoens et al. 1988. Thompson et al, 1996: Pehssier et al . 1996)

The inventors used genetic mapping to unambiguously assign these unanchored contigs to specific centromeres, scoring polymoφhic markers in 48 plants with crossovers informative for the entire genome (Copenhaver et al, 1998). In this manner. several centromeric contigs were connected to the physical maps of^" the chromosome arms (see EXAMPLE 6). and a large set of DNA markers defining centromere boundaries were generated DNA sequence analysis confirmed the structure of the contigs for chromosomes II and IV (Lin et al. 1999)

CEN2 and CEN4 were selected in particular for analysis Both reside on structurally similar chromosomes with a 3 5 Mb rDNA arrays on their distal tips, with regions measuring 3 and 2 Mb. respectivelv . between the rDNA and centromeres, and 16 and 13 Mb regions on their long arms (Copenhaver and Pikaard. 1996)

The virtually complete and annotated sequence of chromosomes II and IV was used to conduct an analysis of centromeres at the nucleotide level (http7/www ncbi.nlm.nih gov Entrez/nucleotide html) The sequence composition was analyzed within the genetically-defined centromere boundaries and compared to the adjacent pericentromenc regions (FIGs 12A-T) Analysis of the two centromeres facilitated comparisons of sequence patterns and identification of conserved sequence elements

The centromere sequences were found to harbour 180 bp repeat sequences These sequences were found to reside in the gaps of each centromeric contig (FIG 3. FIGs 12B. 12L). with few repeats and no long arrays elsewhere in the genome BAC clones near these gaps have end sequences corresponding to repetitive elements that likely constitute the bulk of the DNA between the contigs, including 180 bp repeats, 5S rDNA or 160 bp repeats (FIG 3) Fluorescent in situ hybridization has shown these repetitive sequences are abundant components of Arabidopsis centromeres (Murata et al 1997. Heslop-Harπson et al , 1999. Brandes et al , 1997) Genetic mapping and pulsed-field gel electrophoresis indicate that many 180 bp repeats leside in long arrays measuπng between 0 4 and 1 4 Mb in the centromeric regions (Round et a! 1997), sequence analysis revealed additional interspersed copies near the gaps The inventors specifically contemplate the use of such 180 bp repeats for the construction of minichromosomes The annotated sequence of chromosomes II and IV identified regions with homology to middle repetitive DNA. both within the functional centromeres and in the adjacent regions (FIGs 12B- 12E and 12L- 120)

In a 4 3 Mb sequenced region that includes CEN2 and a 2 8 Mb sequenced region that includes CEN4. retrotransposon homology was found to account for > 10% of the DNA sequence, with a maximum of 62% and 70%, respectively (FIGs 12C. 12M) Sequences with similarity to transposons or middle repetitive elements were found to occupy a similar zone, but weie less common (29%e and 1 1 % maximum density for chromosomes II and IV respectively (FIGs 12D- 12E and FIG 12N-120) Finally, unlike in the case of Diosophila and Neuiospora centromeres (Sun et al 1997 Cambareπ et al , 1998) low complexity DNA. including microsatelhtes, homopolymei tracts, and AT rich isochores. were not found to be enriched in the centromeies of Arabidopsis Neai CEN2. simple repeat sequence densities were comparable to those on the distal chromosome arms, occupying 1 5% of the sequence within the centromere. 3 2% in the flanking regions, and ranging from 20 to 319 bp in length (71 bp on average) Except for an insertion of mitochondπal DNA at CEN2 the DNA in and around the centiomeres did not contain any large regions that deviated signif icantlv f iom the genomic average of - 64% A + T (FIGs 12F 12P) (Bevan et al , 1999)

Unlike the 180 bp repeats, all other lepetitive elements near CEN2 and CEN4 weie less abundant within the genetically-defined centromeres than in the flanking regions The high concentration of repetitive elements outside of the functional centromere domain suggest they may be insufficient for centromere activity Thus. identifying segments of the Arabidopsis genome that are enriched in these repetitive sequences does not pinpoint the regions that provide centromere function, a similar situation may occur in the genomes of other higher eukaryotes

The repetitive DNA flanking the centromeies may play an important role, forming an altered chromatin conformation that serves to nucleate or stabilize centromere structure Alternatively, other mechanisms could result in the accumulation of repetitive elements near centromeres Though evolutionary models predict lepetitive DNA accumulates in regions of low recombination (Charlesworth et al 1986, Charlesworth et al , 1994) many Arabidopsis repetitive elements are more abundant in the recombinationally active peπcentromeπc regions than in the centromeres themselves Instead, retroelements and other transposons may preferentially insert into regions flanking the centromeres or be eliminated from the rest of the genome at a higher rate

III. Centromere Compositions Certain aspects of the present invention concern isolated nucleic acid segments and recombinant vectors comprising a plant centromere In one embodiment of the invention, the plant centromere is an Aiabidopsis thaliana centromere In a further embodiment of the invention, nucleic acid sequences comprising an ,4 thaliana chromosome 2 centromere are provided The sequence of the Aiabidopsis thaliana chromosome 2 centromere is exemplified by the nucleic acid sequences of SEQ ID NO:209 and SEQ ID NO.210. As shown in FIG. 17. the nucleic acid sequences of SEQ ID NO.209 and SEQ ID NO 210 flank a series of 180 bp repeats in centromere 2 of A thaliana As such, the chromosome 2 centromeie may tuithei be defined as compnsmg n number of repeats linked to a nucleic acid sequence included in SEQ ID NO.209 or SEQ ID NO:210. or sequences isolated from both of those sequences In particular embodiments of the invention, the number of repeats (n). is about 2, 4. 8, 15, 25, 40. 70, 100. 200. 400. 600. 800, 1 ,000. 1.500. 2.000. 4.000, 6.000. 8000. 10,000. 30.000. 50.000 or about 100,000. The actual repeat sequence used may vary. Representative samples of repeat sequences that could be used are given in FIGs. 23A-23D and included in the nucleic acid sequences given by SEQ ID NOs 184-208 The length of the repeat used may also vary, and may include repeats of. for example, about 10 bp, 20 bp. 40 bp. 60 bp. 80 bp, 100 bp, 120 bp, 140 bp, 150 bp. 160 bp. 170 bp, 180 bp. 190 bp. or about 200 bp or larger or a repeat sequence, for example, as listed in FIG 23A-FIG 23D and included in the nucleic acid sequences given by SEQ ID NOs 184-208

Isolated segments of the nucleic acid sequences of SEQ ID NO:209 and SEQ ID NO:210 are also contemplated to be of use with the invention, either with or without being linked to a series of repeats. Particularly, contiguous nucleic acid segments of about 100. 200, 400. 800, 1 ,500. 3.000. 5.000, 7.500, 10.000, 15.000. 25.000. 40.000. 75.000. 100,000. 125.000. 150.000. 250.000. 350.000. 450.000. 600.000. 700.00 and about 800.000 bp of the nucleic acid sequences of SEQ ID NO 209 or SEQ ID NO.210 specifically form part of the instant inv ention In particular embodiments of the invention, such nucleic acid sequences may be linked to n number of repeated sequences, for example, where n is 2. 4, 8, 15. 25. 40. 70. 100, 200. 400, 600. 800. 1.000. 1.500. 2.000. 4.000. 6.000. 8000, 10.000. 50.000 or about 100.000 The repeat sequence may comprise, for example, about 10 bp. 20 bp. 40 bp. 60 bp. 80 bp. 100 bp. 120 bp. 140 bp. 150 bp. 160 bp. 170 bp. 180 bp. 190 bp. or about 200 bp or a larger segment of contiguous nucleotides of. for example, a repeat listed in FIG. 23A-FIG.23D and included in the nucleic acid sequences given by SEQ ID NOs 184-208

-4: In another embodiment of the invention, nucleic acid sequences comprising an A thaliana chromosome 4 centromere are provided The sequence of the Aiabidopsis thaliana chromosome 4 centromere is exemplif ied by the nucleic acid sequences of SEQ ID NO 21 1 and SEQ ID NO 212 As shown in FIG 18, the nucleic acid sequences of SEQ ID NO 21 1 and SEQ ID NO 212 in Arabidopsis flank a series of repeated sequences As such, the chromosome 4 centromere may further be defined as comprising n number of repeats linked to a nucleic acid sequence included in SEQ ID NO 21 1 or SEQ ID NO 212, or sequences from both SEQ ID NO.21 1 and SEQ ID NO 212 In particular embodiments of the invention, the number of repeats (n), is about 2. 4, 8. 15, 25. 40. 70, 100, 200, 400. 600, 800, 1 ,000, 1 ,500. 2.000. 4,000, 6,000, 8000. 10.000. 50,000. or about 100,000 The actual repeat sequence used may vary Representative samples of repeat sequences that could be used are given in FIGs 23A-23D wherein these sequences are included in the nucleic acid sequences given by SEQ ID NOs 184- 208 The length of the repeat used may also vary, and may include repeats of, tor example, about 10 bp. 20 bp, 40 bp. 60 bp. 80 bp, 100 bp. 120 bp. 140 bp. 150 bp. 160 bp, 170 bp. 180 bp, 190 bp. or about 200 bp or larger

Isolated segments of the nucleic acid sequences of SEQ ID NO 21 1 and SEQ ID NO 212 are also contemplated to be of use with the invention, either with or without being linked to a series of repeated sequences Particularly, contiguous nucleic acid segments of about 100, 200 400. 800. 1.500. 3,000, 5.000, 7.500. 10.000. 15.000 25.000 40.000, 75.000. 100.000. 125.000. 150.000, 250.000. 350.000. 450.000 600 000, 700.00 bp of the nucleic acid sequences of SEQ ID NO 21 1 or SEQ ID NO 212 specifically form part of the instant invention In particular embodiments of the invention, such nucleic acid sequences may be linked to n number of repeated sequences for example, where n is 2. 4. 8. 15. 25. 40. 70. 100. 200. 400. 600. 800. 1.000. 1.500. 2.000 4.000. 6,000, 8000. 10.000, 50,000 or about 100.000 The repeat sequence may comprise, for example, about 10 bp 20 bp. 40 bp. 60 bp. 80 bp. 100 bp. 120 bp. 140 bp. 150 bp 160 bp, 170 bp. 180 bp 190 bp. or about 200 bp or a larger segment of contiguous nucleotides of the sequence of SEQ ID NO 184-208 Also provided by the invention are regulatoiy regions from the Aiabidopsis polyubiquitin 1 1 gene including piomotei and terminator sequences thereof The nucleic acid sequences of these regulatory regions are exemplified by the nucleic acid sequences of SEQ ID NO 180 and SEQ ID NO 181 Also included with such sequences aie contiguous stretch of from about 10 15. 20, 25. 30 40. 50. 75. 100. 125. 150. 200. 300. 500, 750. 1 ,000. 1.500. and about 2.000 nucleotides of the nucleic acid sequence of SEQ ID NO 180 and SEQ ID NO 181 In particular embodiments of the invention it may be desirable to operably link the Arabidopsis polyubiquitin 1 1 promoter sequences to the 5' end of a coding sequence It may also be desiiable to operably link the Aiabidopsis polyubiquitin 1 1 terminator sequence to the 3^' end of a coding sequence

Still further provided by the invention are regulatory regions from the Aiabidopsis 40S πbosomal protein S 16 gene, including promoter and terminator sequences thereof The nucleic acid sequences of these regulatory regions are exemplified by the nucleic acid sequences of SEQ ID NO 182 and SEQ ID NO 183 Also included with such sequences are contiguous stretch of fiom about 10 15. 20. 25 30 40. 50 75. 100. 125, 150. 200. 300. 500 750. 1.000. 1.500. and about 2.000 nucleotides of the nucleic acid sequence of SEQ ID NO 182 and SEQ ID NO 183 In particular embodiments of the invention, it may be desirable to operably link the Arabidopsis 40S nbosomal protein S 16 gene sequences to the 5 end of a coding sequence It may also be desirable to operably link the Aiabidopsis 40S nbosomal protein S I 6 gene sequence to the 3 end of a coding sequence

Still further provided by the invention are gene sequences and related legulatory elements and sequences w ith other functions from centiomere regions In particular, the invention includes the centromeie sequences giv en by SEQ ID NO 1. SEQ ID NO 2 SEQ ID NO 3. SEQ ID NO 4 SEQ ID NO 5. SEQ ID NO 6. SEQ ID NO 7. SEQ ID NO 8 SEQ ID NO 9 SEQ ID NO 10. SEQ ID NO 1 1 SEQ ID NO 12 SEQ ID NO 1 . SEQ ID NO 14 SEQ ID NO 15 SEQ ID NO 16 SEQ ID NO 17 SEQ ID NO 18 SEQ ID NO.19, SEQ ID NO 20. and SEQ ID NO 21. as well as lengths of about 5. 10. 15. 20. 25. 30, 40, 50. 60. 70. 80, 90, 100. 1 10. 125. 150. 175. 200. 250. 300, 350. 400. 500. 550. 590. 1.000. and about 1.500 contiguous nucleotides of these sequences up to and including the full length of the sequences

Centromere-containing nucleic acid sequences may be provided with other sequences for the creation and use of recombinant minichromosomes Such nucleic acid sequences specifically within the scope of the invention include the nucleic acid sequences listed in the sequence listing provided herewith

The present invention concerns nucleic acid segments, isolatable from A thaliana cells, that are enriched relative to total genomic DNA or other nucleic acids and are capable of conferring centromere activity to a recombinant molecule when incoφorated into the host cell As used herein, the term ' nucleic acid segment" refers to a nucleic acid molecule that has been purified from total genomic nucleic acids of a particular species Therefore, a nucleic acid segment conferring centromere function refers to a nucleic acid segment that contains centromere sequences yet is isolated away from, or purified free from, total genomic nucleic acids of A thaliana Included within the term "nucleic acid segment", are nucleic acid segments and smaller fragments of such segments, and also recombinant vectoi s, including, for example, BACs. YACs, plasmids, cosmids, phage. viruses, and the like

Similarly, a nucleic acid segment comprising an isolated or purified centromeric sequence refers to a nucleic acid segment including centromere sequences and. in certain aspects, regulatory sequences, isolated substantially away from other naturally occurring sequences, or other nucleic acid sequences In this respect, the term "gene" is used for simplicity to refer to a functional nucleic acid segment, protein, polypeptide or peptide encoding unit As will be understood by those in the art. this functional term includes both genomic sequences, cDNA sequences and smaller engineered gene segments that may express, or may be adapted to express, proteins, polypeptides or peptides "Isolated substantially away from other sequences" means that the sequences of interest, in this case centromere sequences, are included within the genomic nucleic acid clones provided herein. Of course, this refers to the nucleic acid segment as originally isolated, and does not exclude genes or coding regions later added to the segment by the hand of man.

In particular embodiments, the invention concerns isolated nucleic acid segments and recombinant vectors incoφorating nucleic acid sequences that encode a centromere functional sequence that includes a contiguous sequence from the centromeres of the current invention. In certain other embodiments, the invention concerns isolated nucleic acid segments and recombinant vectors that include within their sequence a contiguous nucleic acid sequence from an A. thaliana centromere. Again, nucleic acid segments that exhibit centromere function activity will be most preferred.

The nucleic acid segments of the present invention, regardless of the length of the sequence itself, may be combined with other nucleic acid sequences, such as promoters, polyadenylation signals, additional restriction enzyme sites, multiple cloning sites, other coding segments, and the like, such that their overall length may vary considerably. It is therefore contemplated that a nucleic acid fragment of^" almost any length may be employed, with the total length preferably being limited by the ease of preparation and use in the intended recombinant DNA protocol.

(i) Primers and Probes In addition to their use in the construction of recombinant constructs, including minichromosomes, the nucleic acid sequences disclosed herein may find a variety of other uses. For example, the centromere sequences described herein may find use as probes or primers in nucleic acid hybridization embodiments. As such, it is contemplated that nucleic acid segments that comprise a sequence region that consists of at least a 14 nucleotide long contiguous sequence that has the same sequence as, or is complementary to, a 14 nucleotide long contiguous DNA segment of a centromere sequence of the current invention, for example, of the sequences given by SEQ ID NOS 1-212. and particularly. SEQ ID NOS 1 -21 and SEQ ID NOS' 180-212. will find particular utility Longer contiguous identical or complementaiy sequences, e.g . those of about 20. 30. 40. 50. 100, 200. 500, 1.000. 2.000. 5.000 bp. etc . including all intermediate lengths and up to and including the full-length sequence of the sequences given in SEQ ID NOS 1-212. also will be of use in certain embodiments.

As described in detail herein, the ability of such nucleic acid probes to specifically hybridize to centromeric sequences will enable them to be of use in detecting the presence of similar, partially complementary sequences from other plants or animals However, other uses are envisioned, including the use of the centromeres for the preparation of mutant species primers, or primers for use in preparing other genetic constructions

Nucleic acid fragments having sequence regions consisting of contiguous nucleotide stretches of 8, 9, 10. 1 1, 12. 13, 14, 15, 16, 17, 18, 19, 20, 21. 22, 23. 24, 25. 26, 27. 28, 29, 30, 31 , 32, 33, 34. 35. 36. 37. 38. 39, 40. 41. 42, 43. 44. 45, 46, 47. 48. 49. 50. 55, 60. 65. 70, 75. 80, 85, 90. 95. 100 or even of 101 -200 nucleotides or so. identical or complementary to a centromere sequence of the current invention, including the sequences given in SEQ ID NOS 1-212. are particularly contemplated as hybridization probes for use in, e g , Southern and Northern blotting Smaller fragments will generally find use in hybridization embodiments, wherein the length of the contiguous complementary region may be varied, such as between about 10- 14 and about 100 oi 200 nucleotides, but larger contiguous complementarity stretches also may be used, accoiding to the length complementary sequences one wishes to detect

Of course, fragments may also be obtained by other techniques such as. e g . by mechanical shearing or by restriction enzyme digestion Small nucleic acid segments or fragments may be readily prepared by. for example, directly synthesizing the fragment by chemical means, as is commonly practiced using an automated oligonucleotide synthesizer. Also, fragments may be obtained by application of nucleic acid reproduction technology, such as the PCR™ technology of U. S. Patents 4,683, 195 and 4.683,202 (each incoφorated herein by reference), by introducing selected sequences into recombinant vectors for recombinant production, and by other recombinant DNA techniques generally known to those of skill in the art of molecular biology.

Accordingly, the centromere sequences of the current invention may be used for their ability to selectively form duplex molecules with complementary stretches of DNA fragments. Depending on the application envisioned, one will desire to employ varying conditions of hybridization to achieve varying degrees of selectivity of probe towards target sequence. For applications requiring high selectivity, one will typically desire to employ relatively stringent conditions to form the hybrids, e.g., one will elect relatively low salt and/or high temperature conditions, such as provided by about 0.02 M to about 0.15 M NaCl at temperatures of about 50°C to about 70°C. Such selective conditions tolerate little, if any, mismatch between the probe and the template or target strand, and would be particularly suitable for isolating centromeric DNA segments. Nucleic acid sequences hybridizing under these conditions and the conditions below to the nucleic acid sequences provided by the invention, including those given by SEQ ID NOS: 1-212, form a part of the invention. Detection of nucleic acid segments via hybridization is well-known to those of skill in the art, and the teachings of U. S. Patents 4,965.188 and 5, 176,995 (each specifically incoφorated herein by reference in its entirety) are exemplary of the methods of hybridization analyses. Teachings such as those found in the texts of Ma y et al, 1991 ; Segal, 1976; Prokop, 1991 ; and Kuby. 1994. are particularly relevant.

Of course, for some applications, for example, where one desires to prepare mutants employing a mutant primer strand hybridized to an underlying template or where one seeks to isolate centromere function-conferring sequences from related species, functional equivalents, or the like, less stringent hybridization conditions will typically be needed in order to allow formation of the heteroduplex. In these circumstances, one may desire to employ conditions such as about 0 15 M to about 0 9 M salt, at temperatures ranging from about 20°C to about 55°C Cross-hybπdizing species can thereby be readily identified as positiv ely hybπdizing signals with respect to control hybridizations In anv case, it is generally appreciated that conditions can be rendered more stringent by the addition of increasing amounts of formamide which serves to destabilize the hybrid duplex in the same manner as increased temperature or decreased salt Thus hybridization conditions can be readily manipulated, and thus will generally be a method of choice depending on the desired results

In certain embodiments, it will be advantageous to employ nucleic acid sequences of the present invention in combination with an appropriate means, such as a label, for determining hybridization A wide variety of appropriate indicator means are known in the art including fluorescent, radioactive, enzymatic or other ligands such as avidin/biotin. which are capable of giving a detectable signal In preferred embodiments one will likely desire to employ a fluorescent label oi an enzyme tag. such as urease alkaline phosphatase or peroxidase instead of radioactive or other environmentally undesirable reagents In the case of enzyme tags coloπmetπc indicator substrates are known that can be employed to provide a means visible to the human eye or spectrophotometπcally to identify specific hybridization with complementary nucleic acid-containing samples

In general it is envisioned that the hybridization probes described herein will be useful both as reagents in solution hybridization as well as in embodiments employing a solid phase In embodiments involving a solid phase the test DNA (or RNA) is adsorbed or otherwise affixed to a selected matrix or surface This fixed, single-stranded nucleic acid is then subjected to specific hybridization with selected probes under desired conditions The selected conditions will depend on the paiticular circumstances based on the particular criteria required (depending for example on the G+C content, type of target nucleic acid, source of nucleic acid size of h bndization probe, etc ) Following washing of the hybridized surface so as to remove nonspecifically bound probe molecules, specific hybridization is detected or even quantitated, by means of the label

(// Laige Nucleic Acid Segments Using the markers flanking each centiomeie (see FIG 3) it may be possible to purify a contiguous DNA fragment that contains both flanking markers and the centromere encoded between those markers In order to carry this out. very large DNA fragments up to the size of an entire chromosome are prepared by embedding Arabidopsis tissues in agarose using, for example, the method described by Copenhaver et al , ( 1995) These large pieces of DNA can be digested in the agarose with any restriction enzyme Those restriction enzymes which will be particularly useful for isolating intact centromeres include enzymes which yield very large DNA fragments Such restriction enzymes include those with specificities greater than six base pairs such as. for example Asc I Bae I. BbvC I. Fse I. Not I Pac I Pme I PpuM I. Rsr II SanD I, Sap I SexA I. Sfi I. Sgf I SgrA I. Sbf I. Srf I Sse8387 I Sse8647 I. Swa, UbaD I, and UbaE I or any other enzyme that cuts at a low frequency within the Arabidopsis genome, and specifically within the centromeric region Alternatively, a partial digest with a more frequent cutting restriction enzyme could be used

Alternatively large DNA fragments spanning some or all of a centromere could be produced using RecA-Assisted Restriction Endonuclease (RARE) cleavage (Ferπn 1991 ) In order to carry this out v ery large DNA tiagments up to the size of an entne chromosome are prepared by embedding Aiabidopsis tissues in agarose using toi example, the method described by Copenhaver et al ( 1995) Single stranded DNA ohgomers with sequences homologous to sites flanking the region of DNA to be purified are made to form triple stranded complexes with the agarose embedded DNA using the recombinase enzyme RecA The DNA is then treated with a site specific methylase such as, for example. Alu 1 methylase. BamH I methylase, dam methylase EcoR I methylase Hae III methylase Hha I methylase Hpa II methylase or Msp methylase The methylase will modify all the sites specitied by its iecognition sequence except those within the triplex region protected by the RecA/DNA ohgomer complex The RecA/DNA ohgomer complex are then remov ed from the agarose embedded DNA and the DNA is then cleaved with the iestπction enzyme corresponding to the methylase used, tor example, if EcoRI methylase was used then EcoRI restriction endonuclease would be used to perform the cleavage Only those sites protected from modification will be subject to cleavage by the restriction endonuclease Thus by choosing targets flanking the centromeric regions that contain the recognition sequence of a site specific methylase/restriction endonuclease pair RARE can be used to cleave the entire region from the rest of the chromosome. It is important to note that this method can be used to isolate a DNA fragment of unknown composition by using sequence information flanking it Thus, this method may be used to isolate the DNA contained within any gaps in the physical map for the centromeres The DNA isolated by this method can then be sequenced

The large DNA fragments produced by digestion with restriction enzymes or by RARE cleavage aie then separated by size using pulsed-field gel electrophoresis (PFGE) (Schwartz et al, 1982) Specifically, Contour-clamped Homogeneous Electric Field (CHEF) electrophoresis (a variety of PFGE) can be used to separate DNA molecules as large as 10 Mb (Chu et al, 1985) Large DNA fragments resolved on CHEF gels can then be analyzed using standard Southern hybridization techniques to identify and measure the size of those fragments which contain both centromere flanking markers and therefor, the centromere After determining the size of the centromere containing fragment by comparison with known size standaids, the region from the gel that contains the centromere fragment can be cut out of a duplicate gel This centromeric DNA can then be analyzed, sequenced. and used in a variety of applications, as described below. including the construction of minichromosomes As indicated in detail below, minichromosomes can be constructed by attaching telomeres and selectable markers to the centromere fragment cut from the agarose gel using standard techniques which allow DNA gation within the gel slice Plant cells can then be transformed with this hybrid DNA molecule using the techniques described herein below IV. ##Recombinant Constructs Comprising Centromere Sequences ##

In light of the instant disclosure it will be possible for those of ordinary skill in the art to construct the recombinant DNA constiucts described herein Useful construction methods are well-known to those of^" skill in the art (see. foi example, Maniatis et al , 1982) As constructed, the minichromosome will preferably include an autonomous replication sequence (ARS) functional in plants, a centromere functional in plants, and a telomere functional in plants

The basic elements in addition to a plant centromere that may be used in constructing a minichromosome vector are known to those of skill in the art For example, one type of telomere sequence that could be used is an Arabidopsis telomere, which consists of head to tail arrays of the monomer repeat CCCTAAA totaling a few (for example 3-4) kb in length The telomeres of Arabidopsis, like those of other organisms, vary in length and do not appear to have a strict length requirement An example of a cloned telomere can be found in GenBank accession number M20158 (Richards and Ausubel. 1988) Yeast telomere sequences have also been described (see. e.g , Louis. 1994. Genbank accession number S70807) Additionally, a method for isolating a higher eukaryotic telomere from Arabidopsis thaliana was described by Richards and Ausubel ( 1988)

It is commonly believed that higher eukaryotes do not posses a specific sequence that is used as a replication origin, but instead replicate their DNA from random sites distributed along the chromosome In Arabidopsis, it is thought that the cell will form origins of replications about once every 70 kb (Van't Hof, 1978) Thus, because higher eukaryotes have origins of replication at potentially random positions on each chromosome, it is not possible to describe a specific origin sequence, but it may generally be assumed that a segment of plant DNA of a sufficient size will be recognized by the cell and origins will be generated on the construct For example, any piece ot Arabidopsis genomic DNA larger than 70 kb would be expected to contain an ARS By including such a segment of DNA on a recombinant vectoi . ARS function may be provided to the vector. Additionally, many 5. cerevisiae autonomous replicating sequences have been sequenced and could be used to fulfill the ARS function. One example is the Saccharomyces cerevisiae autonomously replicating sequence ARS 131 A (GenBank number L25319). Many origins of replications have been also been sequenced and cloned from E. coli and could be used with the invention, for example, the Col E l origin of replication (Ohmori and Tomizawa, 1979; GenBank number V00270). One Agrohacterium origin that could be used is RiA4. The localization of origins of replication in the plasmids of Agrobacterium rhizogenes strain A4 was described by Jouanin et al (1985).

(i) Considerations in the Preparation of Recombinant Constructs

In addition to the basic elements, positive or negative selectable plant markers

(e.g., antibiotic or herbicide resistance genes), and a cloning site for insertion of foreign

DNA may be included. In addition, a visible marker, such as green fluorescent protein, also may be desirable. In order to propagate the vectors in E. coli, it is necessary to convert the linear molecule into a circle by addition of a stuffer fragment between the telomeres. Inclusion of an E. coli plasmid replication origin and selectable marker also may be preferred. It also may be desirable to include Agrobacterium sequences to improve replication and transfer to plant cells. The inventors have described a number of exemplary minichromosome constructs in FIGs. 7A-7H. although it will be apparent to those in skill art that many changes may be made in the order and types of elements present in these constructs and still obtain a functional minichromosome within the scope of the instant invention.

Artificial plant chromosomes which replicate in yeast also may be constructed to take advantage of the large insert capacity and stability of^" repetitive DNA inserts afforded by this system (see Burke et al, 1987). In this case, yeast ARS and CEN sequences may be added to the vector. The artificial chromosome is maintained in yeast as a circular molecule using a stuffer fragment to separate the telomeres. A fragment of DNA. from any source whatsoever, may be purified and inserted into a minichromosome at any appropriate restriction endonuclease cleavage site The

DNA segment usually w ill include various regulatory signals foi the expression of pioteins encoded by the fragment Alternatively, regulatory signals resident in the minichromosome may be utilized

The techniques and procedures required to accomplish insertion are well-known in the art (see Maniatis et al , 1982) Typically, this is accomplished by incubating a circular plasmid or a linear DNA fragment in the presence of a restriction endonuclease such that the restriction endonuclease cleaves the DNA molecule Endonucleases preferentially break the internal phosphodiester bonds of polynucleotide chains They may be relatively unspecific. cutting polynucleotide bonds regardless of the surrounding nucleotide sequence However, the endonucleases which cleave only a specific nucleotide sequence are called restriction enzymes Restriction endonucleases generally internally cleave DNA molecules at specific recognition sites, making breaks within "recognition" sequences that in many, but not all. cases exhibit two-fold symmetry around a given point Such enzymes typically create double-stranded breaks

Many of these enzymes make a staggered cleavage, yielding DNA fragments with protruding single-stranded 5' or 3^" termini Such ends are said to be "sticky" or "cohesive" because they will hydrogen bond to complementary 3' or 5^" ends As a result, the end of any DNA fragment produced by an enzyme, such as EcoRI. can anneal with any other fragment produced by that enzyme This properly allows splicing of foreign genes into plasmids, for example Some iestπction endonucleases that may be particularly useful with the current invention include Hindlll, Pstl, EcoRI. and BamHl

Some endonucleases create fragments that have blunt ends, that is. that lack any protruding single strands An alternative way to create blunt ends is to use a restriction enzyme that leaves overhangs, but to fill in the overhangs with a polymerase. such as kleno . thereby resulting in blunt ends When DNA has been cleaved with restriction enzymes that cut across both strands at the same position, blunt end ligation can be used to join the fragments directly together The advantage of this technique is that any pair of ends may be |oined together, lπespective of sequence

Those nucleases that preferentially break off terminal nucleotides are referred to as exonucleases For example, small deletions can be produced in any DNA molecule by treatment with an exonuclease which starts from each 3' end of the DNA and chews away single strands in a 3' to 5' direction, creating a population of DNA molecules with single-stranded fragments at each end. some containing terminal nucleotides Similarly, exonucleases that digest DNA from the 5' end or enzymes that remove nucleotides from both strands have often been used Some exonucleases which may be particularly useful in the present invention include Bal3 l. SI. and EλoIII These nucleolytic reactions can be controlled by varying the time of incubation, the temperature, and the enzyme concentration needed to make deletions. Phosphatases and kinases also may be used to control which fragments have ends which can be joined Examples of useful phosphatases include shrimp alkaline phosphatase and calf intestinal alkaline phosphatase An example of a useful kinase is T4 polynucleotide kinase.

Once the source DNA sequences and vector sequences have been cleaved and modified to generate appropriate ends they are incubated together with enzymes capable of mediating the ligation of the two DNA molecules Particularly useful enzymes tor this puφose include T4 hgase. E coli ligase. or other similar enzymes The action of these enzymes results in the sealing of the linear DNA to produce a larger DNA molecule containing the desired fragment (see. for example. U S Patent Nos 4.237,224, 4.264.731 , 4,273,875. 4.322,499 and 4,336,336. which are specifically incorporated herein by reference)

It is to be understood that the termini of the linearized plasmid and the termini of the DNA fragment being inserted must be complementary or blunt in order tor the ligation reaction to be successful Suitable complementarity can be achieved by choosing appropriate restriction endonucleases (i.e., if the fragment is produced by the same restriction endonuclease or one that generates the same overhang as that used to linearize the plasmid. then the termini of both molecules w ill be complementary). As discussed previously, in one embodiment of the invention, at least two classes of the vectors used in the present invention are adapted to receive the foreign oligonucleotide fragments in only one orientation. After joining the DNA segment to the vector, the resulting hybrid DNA can then be selected from among the large population of clones or libraries.

A method useful for the molecular cloning of DNA sequences includes in vitro joining of DNA segments, fragmented from a source of high molecular weight genomic DNA, to vector DNA molecules capable of independent replication. The cloning vector may include plasmid DNA (see Cohen et al, 1973), phage DNA (see Thomas et al, 1974), SV40 DNA (see Nussbaum et al. 1976), yeast DNA, E. coli DNA and most significantly, plant DNA.

A variety of processes are known which may be utilized to effect transformation; i.e., the inserting of a heterologous DNA sequences into a host cell, whereby the host becomes capable of efficient expression of the inserted sequences.

(ii) Regulatory Elements

In one embodiment of the invention, constructs may include a plant promoter, for example, the CaMV 35S promoter (Odell et al, 1985), or others such as CaMV 19S (Lawton et al, 1987). nos (Ebert et al, 1987). Adh (Walker et al, 1987), sucrose synthase (Yang & Russell. 1990), a-tubulin, actin (Wang et al, 1992), cab (Sullivan et al, 1989). PEPCase (Hudspeth & Grula, 1989) or those associated with the R gene complex (Chandler et al, 1989). Tissue specific promoters such as root cell promoters (Conkling et al, 1990) and tissue specific enhancers (Fromm et al. 1989) are also contemplated to be useful, as are inducible promoters such as ABA- and turgor-inducible promoters. In particular embodiments of the invention, a Lat52 promoter may be used (Tvvell et al. 1991). A particularly useful tissue specific promoter is the SCARECROW (Ser) root-specific promoter (DiLaurenzio et al. 1996).

As the DNA sequence between the transcription initiation site and the start of the coding sequence, i.e., the untranslated leader sequence, can influence gene expression. Therefore, one may also wish to employ a particular leader sequence.

It is envisioned that a functional gene could be introduced under the control of novel promoters or enhancers, etc., or perhaps even homologous or tissue specific (for example, root-, collar/sheath-, whorl-, stalk-, earshank-, kernel- or leaf-specific) promoters or control elements. In particular embodiments of the invention, the functional gene may be in an antisense orientation relative to the promoter.

(ii) Terminators It may also be desirable to link a functional gene to a 3' end DNA sequence that acts as a signal to terminate transcription and allow for the poly-adenylation of the mRNA produced by coding sequences. Such a terminator may be the native terminator of the functional gene or, alternatively, may be a heterologous 3' end. Examples of terminators that could be used with the invention are those from the nopaline synthase gene of Agrobacterium tumefaciens (nos 3" end) (Bevan et al, 1983), the terminator for the T7 transcript from the octopine synthase gene of Agrobacterium tumefaciens, and the 3' end of the protease inhibitor I or II genes from potato or tomato.

(Hi) Marker Genes It may be desirable to use one or more marker genes in accordance with the invention. Such markers may be adapted for use in prokaryotic, lower eukaryotic or higher eukaryotic systems, or may be capable of use in any combination of the foregoing classes of organisms. By employing a selectable or screenable marker protein, one can provide or enhance the ability to identify transformants. "Marker genes" are genes that impart a distinct phenotype to cells expressing the marker protein and thus allow such transformed cells to be distinguished from cells that do not have the marker Such genes may encode either a selectable or screenable marker, depending on whether the maiker confers a trait which one can "select^"" for by chemical means. ; e . through the use of a selective agent (e g , a herbicide, antibiotic, or the like), or whether it is simply a trait that one can identify through observation or testing, t e , by "screening"' (e g., the green fluorescent protein) Of course, many examples of suitable marker proteins are known to the art and can be employed in the practice of the invention.

Included within the terms selectable or screenable markers also are genes which encode a "secretable marker" whose secretion can be detected as a means of identifying or selecting for transformed cells Examples include markers which are secretable antigens that can be identified by antibody interaction, or even secretable enzymes which can be detected by their catalytic activity Secretable proteins fall into a number of classes, including small, diffusible proteins detectable, e g . by ELISA. small active enzymes detectable in extracellular solution (e g . α-amylase, β-lactamase, phosphinothπcin acetyltransferase); and proteins that are inserted or trapped in the cell wall (e g , proteins that include a leader sequence such as that found in the expression unit of extensin or tobacco PR-S)

With regard to selectable secretable markers, the use of a gene that encodes a protein that becomes sequestered in the cell wall, and which protein includes a unique epitope is considered to be particularly advantageous Such a secreted antigen markei would ideally employ an epitope sequence that would provide low background in plant tissue, a promoter-leader sequence that would impart efficient expression and targeting across the plasma membrane, and would produce protein that is bound in the cell wall and yet accessible to antibodies A normally secreted wall protein modified to include a unique epitope would satisfy all such requirements

1 Selectable Markers

Manv, selectable marker genes may be used in accordance with invention including but not limited to neo (Potrvkus t al 1985) w hich provides kanamvcin resistance and can be selected for using kanamycin G418 paiomomycin etc bai which confers bialaphos oi phosphinothncm resistance a mutant EPSP synthase protein (Hinchee et al 1988) conferring glyphosate resistance, a nitπlase such as bxn from Klehsiella o aenae which confers resistance to bromoxynil (Stalker ef al 1988), a mutant acetolactate synthase (ALS) which confers resistance to lmidazohnone, sulfonylurea or other ALS inhibiting chemicals (European Patent Application 154 204, 1985), a methotrexate resistant DHFR (Thillet et al 1988), a dalapon dehalogenase that confers resistance to the herbicide dalapon or a mutated anthranilate synthase that confers resistance to 5-methyl tryptophan Where a mutant EPSP synthase is employed, additional benefit may be realized through the incoφoration of a suitable chloioplast transit peptide CTP (U S Patent No 5 188,642) or OTP (U S Patent No 5 633 448) and use of a modified maize EPSPS (PCT Application WO 97/04103)

An illustrative embodiment of selectable marker capable of being used in systems to select transformants are those that encode the enzyme phosphinothncm acetyltransferase such as the bar gene from Stieptoi ces I gi oscopicus or the pat gene from Strepto nces xti idochi omoqenes The enzyme phosphinothncm acetyl transferase (PAT) inactivates the active ingredient in the herbicide bialaphos phosphinothncm (PPT) PPT inhibits glutamine synthetase (Murakami et al 1986 Twell et al 1989) causing rapid accumulation of ammonia and cell death The use of bar as a selectable marker gene and for the production of herbicide-resistant rice plants from protoplasts was described by Rathore et al , ( 1993)

A number of 5 ceievisiae maiker genes are also know n and could be used with the invention, such as foi example the HIS4 gene (Donahue et al 1982 GenBank number JO 1331 ) An example of an £ coli marker gene which has been cloned and sequenced and could be used in accordance with the invention is the Ap gene w hich confers resistance to beta-lactam antibiotics such as ampacillin (nucleotides 4618 to 5478 of GenBank accession number U66885 )

2 Screenable Markers Screenable markers that may be employed include a β-glucuronidase (GUS) or uidA gene w hich encodes an enzyme for which various chromogenic substrates are known, an R-locus gene, which encodes a product that regulates the production of anthocyanin pigments (red color) in plant tissues (Dellaporta et al , 1988), a β-lactamase gene (Sutchffe, 1978), which encodes an enzyme for which various chromogenic substrates are known (e g , PADAC a chromogenic cephalospoπn), a vv/E gene (Zukowsky et al , 1983) which encodes a catechol dioxygenase that can convert chromogenic catechols an α-amylase gene (Ikuta et al , 1990) a tyrosinase gene (Katz et al , 1983) which encodes an enzyme capable of oxidizing tyrosine to DOPA and dopaquinone which in turn condenses to form the easily-detectable compound melanin a β-galactosidase gene which encodes an enzyme for which there are chromogenic substrates a luciferase (lux) gene (Ow et al , 1986) which allows for bioluminescence detection an aequoπn gene (Prasher et al 1985) which may be employed in calcium- sensitive bioluminescence detection, or a gene encoding for green fluorescent protein (Sheen et al 1995 Haseloff et al , 1997 Reichel et al , 1996 Tian et al , 1997 WO 97/41228)

Genes from the maize R gene complex can also be used as screenable markers The R gene complex in maize encodes a protein that acts to regulate the production of anthocyanin pigments in most seed and plant tissue Maize strains can have one or as many as four R alleles which combine to regulate pigmentation in a developmental and tissue specific manner Thus, an R gene introduced into such cells will cause the expression of a red pigment and. if stably incoφorated can be visually scored as a red sector If a maize line carries dominant alleles for genes encoding for the enzymatic intermediates in the anthocvanin biosynthetic pathway (C2 A l A2 Bz l and Bz2), but carries a recessive allele at the R locus transformation of any cell from that line with R will result in red pigment formation Exemplary lines include Wisconsin 22 which contains the rg-Stadler allele and TR1 12. a K55 derivative which is r-g. b, PI Alternatively, any genotype of maize can be utilized if the C I and R alleles are introduced together

Another screenable marker contemplated for use in the present invention is fiiefly luciferase, encoded by the lux gene The presence of the lux gene in transformed cells may be detected using, for example. X-ray film, scintillation counting, fluorescent spectrophotometry, low-light video cameras, photon counting cameras or multiwell luminometry. It also is envisioned that this system may be developed for populational screening for bioluminescence, such as on tissue culture plates, or even for whole plant screening The gene which encodes green fluorescent protein (GFP) is contemplated as a particularly useful reporter gene (Sheen et al . 1995, Haseloff et al , 1997, Reichel et al , 1996; Tian et al. 1997, WO 97/41228). Expression of green fluorescent protein may be visualized in a cell or plant as fluorescence following illumination by particular wavelengths of light

3 Negative Selectable Markers

Introduction of genes encoding traits that can be selected against may be useful for eliminating minichromosomes from a cell or for selecting against cells which comprise a particular minichromosome. An example of a negative selectable marker which has been investigated is the enzyme cytosine deaminase (Stouggard, 1993). In the presence of this enzyme the compound 5-fluorocytosιne is converted to 5-fluorouracιl which is toxic to plant and animal cells. Therefore, cells comprising a minichromosome with this gene could be directly selected against. Other genes that encode proteins that render the plant sensitive to a certain compound will also be useful in this context. For example. T-DNA gene 2 from Agrobacter m tumefaciens encodes a protein that catalyzes the conversion of α-naphthalene acetamide (NAM) to α-naphthalene acetic acid (NAA) renders plant cells sensitive to high concentrations of NAM (Depicker et al , 1988) V. Isolation of Centromeres From Plants

The inventors have provided, for the first time, the nucleic acid sequence of a plant centromere This will allow one of skill in the art to obtain centromere sequences from potentially any species The inventors specifically provide herein below a number of methods which may be employed to isolate such centromeres

(i) Utilization of Conserved Sequences

Numerous of the centromere sequences identified by the inventors were also shown by the inventors to be highly conserved (see e g , Example 5B, Table 3, and Table 4) The novel finding of the inventors that a number of genes reside within the Arabidopsis centromere can therefore be used to find syntenic genes in other organisms (; e , evolutionary conserved relationships in gene order from species to species) For example, the sequence of each Arabidopsis gene can be used to search through sequence databases from other plants An exemplary list of such sequences that could be used is a sequence given by SEQ ID NO 1 , SEQ ID NO 2, SEQ ID NO 3. SEQ ID NO 4 SEQ ID NO 5, SEQ ID NO 6, SEQ ID NO 7, SEQ ID NO 8, SEQ ID NO 9 SEQ ID NO 10 SEQ ID NO 1 1 , SEQ ID NO 12, SEQ ID NO 13, SEQ ID NO 14. SEQ ID NO 15, SEQ ID NO 16, SEQ ID NO 17. SEQ ID NO 18, SEQ ID NO 19, SEQ ID NO 20, and SEQ ID NO 21 Also useful would be the genes listed in Tables 3 and 4 Finding identical or similar genes would identify candidates that may reside within or near centromeric regions Mapping these genes using linked markers would identify potential centromeric regions

Where hybridization is used to obtain centromere sequences, it may be desirable to use less stringent hybridization conditions to allow formation of a heteroduplex In these circumstances, one may desire to employ conditions such as about 0 15 M to about 0 9 M salt at temperatures ranging from about 20°C to about 55°C Cross-hybridizing species can thereby be readily identified as positively hybridizing signals with respect to control hybridizations In any case, it is generally appreciated that conditions can be rendered more stringent by the addition of increasing amounts of formamide which serves to destabilize the hybrid duplex in the same manner as increased temperature or decreased salt Thus hybridization conditions can be readily manipulated and thus will generally be a method of choice depending on the desired results

(u) Identification of Centi omei e- Associated Characteristics

The second method takes advantage of the unique DNA properties that the inventors hav e discovered at the Aiabidopsis centromere and adjacent peπcentromere regions The centromeres are composed of long arrays of 180 bp repeats flanked by regions that are 10-70% retroelements up to 15% pseudogenes and up to 29% transposons (see FIGs 12A-T) This is unique to the centromere since retroelements, transposons and pseudogenes are very rare outside the centromere and peπcentromere region Furthermore, gene density decreases from an average of a gene every 4 5 kb on the chromosomal arm down to one in 150 kb at the centromere This unique centromere composition could be exploited in a number of ways to find centromere legions in other species, for example

1) Markers specific for retroelements, transposons, repeat DNA elements and pseudogenes can be devised to genetically map regions which are dense with similar elements

2) The second method involves in situ hybridization and preferablv fluorescent in situ hybridization (FISH) Fluorescently labeled DNA probes consisting of retroelements transposons and/or repetitive DNA native to a particular species can be combined with microscopy to identify parts of a chromosome with a similar percentage of DNA elements as that found at the Arabidopsis centromere

3) Utilizing sequence databases regions of genomes that have increased numbers of repetitive DNA, pseudogenes, retroelements and transposons, similar to the composition of Aiabidopsis identified by the inventors can be used to identify regions of an organisms chromosome that are centromeric (in) Utilization of Centromei e-Associated Pioteins

The third method involves lmmunoprecipitating known centromere proteins or kinetochore proteins and analyzing bound DNA Antibodies specific to centromere proteins can be incubated with proteins extracted from cells Extiacts can be native or previously treated to cross-link DNA to proteins The antibodies and bound proteins can be purified away from the protein extracts and the DNA isolated The DNA can then be used as a probe for FISH (as talked about above) or to probe libraries to find neighboring centromere sequences

1 Centromere-Associated Protein Specific Antibodies

By identifying, for the first time, centromere-associated genes, the inventors have enabled the production of antibodies to the proteins encoded by such centromere- associated genes The antibodies may be either monoclonal or polyclonal which bind to centromere-associated proteins of the current invention The centromere-associated protein targets of the antibodies, include proteins which bind to the centromere region Further, it is specifically contemplated that these centromere-associated protein specific antibodies would allow for the further isolation and characterization of the centromere-associated proteins For example proteins may be isolated which are encoded by the centromeres Recombinant production of such proteins provides a source of antigen for production of antibodies

Alternatively the centromere may be used as a ligand to isolate using affinity methods, centromere binding proteins Once isolated these protein can be used as antigens for the production polyclonal and monoclonal antibodies A variation on this technique has been demonstrated by Rattner ( 1991 ), by cloning of centromere-associated proteins through the use of antibodies which bind in the vicinity of the centromere

Means for preparing and characterizing antibodies are well known in the art (see e g , Antibodies A Laboratory Manual Cold Spring Harbor Laboratory. 1988, incoφorated herein by reference) The methods for geneiating monoclonal antibodies (mAbs) generally begin along the same lines as those for preparing polyclonal antibodies Briefly a polyclonal antibody is prepared by immunizing an animal with an immunogenic composition in accordance with the present invention and collecting antisera from that immunized animal A wide range of animal species can be used for the production of antisera Typically the animal used for production of antisera is a rabbit, a mouse, a rat, a hamster, a guinea pig or a goat A rabbit is a preferred choice for production of polyclonal antibodies because of the ease of handling, maintenance and relatively large blood volume

As is well known in the art, a given composition may vary in its immunogenicity It is often necessary therefore to boost the host immune system, as may be achieved by coupling a peptide or polypeptide immunogen to a carπei Exemplary and preferred carriers are keyhole limpet hemocyanin (KLH) and bovine serum albumin (BSA) Other albumins such as ovalbumin, mouse serum albumin or rabbit serum albumin also can be used as carπeis Means for conjugating a polypeptide to a carrier protein are well known in the art and include glutaraldehyde. /n-maleimidobencoyl-N-hydroxysuccinimide ester, carbodimide and bis-biazotized benzidine

As is also well known in the art, the immunogenicity of a particular immunogen composition can be enhanced by the use of non-specific stimulators of the immune response, known as adjuvants Exemplary and preferred adjuvants include complete Freund s adjuvant (a non-specific stimulator of the immune response containing killed M cobacter m tubeiciilosis). incomplete Freund's adjuvants and aluminum hydroxide adjuvant

The amount of immunogen composition used in the production of polyclonal antibodies varies upon the nature of the immunogen as well as the animal used for immunization A variety of routes can be used to administer the immunogen (subcutaneous, intramuscular intradermal. intravenous and lntrapeπtoneal ) The production of polyclonal antibodies may be monitored by sampling blood of the immunized animal at various points following immunization A second booster miection also may be giv en The piocess of boosting and titeπng is repeated until a suitable titer is achieved When a desired level of immunogenicity is obtained, the immunized animal can be bled and the serum isolated and stored and/or the animal can be used to generate mAbs

Monoclonal antibodies may be readily prepared through use of well-known techniques, such as those exemplified in U S Patent 4, 196 265, incoφorated herein by reference Typically, this technique involves immunizing a suitable animal with a selected immunogen composition, e g , a purified or partially purified minichromosome -associated protein, polypeptide or peptide The immunizing composition is administered in a manner effective to stimulate antibody producing cells Rodents such as mice and rats are preferred animals however the use of rabbit, sheep or frog cells also is possible The use of rats may provide certain advantages (Goding 1986), but mice are preferred, with the BALB/c mouse being most preferred as this is most routinely used and generally gives a higher percentage of stable fusions

Following immunization somatic cells with the potential for producing antibodies specifically B lymphocytes (B cells), are selected for use in the mAb generating protocol These cells may be obtained from biopsied spleens tonsils or lymph nodes, or from a peripheral blood sample Spleen cells and peripheral blood cells are preferred the former because they are a rich source of antibody-producing cells that are in the dividing plasmablast stage, and the latter because peripheral blood is easily accessible Often, a panel of animals will have been immunized and the spleen of animal with the highest antibody titer will be removed and the spleen lymphocytes obtained by homogenizing the spleen with a syringe Typically a spleen from an immunized mouse contains approximately 5 x 10⁷ to 2 x 10⁸ lymphocytes The antibody-producing B lymphocytes from the immunized animal are then fused with cells of an immortal myeloma cell generally one of the same species as the animal that w as immunized Myeloma cell lines suited for use in hybπdoma-producing fusion procedures preferably are non-antibody-producing have high fusion efficiency, and enzyme deficiencies that render them incapable of growing in certain selective media which support the growth of only the desired fused cells (hybπdomas)

Any one of a number of myeloma cells may be used, as are known to those of skill in the art (Goding 1986 Campbell 1984) For example where the immunized animal is a mouse, one may use P3-X63/Ag8, X63-Ag8 653 NS l/1 Ag 4 1 , Sp210-Agl4 FO, NSO/U, MPC- 1 1 MPC1 1-X45-GTG 1 7 and S 194/5XX0 Bui, for rats, one may use R210 RCY3, Y3-Ag 1 2 3 IR983F and 4B210 and U-266, GM 1500-GRG2 LICR-LON-HMy2 and UC729-6 are all useful in connection with human cell fusions

One preferred muπne myeloma cell is the NS- 1 myeloma cell line (also termed

P3-NS-l-Ag4- l ) which is readily available from the NIGMS Human Genetic Mutant Cell Repository by requesting cell line repository number GM3573 Another mouse myeloma cell line that may be used is the 8-azaguanιne-resιstant mouse muπne myeloma SP2/0 non-producer cell line

Methods for generating hybrids of antibody-producing spleen or lymph node cells and myeloma cells usually comprise mixing somatic cells with myeloma cells in a 2 1 ratio, though the ratio may vary from about 20 1 to about 1 1 respectively, in the presence of an agent or agents (chemical or electrical) that promote the fusion of cell membranes Fusion methods using Sendai virus have been described

(Kohler et al 1975 1976). and those using polyethylene glycol (PEG), such as 37% (v/v) PEG, (Gefter et c// 1977) The use of electπcallv induced fusion methods also is appropriate (Goding 1986) Fusion procedures usually produce viable hybrids at low frequencies, about 1 x 10 ⁶ to 1 x 10 ^s However, this does not pose a problem as the viable, fused hybrids are diffeientiated from the parental unfused cells (particularly the unfused myeloma cells that would normally continue to divide indefinitely) by cultuπng in a selective medium The selective medium is generally one that contains an agent that blocks the de novo synthesis of nucleotides in the tissue culture media Exemplary and preferred agents are aminopteπn, methotrexate, and azaseπne Aminopteπn and methotrexate block de novo synthesis of both puπnes and pynmidmes. whereas azaseπne blocks only puπne synthesis Where aminopteπn or methotrexate is used, the media is supplemented with hypoxanthine and thymidine as a source of nucleotides (HAT medium) Where azaseπne is used, the media is supplemented with hypoxanthine

The preferred selection medium is HAT Only cells capable of opeiating nucleotide salvage pathways are able to survive in HAT medium The myeloma cells are defective in key enzymes of the salvage pathway, e g . hypoxanthine phosphoπbosyl transferase (HPRT), and they cannot survive The B-cells can operate this pathway, but they have a limited life span in culture and generally die within about two weeks Therefore, the only cells that can survive in the selective media are those hybrids formed from myeloma and B-cells

This cultuπng provides a population of hybπdomas from which specific hybπdomas are selected Typically selection of hybπdomas is performed by cultuπng the cells by single-clone dilution in microtiter plates, followed by testing the individual clonal supernatants (after about two to three weeks) for the desired reactivity The assay should be sensitive, simple and rapid, such as radioimmunoassays enzyme immunoassays, cytotoxicity assays plaque assays, dot lmmunobinding assays, and the

The selected hybπdomas would then be serially diluted and cloned into individual antibody-producing cell lines which clones can then be propagated indefinitely to provide mAbs The cell lines may be exploited for mAb production in two basic ways A sample of the hybridoma can be injected (often into the peritoneal cav ity) into a histocompatible animal of the type that w s used to provide the somatic and myeloma cells for the original fusion The injected animal develops tumois secreting the specific monoclonal antibody produced by the fused cell hybrid The body fluids of the animal, such as serum or ascites fluid, can then be tapped to provide mAbs in high concentration The individual cell lines also could be cultured in vitio where the mAbs are naturally secreted into the culture medium from which they can be readily obtained in high concentrations mAbs produced by either means may be further purified, if desired using filtration, centπfugation and various chromatographic methods such as HPLC or affinity chromatography

2 ELISAs and Immunoprecipitation

ELISAs may be used in conjunction with the invention, for example, in identifying expression of a centromere-associated protein in a candidate centromere sequence Such an assay could thereby facilitate the isolation of centromeres from species other than Arabidopsis By identifying conserved centromere-associated coding sequences, the inventors have provided the essential tools for such a screen

In an ELISA assay, proteins or peptides comprising minichromosome-encoded protein antigen sequences are immobilized onto a selected surface, preferablv a surface exhibiting a protein affinity such as the wells of a polystyrene microtiter plate After washing to remove incompletely adsorbed material it is desirable to bind or coat the assay plate wells with a nonspecific protein that is known to be antigenically neutral with regard to the test antisera such as bovine serum albumin (BSA), casein or solutions of milk powdei This allows for blocking of nonspecific adsoφtion sites on the immobilizing surface and thus reduces the background caused by nonspecific binding of antisera onto the surface After binding of antigemc material to the well, coating with a non-reactive material to reduce background, and washing to lemove unbound material, the immobilizing surface is contacted with the antiseia or clinical or biological extract to be tested in a manner conducive to immune complex (antigen/antibody) formation Such conditions preferably include diluting the antisera with diluents such as BSA, bovine gamma globulin (BGG) and phosphate buffered saline (PBS Tween These added agents also tend to assist in the reduction of nonspecific background The layered antisera is then allowed to incubate tor from about 2 to about 4 hours, at temperatures preferably on the order of about 25° to about 27°C Following incubation, the antisera-contacted surface is washed so as to remove non-immunocomplexed material A preferred washing procedure includes washing with a solution such as PBS/Tween^®, oi borate buffer

Following formation of specific immunocomplexes between the test sample and the bound antigen, and subsequent washing, the occurrence and even amount of immunocomplex formation may be determined by subjecting same to a second antibody having specificity for the first To provide a detecting means, the second antibody will preferably have an associated enzyme that will generate color or light development upon incubating with an appropriate chromogenic substrate Thus, for example, one will desire to contact and incubate the antisera-bound surface with a urease or peroxidase-conjugated anti-human IgG for a period of time and under conditions which favor the development of immunocomplex formation (e g . incubation for 2 hours at room temperature in a PBS-containing solution)

After incubation with the second enzyme-tagged antibody, and subsequent to washing to remove unbound material, the amount of label is quantified by incubation with a chromogenic substrate such as urea and bromocresol purple or 2.2'-azιno-dι-(3-ethyl-benzthιazolιne)-6-sulfonιc acid (ABTS) and H₂0₂. in the case of peroxidase as the enzyme label Quantitation is then achieved by measuring the degree of color generation, e g . using a visible spectra spectrophotometer 3 Western Blots

Centromere- associated antibodies may find use in immunoblot or western blot analysis, for example, for the identification of proteins immobilized onto a solid support matrix, such as nitrocellulose, nylon or combinations thereof In conjunction with immunoprecipitation followed by gel electrophoresis. these may be used as a single step reagent for use in detecting antigens against which secondary reagents used in the detection of the antigen cause an adveise background This is especially useful when the antigens studied are immunoglobulins (precluding the use of immunoglobulins binding bacterial cell wall components), the antigens studied cross-react with the detecting agent. or they migrate at the same relative molecular weight as a cross-reacting signal

Immunologically-based detection methods for use in conjunction with Western blotting include enzymatically-, radiolabel- or fluorescently-tagged secondary antibodies against the protein moiety are considered to be of particular use in this regard

(iv) Genetic Mapping Based Approaches

The genetic mapping techniques outlined here for the identification of centromeres in Arabidopsis may find use in other species In one aspect, this may comprise actual use of the mapping data piovided herein based on synteny between Arabidopsis chromosomes and those of other species Further new mapping data may be obtained using the techniques described herein For example in any plant that makes tetrads, the detailed methodology described herein for tetrad analysis could be used for the isolation of centromeres Briefly, tetrad analysis measures the recombination frequency between genetic makers and a centromere by analyzing all four pioducts of individual meiosis A particular advantage arises from the quartet (qi t 1 ) mutation in Aiabidopsis which causes the four products of pollen mother cell meiosis in Aiabidopsis to remain attached Sev eral naturally occurring plant species in addition to Aiabidopsis are known to release pollen clusters, including water lilies, cattails heath (Ei icaceae and Epaci idceae) ev ening primrose (Onagiaceae) sundews (Dioseiaceae) orchids (Oichidaceae) and acacias (Mimosaceae) (Preuss 1994 Smyth 1994) However none of these species has been developed into an experimental system limiting their use tor genetic analysis However, it is contemplated by the inventors that the cloning and introduction of the quaitet mutation or an antisense copy of a non-mutated Quartet gene, could allow the use of tetrad analysis in potentially any species

Southern genomic DNA blots in combination with RFLP analysis may be used to map centromeres with a high degree of resolution The stored seedling tissue provides the necessary amount of DNA for analysis of the restriction fragments Southern blots are hybridized to probes labeled by radioactive or non-radioactive methods

It may, in many cases, be desired to identify new polymoφhic DNA markers which are closely linked to the target region In some cases this can be readily done For example in many plant genomes, a polymoφhic Sau3A site can be found for about every 8 to 20 kB surveyed Subtractive methods are available for identifying such polymoφhisms (Rosenberg et al 1994) and these subtractions may be performed using DNA from selected centromeric YAC oi BAC clones Screens for RFLP markers potentially linked to centromeres also can be performed using DNA fragments from a centromere-linked YAC clone to probe blots of genomic DNA from a target organism that has been digested with a panel of restriction enzvmes

To be certain that an entire centromeric region has been cloned, clones or a series of clones, are identified that hybridize to markers on either side of each centromere These efforts can be complicated by the presence of repetitive DNA in the centromere as well as by the potential instability of centromere clones Thus, identification of large clones with unique sequences that will sei ve as useful probes simplifies a chromosome walking strategy Blot hybridization allows comparison of the structure of the clones ith that of genomic DNA and thus determines whether the clones have suffered deletions oi rearrangements The centromenc clones identified aie useful for hybridization experiments that can be used to deteimine whether they share common sequences whether they localize /// situ to the cytologically defined centromeric region, and whethei they contain repetitive sequences thought to map near Aiabidopsis centromeres (Richards et al 1991. Maluszynska et al 1991 )

Exemplary methods for conducting PFGE and YAC genome analysis described

(Ecker, 1990) A large insert YAC library for genome mapping in Aiabidopsis thaliana was described in Creusot ( 1995) The analysis of clones carrying repeated DNA sequences in two YAC libraries of Arabidopsis thaliana DNA was discussed by Schmidt et al , ( 1994) The construction and characterization of a yeast artificial chromosome library of Aiabidopsis was described by Grill and Somerville ( 1991 )

A particularly useful type of clone is the bacterial artificial chromosome (BAC) as data has suggested that YAC clones may sometimes not span centromeres (Willard, 1997) The construction and characterization of a bacterial artificial chromosome library from, for example Aiabidopsis thaliana has been described (Choi et al 1995) The complementation of plant mutants with large genomic DNA fragments can be achieved using transformation-competent minichromosome vectoi s, thereby speeding positional cloning (Liu et al . 1999) The construction and characterization of the IGF Aiabidopsis BAC library was described by Mozo et al ( 1998 ) A complete BAC-based physical map of the Aiabidopsis thaliana genome has been described (Mozo et al . 1998)

VI. Site Specific Integration and Excision of Nucleic Acid Segments

It is specifically contemplated by the inventois that one could employ techniques for the site-specific integration or excision of nucleic acid segments for the constiuction of minichromosomes (see. e g . Example 8B below) Such techniques also could be used for the site-specific integration or excision of transgenes w hich are introduced into a plant including minichromosome ectors

Site-specific integration or excision of nucleic acid molecules can be achieved by means of homologous recombination (see for example U S Patent No 5 527 695 specifically incoφorated herein by reference in its entirety) Homologous recombination is a reaction between any pair of DNA sequences having a similar sequence of nucleotides where the two sequences interact (recombine) to form a new recombinant DNA species The frequency of homologous recombination increases as the length of the shared nucleotide DNA sequences increases and is higher with linearized plasmid molecules than with circularized plasmid molecules Homologous recombination can occur between two DNA sequences that are less than identical but the recombination frequency declines as the di ergence between the two sequences increases

Introduced DNA sequences can be targeted via homologous recombination by linking a DNA molecule of interest to sequences sharing homology with endogenous sequences of the host cell Once the DNA enters the cell the two homologous sequences can interact to insert the introduced DNA at the site where the homologous genomic DNA sequences were located Therefore, the choice of homologous sequences contained on the introduced DNA will determine the site where the introduced DNA is integrated via homologous recombination For example if the DNA sequence of interest is linked to DNA sequences sharing homology to a single copy gene ot a host plant cell the DNA sequence of interest will be inserted via homologous recombination at only that single specific site However if the DNA sequence ot interest is linked to DNA sequences sharing homology to a multicopy gene of the host eukaryotic cell, then the DNA sequence of interest can be inserted via homologous iecombination at each of the specific sites where a copy of the gene is located

DNA can be inserted into a host chromosome or vector by a homologous recombination reaction involv ing either a single reciprocal recombination (resulting in the insertion of the entire length of the introduced DNA) or through a double reciprocal recombination (resulting in the insertion of only the DNA located between the two iecombination events ) For example, if one wishes to insert a foreign gene into the genomic site where a selected gene is located, the introduced DNA should contain sequences homologous to the selected gene A single homologous recombination event would then result in the entire introduced DNA sequence being inserted into the selected gene Alternatively, a double recombination event can be achieved by flanking each end of the DNA sequence of interest (the sequence intended to be inserted into the genome) with DNA sequences homologous to the selected gene. A homologous recombination event involving each of the homologous flanking regions will result in the insertion of the foreign DNA Thus only those DNA sequences located between the two regions sharing genomic homology become integrated into the genome

Although introduced sequences can be targeted for insertion into a specific site via homologous recombination, in higher eukaryotes homologous recombination is a relatively rare event compared to random insertion events In plant cells, foreign DNA molecules find homologous sequences in the cell's genome and recombine at a frequency of approximately 0 5-4.2X 10^"4 Thus any transformed cell that contains an introduced

DNA sequence integrated via homologous recombination will also likely contain numerous copies of randomly integrated introduced DNA sequences Therefore, it may be desirable to use more precise mechanisms for site-specific recombination. A preferred manner for carrying out site-specific recombination comprises use of^" a site-specific recombinase system In general, a site specific recombinase system consists of three elements: two pairs of DNA sequence (first and second site-specific recombination sequences) and a specific enzyme (the site-specific recombinase) The site-specific recombinase will catalyze a recombination reaction only between two site-specific recombination sequences

A number of different site specific recombinase systems could be employed in accordance with the instant invention, including, but not limited to. the Cre/lox s tem of bactenophage P I (Hoess et al . 1982. U S Patent No 5.658.772, specifically incoφorated herein by reference in its entirety), the FLP FRT system of yeast (Gohc and Lindquist. 1989). the Gin recombinase of phage Mu (Maeser and Kahmann. 1991 ). the Pin recombinase of E coli (Εnomoto et al 1983). the recombinase encoded by the sre gene (ORF469) and which is capable of mediating integration of the R4 phage genome (Matsuura et al . 1996), the site-specific recombinase encoded by pinD of Shigella chsenteriae (Tominaga. 1997). the site-specific recombinase encoded in the major 'pathogenicity island' of Salmonella rs'phi (Zhang et al . 1997) the Int-B 13 site-specific recombinase of the bactenophage P4 integrase family (Ravatn et al, 1998), as well as the and the R/RS system of the pSR l plasmid (Araki et al , 1992) The bactenophage PI Cre/lox and the yeast FLP/FRT systems constitute two particularly useful systems for site specific recombination In these systems, a recombinase (Cre or FLP) will interact specifically with its respective site-specific recombination sequence (lox oi FRT. respectively) to invert or excise the intervening sequences The sequence for each of these two systems is relatively short (34 bp for lox and 47 bp for FRT) and therefore, convenient for use with transformation vectors

The FLP/FRT recombinase system has been demonstrated to function efficiently in plant cells, but could also be used in. for example, a bacterial cell or /;; vitro The performance of the FLP/FRT system indicates that FRT site structure, and amount of the FLP protein present affect excision activity In general, short incomplete FRT sites lead to higher accumulation of excision products than the complete full-length FRT sites The systems can catalyze both intra- and intermolecular reactions, indicating their utility foi DNA excision as well as integration reactions The recombination reaction is reversible and this reversibility can compromise the efficiency of the reaction in each direction Altering the structure of the site-specific recombination sequences is one approach to remedying this situation The site-specific recombination sequence can be mutated in a manner that the product of the recombination reaction is no longer recognized as a substrate for the reverse reaction, thereby stabilizing the integration oi excision event In the Cre-lox system, discovered in bactenophage PI . recombination between loxP sites occurs in the presence of the Cre recombinase (see. e.g . U S Patent No 5.658.772. specifically incoφorated herein by refeience in its entuety) This sy stem has been utilized to excise a gene located between two lox sites which had been introduced into a yeast genome (Sauer. 1987) Cre was expressed from an mducible yeast GAL1 promoter and this Cre gene was located on an autonomously lephcating yeast vector

Since the lox site is an asymmetrical nucleotide sequence, lox sites on the same DNA molecule can have the same or opposite orientation with respect to each other Recombination between lox sites in the same orientation results in a deletion of the DNA Segment located between the two lox sites and a connection between the resulting ends of the original DNA molecule The deleted DNA segment forms a circular molecule of DNA The original DNA molecule and the resulting circular molecule each contain a single lox site Recombination between lox sites in opposite orientations on the same DNA molecule result in an inversion of the nucleotide sequence of the DNA segment located between the two lox sites In addition, reciprocal exchange of DNA segments proximate to lox sites located on two different DNA molecules can occur. All of these recombination events are catalyzed by the product of the Cre coding region

VII. Transformed Host Cells and Transgenic Plants

Methods and compositions for transforming a bacterium, a yeast cell, a plant cell. or an entire plant with one or more minichromosomes are further aspects of this disclosure A transgenic bacterium, yeast cell, plant cell or plant derived from such a transformation process or the progeny and seeds from such a transgenic plant also are further embodiments of the invention

Means for transforming bacteria and yeast cells aie well known in the art

Typically, means ot transformation are similar to those well known means used to transform other bacteria or yeast such as E coli or Saccharoimces cerevisiae Methods for DNA transformation of plant cells include plant transformation protoplast transformation (as used herein protoplast transformation includes PEG-mediated transformation electroporation and protoplast fusion tiansformation) gene transfer into pollen injection into reproductiv e organs injection into immature embryos and particle bombaidment Each of these methods has distinct advantages and disadvantages Thus one paiticular method of introducing genes into a particular plant strain may not necessaπly be the most effective for another plant strain but it is well known in the art which methods are useful for a particular plant strain

There are many methods for introducing transforming DNA segments into cells but not all are suitable for delivering DNA to plant cells Suitable methods are believed to include virtually any method by which DNA can be introduced into a cell such as by Agrobactermm infection direct delivery of DNA such as, foi example by PEG-mediated transformation ot protoplasts (Omirulleh et al 1993), by desiccation/inhibition-mediated DNA uptake by electroporation, by agitation with silicon carbide fibers by acceleration of DNA coated particles, etc In certain embodiments acceleration methods are preferred and include, for example, microprojectile bombardment and the like

Technology for introduction of DNA into cells is well-known to those of skill in the art Four general methods for delivering a gene into cells have been described ( 1 ) chemical methods (Graham et al 1973, Zatloukal et al 1992) (2) physical methods such as microinjection (Capecchi, 1980) electroporation (Wong et al 1982 Fromm et al 1985 U S Patent No 5 384 253) and the gene gun (Johnston et al 1994 Fynan et c;/ 1993), (3) viral vectors (Clapp 1993 Lu et al 1993 Eglitis et α/ 1988a 1988b) and (4) receptor-mediated mechanisms (Cuπel et al 1991 , 1992 Wagner et al 1992)

(i) Elect i opoi ation

The application of brief, high-voltage electric pulses to a variety of animal and plant cells leads to the formation of nanometer-sized pores in the plasma membrane DNA is taken directly into the cell cytoplasm either through these pores or as a consequence of the redistribution of membrane components that accompanies closure of the pores Electroporation can be extremely efficient and can be used both for transient expression of cloned genes and for establishment of cell lines that carry integrated copies of the gene of interest Electroporation in contrast to calcium phosphate-mediated transfection and protoplast fusion, frequently gives rise to cell lines that carry one, or at most a few integrated copies of the foreign DNA

The introduction of DNA by means of electroporation is well-known to those of skill in the art In this method, certain cell wall-degrading enzymes such as pectin-degrading enzymes, are employed to render the target recipient cells more susceptible to transformation by electroporation than untreated cells Alternatively recipient cells are made more susceptible to transformation, by mechanical wounding To effect transformation by electroporation one may employ either friable tissues such as a suspension culture of cells, or embryogenic callus or alternatively one may transform immature embryos or other organized tissues directly One would partially degrade the cell walls of the chosen cells by exposing them to pectin-degrading enzymes (pectolyases) or mechanically wounding in a controlled manner Such cells would then be recipient to DNA transfer by electroporation which may be carried out at this stage and transformed cells then identified by a suitable selection or screening protocol dependent on the nature of the newly incoφorated DNA

(;/) Microprojectile Bombai dment

A further advantageous method for delivering transforming DNA segments to plant cells is microprojectile bombai dment In this method particles may be coated with nucleic acids and delivered into cells by a propelling force Exemplary particles include those comprised of tungsten gold platinum and the like An advantage of microprojectile bombardment, in addition to it being an effective means of reproducibly stably transforming monocots. is that neither the isolation of protoplasts (Cπstou et al , 1988) nor the susceptibility to Agrobacterium infection is required An illustrative embodiment of a method for delivering DNA into maize cells by acceleration is a Biohstics Particle Delivery System, which can be used to propel particles coated with DNA or cells through a screen, such as a stainless steel or Nytex screen, onto a filter surface covered with plant cells cultured in suspension. The screen disperses the particles so that they are not delivered to the recipient cells in large aggregates. It is believed that a screen intervening between the projectile apparatus and the cells to be bombarded reduces the size of projectiles aggregate and may contribute to a higher frequency of transformation by reducing damage inflicted on the recipient cells by projectiles that are too large.

For the bombardment, cells in suspension are preferably concentrated on filters or solid culture medium Alternatively, immature embryos or other target cells may be arranged on solid culture medium The cells to be bombarded are positioned at an appropriate distance below the macroprojectile stopping plate. If desired, one or more screens also are positioned between the acceleration device and the cells to be bombarded Through the use of techniques set forth herein one may obtain up to 1.000 or more foci of cells transiently expressing a marker gene The number of cells in a focus which express the exogenous gene product 48 hours post-bombardment often range from 1 to 10 and average 1 to 3

In bombardment transformation, one may optimize the prebombardment cultuπng conditions and the bombardment parameters to yield the maximum numbers of stable transformants Both the physical and biological parameters for bombardment are important in this technology Physical factors are those that involve manipulating the DNA/microprojectile precipitate or those that affect the flight and velocity of either the macro- or microprojectilcs. Biological factors include all steps involved in manipulation of cells before and immediately after bombai dment the osmotic adjustment ot target cells to help alleviate the trauma associated with bombai dment and also the nature of the tiansforming DNΛ such as linearized DNA or intact supercoiled plasmids It is believed that pre-bombardment manipulations aie especially important for successful transformation of immature embryos

Accordingly it is contemplated that one may wish to adjust various of the bombardment parameters in small scale studies to fully optimize the conditions One may particularly wish to adjust physical parameters such as gap distance flight distance, tissue distance, and helium pressure One also may minimize the trauma reduction factors (TRFs) by modifying conditions which influence the physiological state of the recipient cells and which may therefore influence transformation and integration efficiencies For example the osmotic state tissue hydration and the subculture stage oi cell cycle of the recipient cells may be adjusted foi optimum transformation The execution of other routine adjustments will be known to those of skill in the art in light ot the present disclosure

(in) Agi obactei mm-Mediated Transfei

A robactermm-mediaied transfer is a widely applicable system for introducing genes into plant cells because the DNA can be introduced into whole plant tissues, thereby bypassing the need for regeneration ot an intact plant from a protoplast The use of Aαiohαcterium-mcdialed plant integrating vectors to introduce DNA into plant cells is well known in the art See tor example the methods described (Fralev et αl 1985, Rogers et αl 1987) Advances in A,i,'/ofr_<./ctetπ//?;-medιated transfer now allow introduction of large segments of DNA (Hamilton 1997 Hamilton et αl 1996)

Using conventional transformation vectors chiomosomal integration is required for stable inheritance of the foreign DNA However the vector described herein may be used for transformation with or without integration as the centromere function required for stable inheritance is encoded within the minichromosome In particulai embodiments transformation events in which the minichromosome is not chromosomally integrated may be preferred in that problems w ith site-specific v ariations in expression and insertional mutagenesis mav be avoided

The integration of the Ti-DNA is a relatively precise process resulting in few rearrangements The region of DNA to be transferred is defined by the border sequences and intervening DNA is usually inserted into the plant genome as described (Spielmann et al , 1986, Jorgensen et al , 1987) Modem Agrobacterium transformation vectors are capable of replication in E coli as well as Agrobacterium, allowing for convenient manipulations as described (Klee et α/ 1985) Moreover recent technological advances in vectors for Agiobacteiium-mediated gene transfer have improved the arrangement of genes and restriction sites in the vectors to facilitate construction of vectors capable of expiessing various polypeptide coding genes The vectors described (Rogers et al 1987) have convenient multi-linker regions flanked by a promoter and a polyadenvlation site for direct expression of inserted polypeptide coding genes and are suitable for present puφoses In addition Agi obactei mm containing both armed and disarmed Ti genes can be used for the transformations In those plant stiains where A qrohacterium-mediated transfoimation is efficient, it is the method of choice because of the facile and defined nature of the gene transfer

Agro/w teπ-fw-mediated transformation ot leaf disks and other tissues such as cotyledons and hypocotvls appears to be limited to plants that Agiobαcteπum naturally infects Agiobαctenum-mediated transformation is most efficient in dicotyledonous plants Few monocots appear to be natural hosts for Agrobacterium although transgenic plants have been produced in asparagus and more significantly in maize using Agrobacterium vectors as described (Bytebier et al 1987 U S Patent No 5 591 616 specifically incoφorated herein by reference) Therefore commercially important cereal grains such as rice corn and wheat must usually be tiansformed using alternative methods However as mentioned abov e the transformation of asparagus using Aiξi obacteriiim also can be achieved (sec, for example Bytebier et al 1987) transfer may be made more efficient through the use of^" a mutant that is defective in integration of the Agrobactermm T-DNA but competent for delivery of the DNA into the cell (Mysore et al . 2000a) Additionally, even in Arabidopsis ecotypes and mutants that are recalcitrant to Agrohacterium root transformation, germ- line transformation may be carried out (Mysore et al . 2000b)

A transgenic plant formed using Agrobacterium transformation methods typically contains a single gene on one chromosome Such transgenic plants can be referred to as being hemizygous for the added gene. A more accurate name for such a plant is an independent segregant. because each transformed plant represents a unique T-DNA integration event.

More preferred is a transgenic plant that is homozygous for the added foreign DNA, i.e . a transgenic plant that contains two copies of a transgene. one gene at the same locus on each chromosome of^" a chromosome pair A homozygous transgenic plant can be obtained by sexually mating (selfing) an independent segregant transgenic plant that contains a single added transgene. germinating some of the seed produced and analyzing the resulting plants produced for enhanced activ ity relative to a control (native, non-transgenic) or an independent segregant transgenic plant

Even more preferred is a plant in which the minichromosome has not been chromosomally integrated. Such a plant may be termed 2n + x. wheie 2n is the diploid number of chromosomes and where x is the number of minichromosomes Initially, transformants may be 2n+l . i.e. having 1 additional minichromosome In this case, it may be desirable to self the plant or to cross the plant with another 2n + 1 plant to yield a plant which is 2n + 2 The 2n + 2 plant is preferred in that it is expected to pass the minichromosome through meiosis to all its offspring

It is to be understood that two different transgenic plants also can be mated to produce offspring that contain two independently segregating added, exogenous minichromosomes Selfing of appropriate progeny can produce plants that are homozygous tor both added, exogenous minichromosomes that encode a poly peptide of interest Back-crossing to a parental plant and out-crossing with a non-transgenic plant also are contemplated

Civ) Other Transformation Methods

Transformation of plant protoplasts can be achieved using methods based on calcium phosphate precipitation, polyethylene glycol treatment, electroporation, and combinations of these treatments (see. e.g , Potrykus et al, 1985. Lorz et al , 1985, Fromm et al , 1986; Uchimiya et al, 1986. Calhs et al, 1987: Marcotte et al, 1988)

Application of these systems to different plant strains for the puφose of making transgenic plants depends upon the ability to regenerate that particular plant strain from protoplasts Illustrative methods for the regeneration of cereals from protoplasts are described (Fujimura et al, 1985. Toπyama et al, 1986; Yamada et al , 1986.

Abdullah et al, 1986).

To transform plant strains that cannot be successfully regenerated from protoplasts, other ways to introduce DNA into intact cells or tissues can be utilized. For example, regeneration of cereals from immature embryos or explants can be effected as described (Vasil 1988). In addition, "particle gun" or high-velocity microprojectile technology can be utilized (Vasil 1992)

Using that latter technology, DNA is carried through the cell wall and into the cytoplasm on the surface of small metal particles as described (Klein et al , 1987. Klein et al, 1988. McCabe et al . 1988) The metal particles penetrate through several layers of cells and thus allow the transformation of cells within tissue explants

Protoplast fusion, for example, could be used to integrate a minichromosome constructed in a host cell, such as a yeast cell, and then fuse those cells to plant protoplasts The chromosomes lacking plant centromeres (such as yeast chromosomes in this example) would be eliminated by the plant cell while the minichromosome would be stably maintained Numerous examples of protocols foi protoplast fusion that could be used with the invention have been described (see. e g . Negrutiu et al . 1992. and Peterson)

Liposome fusion could be used to intioduce a recombinant construct comprising a centromere, such as a minichromosome, by. for example, packaging the recombinant construct into small droplets of lipids (hposomes) and then fusing these hposomes to plant protoplasts thus delivering the AC into the plant cell (see Lurqui and Rollo, 1993).

VIII. Exogenous Genes for Expression in Plants

One particularly important advance of the present invention is that it provides methods and compositions for expression of exogenous genes in plant cells One advance of the constructs of the current invention is that they enable the introduction of multiple genes, potentially representing an entire biochemical pathway Significantly, the current invention allows for the transformation of plant cells with a minichromosome comprising a number of structural genes Another advantage is that more than one minichromosome could be introduced, allowing combinations of genes to be moved and shuffled Moreover, the ability to eliminate a minichromosome from a plant would provide additional flexibility, making it possible to alter the set of genes contained within a plant Further, by using site-specific recombinases. it should be possible to add genes to an existing minichromosome once it is in a plant

Added genes often will be genes that direct the expression of a particular protein or polypeptide product, but they also may be non-expressible DNA segments, e g . transposons such as Ds that do not direct their own transposition As used herein, an ' expressible gene" is any gene that is capable of being transcribed into RNA (e g . mRNA. antisense RNA. etc ) or translated into a protein, expressed as a trait of interest. or the like, etc . and is not limited to selectable, screenable or non-selectable marker genes The inventors also contemplate that where both an expressible gene that is not necessarily a marker gene is employed in combination w ith a marker gene, one may employ the separate genes on eithei the same 01 different DNA segments for transformation In the lattei case, the different vectors are delivered concuirently to recipient cells to maximize cotranstormation

The choice of the particular DNA segments to be delivered to the recipient cells often will depend on the puφose of the transformation One of the major puφoses of transformation of crop plants is to add some commercially desirable, agronomically important traits to the plant Such traits include but are not limited to. herbicide resistance or tolerance, insect resistance or tolerance, disease resistance or tolerance (viral, bacterial fungal nematode) stress tolerance and/or resistance, as exemplified by resistance or tolerance to diought. heat chilling fieezing excessive moistuie, salt stress, oxidative stress increased yields, food content and makeup physical appearance male sterility, drydown, standabihty, prolificacy starch quantity and quality oil quantity and quality, protein quality and quantity, amino acid composition and the like One may desire to incoφorate one or more genes conferring any such desirable trait or traits, such as, tor example a gene or genes encoding herbicide resistance

In certain embodiments the present invention contemplates the transformation of a recipient cell with minichromosomes comprising more than one exogenous gene As used herein, an ' exogenous gene " is a gene not normally found in the host genome in an identical context By this it is meant that the gene may be isolated from a different species than that of the host genome or alternatively isolated from the host genome but operably linked to one or more regulatory regions which differ from those found in the unaltered, native gene Two or more exogenous genes also can be supplied in a single transformation event using either distinct tiansgene-encoding vectors or using a single vector incoφorating two or more gene coding sequences For example, plasmids bearing the bai and aroA expression units in either convergent divergent or cohnear orientation are considered to be particularly useful Further preferred combinations arc those of an insect resistance gene such as a Bt gene, along with a protease inhibitoi gene such as pinll. or the use of bai in combination with either ot the above genes Of course any two or more transgenes ot any description such as those conferring herbicide insect disease (vital, bacterial, fungal nematode) oi drought lesistance male sterility drydown standabihty piohficacy. starch properties oil quantity and quality or those incieasing yield or nutritional quality may be employed as desired

(i) Heibicide Resistance

The genes encoding phosphinothncm acetyltransferase (bai and pat), glyphosate tolerant EPSP synthase genes the glyphosate degradative enzyme gene gox encoding glyphosate oxidoreductase, deli (encoding a dehalogenase enzyme that inactivates dalapon) herbicide resistant (e g , sulfonylurea and lmidazohnone) acetolactate synthase and bxn genes (encoding a nitπlase enzyme that degrades bromoxynil) are good examples of herbicide resistant genes for use in transformation The bai and pat genes code lor an enzyme phosphinothncm acetyltransferase (PAT) which inactivates the herbicide phosphinothncm and prevents this compound from inhibiting glutamine synthetase enzymes The enzyme 5-enolpyruvylshιkιmate 3-phosphate synthase (EPSP Synthase), is normally inhibited by the herbicide N-(phosphonomethyl)glycιne (glyphosate) However genes are known that encode glyphosate-resistant EPSP synthase enzymes These genes are particularly contemplated for use in plant transformation The deh gene encodes the enzyme dalapon dehalogenase and confei s resistance to the herbicide dalapon The bxn gene codes foi a specific nitπlase enzyme that converts bromoxynil to a non-herbicidal degradation product

(//) insect Resistance

Potential insect resistance genes that can be intioduced include Bacillus thuiinmeiisis ciystal toxin genes or Bt genes (Watrud et al 1985) Bt genes may piovide resistance to lepidopteran or coleopteran pests such as Euiopean Corn Boier (ECB) Preferred Bt toxin genes for use in such embodiments include the and CnΙA(c) genes Endotoxin genes trom other species of B thurιιii>ιeιιsιs which affect insect growth or development also may be employed in this regard

It is contemplated that preferred Bt genes foi use in the transformation protocols disclosed herein will be those in which the coding sequence has been modified to effect increased expiession in plants and more particularly, in monocot plants Means foi preparing synthetic genes are well known in the art and are disclosed in. for example. U S Patent No 5.500.365 and U S Patent Number No 5.689.052 each of the disclosures of which are specifically incoφorated herein by reference in their entirety Examples of such modified Bt toxin genes include a synthetic Bt CnΙA(b) gene (Perlak et al , 1991 ), and the synthetic CIΛIA(C) gene termed 1800b (PCT Application WO 95/06128) Some examples of other Bt toxin genes known to those of skill in the art are given in Table 1 below

''Adapted from. http://epunιx biols.susx.ac.uk/Home/Neil_Cnckmore/Bt/index.html

Protease inhibitors also may provide insect resistance (Johnson et al, 1989). and will thus hav e utility in plant transformation The use ot a protease inhibitor II gene, pinll. from tomato or potato is envisioned to be particularly useful Even more advantageous is the use of a pinll gene in combination with a Bt toxin gene, the combined effect of which has been discovered to produce synergistic insecticidal activity Other genes which encode inhibitors of the insect^'s digestive system, or those that encode enzymes or co-factors that facilitate the production of inhibitoi s. also may be useful This group may be exemplified by oryzacystatin and amylase inhibitors such as those from wheat and barley.

Also, genes encoding lectins may confer additional or alternative insecticide properties Lectins (originally termed phytohemagglutinins) arc multivalent carbohydrate-binding proteins which have the ability to agglutinate red blood cells from a range of species. Lectins have been identified recently as insecticidal agents with activity against weevils. ECB and rootworm (Murdock et al , 1990. Czapla & Lang. 1990) Lectin genes contemplated to be useful include, for example, barley and wheat germ agglutinin (WGA) and rice lectins (Gatehouse et al, 1984). with WGA being preferred

Genes controlling the production of large or small polypeptides active against insects when introduced into the insect pests, such as, e g . lytic peptides. peptide hormones and toxins and venoms, form another aspect of the invention. For example, it is contemplated that the expression of juvenile hormone esterase. directed towards specific insect pests, also may result in insecticidal activity, or perhaps cause cessation of metamoφhosis (Hammock et al , 1990)

Transgenic plants expressing genes which encode enzymes that affect the integrity of the insect cuticle form yet another aspect of the invention Such genes include those encoding, e.g.. chitinasc. proteases, hpases and also genes for the production of nikkomycin. a compound that inhibits chitin synthesis, the introduction of any of which is contemplated to produce insect resistant plants Genes that code for activities that aflect insect molting, such as those affecting the production of ecdysteroid UDP-glucosyl transferase also fall within the scope of the useful transgenes of the present invention

Genes that code for enzymes that facilitate the pioduction of compounds that reduce the nutritional quality of the host plant to insect pests also are encompassed by the present invention It may be possible, for instance to confer insecticidal activity on a plant by altering its sterol composition Sterols aie obtained by insects from their diet and are used for hormone synthesis and membrane stability Therefore alterations in plant sterol composition by expression of novel genes e g , those that directly promote the production of undesirable sterols or those that conv ert desirable sterols into undesirable forms, could have a negative effect on insect grow th and/or development and hence endow the plant with insecticidal activity Lipoxygenases arc naturally occurring plant enzymes that have been shown to exhibit anti-nutπtional effects on insects and to i educe the nutritional quality of their diet Therefore further embodiments of the invention concern transgenic plants with enhanced hpoxygenase activity which may be resistant to insect feeding

Ti ipsacum dactxloides is a species of grass that is resistant to certain insects including corn root worm It is anticipated that genes encoding proteins that are toxic to insects or are involved in the biosynthesis of compounds toxic to insects w ill be isolated from Tiipsacum and that these novel genes w ill be useful in conferring resistance to insects It is known that the basis of insect resistance in Ti ipsacum is genetic because said resistance has been transferred to Zea nun s v ia sexual crosses (Branson and Guss 1972) It is furthei anticipated that other cereal monocot or dicot plant species may have genes encoding proteins that are toxic to insects which would be useful for producing insect resistant plants

Further genes encoding proteins characterized as having potential insecticidal activity also may be used as tiansgenes in accoidance herewith Such genes include foi example, the covvpea trypsin inhibitor (CpTI. Hilder et al 1987) which may be used as a iootworm deterrent, genes encoding avermectin (Aveimecttn and Abamectin . Campbell. W C . Ed 1989 Ikeda et al 1987) which may prove particulaily useful as a corn rootworm deterrent πbosome inactivating piotein genes and even genes that regulate plant structures Transgenic plants including anti-insect antibody genes and genes that code foi enzymes that can convert a non-toxic insecticide (pro-insecticide) applied to the outside of the plant into an insecticide inside the plant also are contemplated

(in) Envu onment or Stress Resistance Improvement of a plants ability to tolerate various environmental stresses such as. but not limited to. drought, excess moisture, chilling, freezing, high temperature, salt, and oxidative stress, also can be effected through expression of novel genes It is proposed that benefits may be realized in terms of increased resistance to freezing temperatures through the introduction of an antifreeze" protein such as that of the Winter Flounder (Cutler et al , 1989) or synthetic gene derivatives thereof Improved chilling tolerance also may be conferred through increased expiession of glyceιol-3-phosphate acetyltransferase in chloroplasts (Wolter et al , 1992) Resistance to oxidative stress (often exacerbated by conditions such as chilling temperatures in combination with high light intensities) can be conferred by expression of superoxide dismutase (Gupta et al , 1993). and may be improved by glutathione leductase (Bowler et al , 1992) Such strategies may allow for tolerance to freezing in newly emerged fields as well as extending later maturity higher yielding varieties to earlier ielative maturity zones

It is contemplated that the expression of novel genes that favorably effect plant water content, total water potential, osmotic potential, and turgor will enhance the ability of the plant to tolerate drought As used herein, the terms ' drought resistance and "drought tolerance ' are used to refer to a plants increased resistance or tolerance to stress induced by a reduction in water availability as compared to normal circumstances and the ability ot the plant to function and survive in lower-water environments In this aspect of the invention it is proposed, for example, that the expiession of genes encoding for the bios nthesis of osmotically-active solutes such as polyol compounds mav impart protection against drought Within this class are genes encoding foi mannitol-L-phosphate dehydrogenase (Lee and Saicr 1982) and trehalose-6-phosphate synthase (Kaasen et al 1992) Through the subsequent action of native phosphatases in the cell or by the introduction and coexpression of a specific phosphatase these introduced genes will result in the accumulation of either mannitol or trehalose respectively both of which have been well documented as protective compounds able to mitigate the effects of stress Mannitol accumulation in transgenic tobacco has been verified and preliminary results indicate that plants expressing high levels of this metabolite are able to tolerate an applied osmotic stress (Tarczynski et al 1992 1993)

Similarly the efficacy of other metabolites in protecting either enzyme function (e t> alanopine or propionic acid) or membrane integrity (e g alanopine) has been documented (Loomis ef ci/ 1989) and therefore expression of genes encoding tor the biosynthesis of these compounds might confer drought resistance in a manner similar to or complimentary to mannitol Other examples of naturally occurring metabolites that are osmotically active and/or provide some direct protective effect during drought and/or desiccation include fructose, erythπtol (Coxson et α/ 1992), sorbπol dulcitol (Karsten et ci/ 1992) glucosylglycerol (Reed et al 1984 ErdMann et al 1992), sucrose stachyose (Koster and Leopold 1988 Blackman et al 1992), raffinose (Bernal-Lugo and Leopold 1992), prohne (Rensburg et al 1993), glycine betaine ononitol and pinitol (Vernon and Bohneit 1992) Continued canopy growth and increased reproductive fitness during times of stress will be augmented by introduction and expression of genes such as those controlling the osmotically active compounds discussed above and other such compounds Currently preferred genes which promote the synthesis of an osmotically active polyol compound are genes which encode the enzymes mannitol- 1 -phosphate dehydrogenase trehalose-6-phosphate synthase and myoinositol O-methyltransferase It is contemplated that the expression of specific proteins also may increase drought tolerance. Three classes of Late Embryogenic Proteins have been assigned based on structural similarities (see Dure et al. 1989). All three clas.ses of^" LEAs have been demonstrated in maturing (i.e. desiccating) seeds. Within these 3 types of LEA proteins. the Type-II (dehydrin-type) have generally been implicated in drought and/or desiccation tolerance in vegetative plant parts (i.e. Mundy and Chua, 1988; Piatkowski et al, 1990; Yamaguchi-Shinozaki et al, 1992). Recently, expression of a Type-Ill LEA (HVA- 1) in tobacco was found to influence plant height, maturity and drought tolerance (Fitzpatrick, 1993). In rice, expression of the HVA-1 gene influenced tolerance to water deficit and salinity (Xu et al, 1996). Expression of structural genes from all three LEA groups may therefore confer drought tolerance. Other types of proteins induced during water stress include thiol proteases, aldolases and transmembrane transporters (Guerrero et al, 1990), which may confer various protective and/or repair-type functions during drought stress. It also is contemplated that genes that effect lipid biosynthesis and hence membrane composition might also be useful in conferring drought resistance on the plant.

Many of these genes for improving drought resistance have complementary modes of action. Thus, it is envisaged that combinations of these genes might have additive and/or synergistic effects in improving drought resistance in plants. Many of these genes also improve freezing tolerance (or resistance): the physical stresses incurred during freezing and drought are similar in nature and may be mitigated in similar fashion. Benefit may be conferred via constitutive expression of these genes, but the preferred means of expressing these novel genes may be through the use of a turgor-induced promoter (such as the promoters for the turgor-induced genes described in Guerrero et al. 1990 and Shagan et al, 1993 which are incoφorated herein by reference). Spatial and temporal expression patterns of^" these genes may enable plants to better withstand stress.

It is proposed that expression of genes that are involved with specific moφhological traits that allow for increased water extractions from drying soil would be of benefit For example introduction and expiession of genes that alter root characteristics may enhance water uptake It also is contemplated that expression of genes that enhance reproductive fitness during times of stress would be of signif icant v alue Foi example expiession of genes that improve the synchiony of pollen shed and receptiveness of the female flower parts ; e silks would be of benefit In addition it is proposed that expression of genes that minimize kernel abortion during times of stress ould increase the amount of grain to be harvested and hence be of value

Given the oveiall role of water in determining yield, it is contemplated that enabling plants to utilize water more efficiently through the introduction and expression of novel genes will improve overall performance even when soil water availability is not limiting By introducing genes that improve the ability of plants to maximize water usage across a full range of stresses relating to water availability, yield stability or consistency of yield performance may be realized

(ι\ ) Di sea se Resistance

It is proposed that increased resistance to diseases may be realized through introduction of genes into plants, for example into monocotyledonous plants such as maize It is possible to produce resistance to diseases caused by viruses, bacteria fungi and nematodes It also is contemplated that control of mycotoxin producing organisms may be realized through expression of introduced genes

Resistance to viruses may be produced thiough expression of novel genes For example, it has been demonstrated that expression of a viral coat protein in a transgenic plant can impart resistance to infection of the plant by that virus and perhaps other closely related viruses (Cuozzo et al 1988 Hemenway et al 1988 Abel et al 1986) It is contemplated that expression of antisense genes targeted at essential viral functions mav also impart resistance to viruses For example an antisense gene targeted at the gene responsible for replication of viral nucleic acid may inhibit replication and lead to resistance to the virus It is believed that lnteiference with other viral functions through the use of antisense genes also may increase resistance to viruses. Further, it is proposed that it may be possible to achieve resistance to viruses through other approaches, including, but not limited to the use of satellite viruses.

It is proposed that increased resistance to diseases caused by bacteria and fungi may be realized through introduction of novel genes. It is contemplated that genes encoding so-called "peptide antibiotics," pathogenesis related (PR) proteins, toxin resistance, and proteins affecting host-pathogen interactions such as moφhological characteristics will be useful. Peptide antibiotics are polypeptide sequences which are inhibitory to growth of bacteria and other microorganisms. For example, the classes of peptides referred to as cecropins and magainins inhibit growth of many species of bacteria and fungi. It is proposed that expression of PR proteins in monocotyledonous plants such as maize may be useful in conferring resistance to bacterial disease. These genes are induced following pathogen attack on a host plant and have been divided into at least five classes of proteins (Bol, Linthorst, and Cornelissen, 1990). Included amongst the PR proteins are β-1 , 3-glucanases, chitinases, and osmotin and other proteins that are believed to function in plant resistance to disease organisms. Other genes have been identified that have antifungal properties, e.g., UDA (stinging nettle lectin) and hevein (Broakaert et a , 1989; Barkai-Golan et al, 1978). It is known that certain plant diseases are caused by the production of phytotoxins. It is proposed that resistance to these diseases would be achieved through expression of a novel gene that encodes an enzyme capable of degrading or otherwise inactivating the phytotoxin. It also is contemplated that expression of novel genes that alter the interactions between the host plant and pathogen may be useful in reducing the ability of the disease organism to invade the tissues of the host plant, e.g., an increase in the waxiness of the leaf cuticle or other moφhological characteristics.

(v) Plant Agronomic Characteristics

Two of the factors determining where crop plants can be grown are the average daily temperature during the growing season and the length of time between frosts. Within the areas where it is possible to grow a particular crop, there aie varying limitations on the maximal time it is allowed to grow to maturity and be harvested For example a v ariety to be grown in a particular area is selected foi its ability to mature and dry down to harvestable moistuie content within the required period of time with maximum possible yield Therefore crops of varying maturities is developed for different growing locations Apart from the need to dry down sufficiently to permit harvest it is desirable to have maximal drying take place in the field to minimize the amount of energy required for additional drying post-harvest Also, the more readily a product such as grain can dry down, the more time there is available for growth and kernel fill It is considered that genes that influence maturity and/or dry down can be identified and introduced into plant lines using transformation techniques to create new varieties adapted to different growing locations or the same growing location but having improved yield to moisture ratio at harvest Expression of genes that are involved in regulation of plant development may be especially useful

It is contemplated that genes may be introduced into plants that would improve standabihty and other plant growth characteristics Expression of novel genes in plants which confer stronger stalks, improved root systems, or prev ent or reduce ear droppage would be of great value to the farmer It is proposed that introduction and expression of genes that increase the total amount of photoassimilate available by, for example, increasing light distribution and/or interception would be advantageous In addition the expression of genes that increase the efficiency of photosynthesis and/or the leaf canopy would further increase gains in productivity It is contemplated that expression of a phytochrome gene in crop plants may be advantageous Expression of such a gene may reduce apical dominance, confer semidwarfism on a plant, and increase shade tolerance (U S Patent No 5 268,526) Such approaches would allow for increased plant populations in the field

(vi) Nutrient Utilization

The ability to utilize available nutrients may be a limiting factor in growth of crop plants It is proposed that it would be possible to altei nutrient uptake, tolerate pH extremes, mobilization through the plant, storage pools, and availability for metabolic activities by the introduction of novel genes. These modifications would allow a plant such as maize to more efficiently utilize available nutrients It is contemplated that an increase in the activity of, for example, an enzyme that is normally present in the plant and involved in nutrient utilization would increase the availability of a nutrient An example of such an enzyme would be phytase It is further contemplated that enhanced nitrogen utilization by a plant is desirable Expression of a glutamate dehydrogenase gene in plants, e g . E coli gdhA genes, may lead to increased fixation of nitrogen in organic compounds Furthermore, expression of gdhA in plants may lead to enhanced resistance to the herbicide glufosinate by incorporation of excess ammonia into glutamate. thereby detoxifying the ammonia It also is contemplated that expression of a novel gene may make a nutrient source available that was previously not accessible, e g.. an enzyme that releases a component of nutrient value from a more complex molecule, perhaps a macromolecule

(vii) Male Sterihtx Male sterility is useful in the production of hybrid seed It is proposed that male sterility may be produced through expression of novel genes For example, it has been shown that expression of genes that encode proteins that interfere with development of the male inflorescence and/or gametophyte result in male sterility Chimeric πbonuclease genes that express in the anthers of transgenic tobacco and oilseed rape have been demonstrated to lead to male sterility (Maπani et al , 1990)

A number of mutations were discovered in maize that confer cytoplasmic male sterility One mutation in particular, referred to as T cytoplasm, also correlates with sensitivity to Southern corn leaf blight A DNA sequence, designated TURF- 13 (Levings. 1990). was identified that correlates with T cytoplasm It is proposed that it would be possible through the introduction of TURF- 13 via transformation, to separate male sterility from disease sensitivity As it is necessary to be able to restore male fertility for breeding purposes and for grain production, it is proposed that genes encoding restoration of male fertility also may be introduced

(viu) Improved Nutritional Content

Genes may be introduced into plants to improve the nutrient quality or content of a particular crop Introduction of genes that alter the nutrient composition of a crop may greatly enhance the feed or food value. For example, the protein of^" many grains is suboptimal for feed and food puφoses. especially when fed to pigs, poultry, and humans. The protein is deficient in several amino acids that are essential in the diet of these species, requiring the addition of supplements to the grain. Limiting essential amino acids may include lysine, methionine. tryptophan. threonine, vahne. argimne. and histidine Some amino acids become limiting only after corn is supplemented with other inputs for feed formulations. The levels of these essential amino acids in seeds and grain may be elevated by mechanisms which include, but are not limited to. the introduction of genes to increase the biosynthesis of the amino acids, decrease the degradation of the amino acids, increase the storage of the amino acids in proteins, or increase transport of the amino acids to the seeds or grain

The protein composition of a crop may be altered to improve the balance of amino acids in a variety of ways including elevating expression of native proteins, decreasing expression of those with poor composition, changing the composition of native proteins, or introducing genes encoding entirely new proteins possessing superior composition

The introduction of genes that alter the oil content of a crop plant may also be of value Increases in oil content may result in increases in metabohzable-energy-content and density of the seeds for use in feed and food The introduced genes may encode enzymes that remove or reduce rate-limitations or regulated steps in fatty acid or hpid biosynthesis. Such genes may include, but are not limited to. those that encode acetyl- CoA carboxylase. ACP-acyltransferase. β-ketoacyl-ACP synthase. plus other well known fatty acid biosynthetic activities. Other possibilities are genes that encode proteins that do not possess enzymatic activity such as acyl carrier protein Genes may be introduced that alter the balance of fatty acids present in the oil providing a more healthful or nutritive feedstuff The introduced DNA also may encode sequences that block expression of enzymes involved in fatty acid biosynthesis, altering the proportions of fatty acids present in crops.

Genes may be introduced that enhance the nutritive value of the starch component of crops, for example by increasing the degree of branching, resulting in improved utilization of the starch in livestock by delaying its metabolism Additionally, other major constituents of a crop may be altered, including genes that affect a variety ot other nutritive, processing, or other quality aspects For example, pigmentation may be increased or decreased

Feed or food crops may also possesses insufficient quantities of vitamins, requiring supplementation to provide adequate nutritive value Introduction of genes that enhance vitamin biosynthesis may be envisioned including, for example, vitamins A. E, B|₂. choline. and the like Mineral content may also be sub-optimal. Thus genes that affect the accumulation or availability of compounds containing phosphorus, sulfur, calcium, manganese, zinc, and iron among others would be valuable

Numerous other examples of improvements of crops may be used w ith the invention. The improvements may not necessarily involve grain, but may, for example. improve the value of a crop for silage Introduction of DNA to accomplish this might include sequences that alter lignin production such as those that result in the ' brown midrib" phenotype associated with supeπor feed value foi cattle

In addition to direct improvements in feed or food value, genes also may be introduced which improve the processing of^" crops and improve the value ot the products resulting from the piocessing One use of crops if via wetmilling Thus novel genes that increase the efficiency and reduce the cost of such processing, foi example by deci easing steeping time may also find use Impioving the value of wetmilling products may include altering the quantity 01 quality ot staich. oil. coin gluten meal, or the components of gluten feed Elevation of starch may be achieved through the identification and elimination of rate limiting steps in starch biosynthesis or by decreasing levels of the other components of crops resulting in proportional increases in starch

Oil is another product of wetmilling, the value of which may be improved by introduction and expiession of genes Oil properties may be altered to improve its performance in the production and use of cooking oil. shortenings, lubricants oi other oil- deπved products or improvement of its health attributes when used in the food-related applications Novel fatty acids also may be synthesized which upon extraction can serve as starting materials tor chemical syntheses The changes in oil properties may be achieved by altering the type level, or hpid arrangement of the fatty acids present in the oil This in turn may be accomplished by the addition of genes that encode enzymes that catalyze the synthesis of novel fatty acids and the lipids possessing them or by increasing levels of nativ e fatty acids while possibly reducing levels of precursors Alternatively, DNA sequences may be introduced which slow or block steps in fatty acid biosynthesis resulting in the increase in precursor fatty acid intermediates Genes that might be added include desaturases. epoxidases. hydratases dehydratases and othei enzymes that catalyze reactions involving tatty acid intermediates Repiesentative examples of catalytic steps that might be blocked include the desaturations from steaπc to oleic acid and oleic to hnolenic acid resulting in the respective accumulations ot steaπc and oleic acids Another example is the blockage of elongation steps resulting in the accumulation of C₈ to Ci: saturated fatty acids

(ix) Production or Assimilation of Chemicals or Biologicals

It may further be considered that a transgenic plant prepared in accordance with the invention may be used for the production or manufacturing of useful biological compounds that were either not produced at all, or not produced at the same level, in the corn plant previously. Alternatively, plants produced in accordance with the invention may be made to metabolize certain compounds, such as hazardous wastes, thereby allowing bioremediation of these compounds.

The novel plants producing these compounds are made possible by the introduction and expression of one or potentially many genes with the constructs provided by the invention. The vast array of possibilities include but are not limited to any biological compound which is presently produced by any organism such as proteins, nucleic acids, primary and intermediary metabolites, carbohydrate polymers, enzymes for uses in bioremediation, enzymes for modifying pathways that produce secondary plant metabolites such as flavonoids or vitamins, enzymes that could produce pharmaceuticals. and for introducing enzymes that could produce compounds of interest to the manufacturing industry such as specialty chemicals and plastics. The compounds may be produced by the plant, extracted upon harvest and/or processing, and used for any presently recognized useful purpose such as pharmaceuticals, fragrances, and industrial enzymes to name a few.

(x) Non-Protein-Expressing Sequences

DNA may be introduced into plants for the puφose of expressing RNA transcripts that function to affect plant phenotype yet are not translated into protein. Two examples are antisense RNA and RNA with ribozyme activity. Both may serve possible functions in reducing or eliminating expression of native or introduced plant genes. However, as detailed below, DNA need not be expressed to effect the phenotype of a plant.

1 Antisense RNA

Genes may be constructed oi isolated which when transcribed, produce antisense RNA that is complementary to all or part(s) of a targeted messenger RNA(s) The antisense RNA leduces pioduction of the polypeptide product of the messenger RNA The polypeptide pioduct may be any piotein encoded by the plant genome The aforementioned genes will be referred to as antisense genes An antisense gene may thus be introduced into a plant by transformation methods to produce a novel transgenic plant with reduced expression of a selected protein of interest For example, the protein may be an enzyme that catalyzes a reaction in the plant Reduction of the enzyme activity may reduce or eliminate products of the reaction which include any enzymatically synthesized compound in the plant such as fatty acids, amino acids, carbohydrates, nucleic acids and the like Alternatively, the protein may be a storage protein such as a zein or a structural protein, the decreased expression of which may lead to changes in seed amino acid composition or plant morphological changes respectively The possibilities cited above are provided only by way of example and do not lepresent the full range of applications

2 Ribozymes

Genes also may be constructed or isolated which when transcribed produce RNA enzymes (ribozymes) which can act as endonbonucleases and catalyze the cleavage of RNA molecules with selected sequences The cleavage of selected messenger RNAs can result in the reduced production of their encoded polypeptide products These genes may be used to prepare novel transgenic plants which possess them The transgenic plants may possess reduced levels of polypeptides including, but not limited to the polypeptides cited above

Ribozymes are RNA-protein complexes that cleave nucleic acids in a site-specific fashion Ribozymes have specific catalytic domains that possess endonuclease activity

(Kim and Cech 1987 Gerlach et al 1987 Forster and Symons 1987) For example, a large number of ribozymes accelerate phosphoester transfer reactions ith a high degree of specificity often cleaving onlv one of several phosphoesters in an oligonucleotide substrate (Cech et al , 1981. Michel and Westhof, 1990. Reinhold-Huiek and Snub. 1992). This specificity has been attributed to the requirement that the substrate bind via specific base-pairing interactions to the internal guide sequence ("IGS") ot the ribozyme prior to chemical reaction

Ribozyme catalysis has primarily been observed as part of sequence-specific cleavage/ligation reactions involving nucleic acids (Joyce. 1989, Cech et al . 1981 ) For example, U. S. Patent 5.354.855 reports that certain ribozymes can act as endonucleases with a sequence specificity greater than that of known πbonucleases and approaching that of the DNA restriction enzymes

Several different ribozyme motifs have been described with RNA cleavage activity (Symons, 1992) Examples include sequences from the Group I self splicing introns including Tobacco Ringspot Virus (Prody et al , 1986), Avocado Sunblotch Viroid (Palukaitis et al , 1979. Symons, 1981). and Lucerne Transient Streak Virus (Forster and Symons. 1987) Sequences from these and related viruses are referred to as hammerhead ribozyme based on a predicted folded secondary structure

Other suitable ribozymes include sequences from RNase P with RNA cleavage activity (Yuan et al , 1992. Yuan and Altman, 1994, U S Patents 5, 168,053 and 5.624,824). haiφin ribozyme structures (Berzal-Hcrranz et al . 1992.

Chownra et al . 1993) and Hepatitis Delta virus based ribozymes (U S Patent 5.625.047) The general design and optimization of ribozyme directed RNA cleavage activity has been discussed in detail (Haseloff and Gerlach, 1988, Symons. 1992, Chownra et al, 1994. Thompson et al, 1995)

The other variable on ribozyme design is the selection of a cleavage site on a given target RNA Ribozymes are targeted to a given sequence by virtue of annealing to a site by complimentary base pair interactions Two stretches of homology are required for this targeting These stretches of homologous sequences flank the catalytic ribozyme structure defined above Each stretch of homologous sequence can vary in length from 7 to 15 nucleotides The only requirement foi defining the homologous sequences is that, on the target RNA. they are separated by a specific sequence which is the cleavage site For hammerhead ribozyme. the cleavage site is a dinucleotide sequence on the target RNA is a uracil (U) followed by either an adenine. cytosine or uracil (A.C or U) (Perπman et al , 1992, Thompson et al , 1995) The frequency of this dinucleotide occurring in any given RNA is statistically 3 out of 16 Therefore, for a given target messenger RNA of 1.000 bases. 187 dinucleotide cleavage sites are statistically possible

Designing and testing ribozymes for efficient cleavage of a target RNA is a process well known to those skilled in the art Examples of scientific methods for designing and testing ribozymes are described by Chownra et al , ( 1994) and Lieber and Strauss ( 1995). each incoφorated by reference The identification of operative and preferred sequences for use in down regulating a given gene is simply a matter of preparing and testing a given sequence, and is a routinely practiced "screening" method known to those of skill in the art

3 Induction of Gene Silencing

It also is possible that genes may be introduced to produce novel transgenic plants which have reduced expression of a native gene product by the mechanism of co-suppression It has been demonstrated in tobacco, tomato, and petunia (Goring et al , 1991. Smith et al , 1990. Napoli et al , 1990, van der Krol et al , 1990) that expression of the sense transcript of a native gene ill reduce or eliminate expression of the native gene in a manner similar to that observed for antisense genes The introduced gene may encode all or part of the targeted native protein but its translation may not be required for reduction of levels of that native protein

4 Non-RNA-Expressing Sequences

DNA elements including those of transposable elements such as Ds. Ac. or Mu. may be inserted into a gene to cause mutations These DNA elements may be inserted in order to inactivate (or activate) a gene and thereby tag" a particular trait In this instance the transposable element does not cause instability of the tagged mutation because the utility of the element does not depend on its ability to move in the genome Once a desired trait is tagged, the introduced DNA sequence may be used to clone the corresponding gene, e g , using the introduced DNA sequence as a PCR primer together with PCR gene cloning techniques (Shapuo 1983 Dellaporta et al , 1988) Once identified, the entire gene(s) for the particular trait, including control or regulatory regions where desired, may be isolated, cloned and manipulated as desired The utility of DNA elements introduced into an organism for puφoses of gene tagging is independent of the DNA sequence and does not depend on any biological activity of the DNA sequence, z e , transcription into RNA or translation into protein The sole function of the DNA element is to disrupt the DNA sequence of a gene

It is contemplated that unexpressed DNA sequences including novel synthetic sequences, could be introduced into cells as proprietary ' labels" of those cells and plants and seeds thereof It would not be necessary for a label DNA element to disrupt the function of a gene endogenous to the host organism, as the sole function of this DNA would be to identify the origin of the organism For example, one could introduce a unique DNA sequence into a plant and this DNA element would identify all cells, plants. and progeny of these cells as having arisen from that labeled source It is proposed that inclusion of label DNAs would enable one to distinguish proprietary gcrmplasm or germplasm derived from such from unlabelled germplasm

Another possible element which may be introduced is a matrix attachment region element (MAR), such as the chicken l sozyme A element (Stief, 1989). which can be positioned around an expressible gene of interest to effect an increase in overall expression of the gene and diminish position dependent effects upon incoφoration into the plant genome (Stief et al 1989 Phi- Van et al 1990)

5 Other Other examples of non-protein expressing sequences specifically envisioned for use with the invention include tRiNA sequences, for example, to alter codon usage, and rRNA val iants, for example which may confer resistance to v arious agents such as antibiotics

IX. Biological Functional Equiv alents

Modification and changes may be made in the centromeric DNA segments of the current invention and still obtain a functional molecule with desirable characteristics The following is a discussion based upon changing the nucleic acids of a centromere to create an equivalent, or even an improved, second-generation molecule

In particular embodiments of the invention, mutated centromeric sequences are contemplated to be useful for increasing the utility of the centromere It is specifically contemplated that the function of the centromeres of the current invention may be based upon the secondary structure of the DNA sequences of the centromere and / or the proteins which interact with the centromere By changing the DNA sequence ot the centromere, one may alter the affinity of one or more centromere-associated proteιn(s) for the centromere and / or the secondary structuie of the centromeric sequences thereby changing the activity of the centromere Alternatively changes may be made in the centromeres of the invention which do not effect the activity of the centromere Changes in the centromeric sequences which reduce the size of the DNA segment needed to confer centiomere activity are contemplated to be particularly useful in the current invention, as would changes which increased the fidelity with which the centromere was transmitted during mitosis and meiosis

X. Plants

The term plant " as used herein refers to any type of plant The inventois have provided below an exemplary description ot some plants that may be used with the invention However, the list is not in any way limiting as other types of plants will be known to those of skill in the art and could be used with the invention A common class of plants exploited in agriculture are vegetable crops, including artichokes, kohlrabi, arugula. leeks, asparagus, lettuce (e g . head. leaf, romaine). bok choy. malanga. broccoli, melons (e g . muskmelon. watermelon, crenshaw. honeydew. cantaloupe), brussels sprouts, cabbage, cardoni. carrots, napa. cauliflower, okra. onions, celery, parsley, chick peas, parsnips, chicory. Chinese cabbage, peppers, collards, potatoes, cucumber plants (marrows, cucumbeis). pumpkins, cucurbits, radishes, dry bulb onions, rutabaga, eggplant, salsify, escarole. shallots, endive, garlic, spinach, green onions, squash, greens, beet (sugar beet and fodder beet), sweet potatoes, swiss chard, horseradish, tomatoes, kale, turnips, and spices

Other types of plants frequently finding commercial use include fruit and vine crops such as apples, apricots, cherries, nectarines, peaches, pears, plums, prunes, quince almonds, chestnuts, filberts, pecans, pistachios, walnuts, citrus, blueberries. boysenberπes. cranberries, currants, loganberries, raspberries, strawberries, blackberries, grapes, avocados, bananas, kiwi, persimmons, pomegranate, pineapple, tropical fruits, pomes, melon, mango, papaya, and lychee

Many of the most widely grown plants are field crop plants such as evening primrose, meadow foam, corn (field, sweet, popcorn), hops, jojoba, peanuts, rice. safflower. small grains (barley, oats, rye. wheat, etc ). sorghum, tobacco, kapok. leguminous plants (beans, lentils, peas, soybeans), oil plants (rape, mustard, poppy. olives, sunflowers, coconut, castor oil plants, cocoa beans, groundnuts), fibre plants

(cotton, flax, hemp, jute), lauraceae (cinnamon, camphor), or plants such as coffee. sugarcane, tea. and natural rubber plants

Still other examples of plants include bedding plants such as flowers, cactus, succulents and ornamental plants, as well as tiees such as forest (broad-leaved trees and evergreens, such as conifers), fruit, ornamental, and nut-bearing trees, as well as shrubs and other nursery stock XI. Definitions

As used herein, the terms ''autonomous replicating sequence" oi "ARS^"' or "ongin of replication ^" refer to an origin of DNA replication recognized by pioteins that initiate DNA replication

As used herein, the terms "binary BAC" oi "binary bacterial artificial chromosome^" refer to a bacterial vector that contains the T-DNA border sequences necessary for Agrobactermm mediated transformation (see. for example. Hamilton et al . 1996, Hamilton. 1997, and Liu et al , 1999

As used herein, the term "candidate centromere sequence" refers to a nucleic acid sequence which one wishes to assay for potential centromere function

As used herein, a "centromere" is any DNA sequence that confers an ability to segregate to daughter cells through cell division. In one context, this sequence may produce a segregation efficiency to daughter cells ranging from about 1 % to about 100%:. including to about 5%, 10%, 20%, 30%. 40%, 50%. 60%, 70%, 80%, 90% or about 95% of daughter cells Variations in such a segregation efficiency may find important applications within the scope of the invention, for example, mini-chromosomes carrying centromeres that confer 100% stability could be maintained in all daughter cells without selection, while those that confer 1 % stability could be temporarily introduced into a transgenic organism, but be eliminated when desired In particular embodiments of the invention, the centromere may confer stable segregation of a nucleic acid sequence. including a recombinant construct comprising the centromere, through mitotic or meiotic divisions, including through both meiotic and meitotic divisions A plant centromere is not necessarily derived from plants, but has the ability to promote DNA segregation in plant cells As used herein, the term "centromere-associated protein" refers to a protein encoded by a sequence of the centromere or a protein which is encoded by host DNA and binds with relatively high affinity to the centromere.

As used herein, "eukaryote" refers to living organisms whose cells contain nuclei.

A eukaryote may be distinguished from a "prokaryote" which is an organism which lacks nuclei. Prokaryotes and eukaryotes differ fundamentally in the way their genetic information is organized, as well as their patterns of RNA and protein synthesis.

As used herein, the term "expression" refers to the process by which a structural gene produces an RNA molecule, typically termed messenger RNA (mRNA). The mRNA is typically, but not always, translated into polypeptide(s).

As used herein, the term "genome" refers to all of the genes and DNA sequences that comprise the genetic information within a given cell of an organism. Usually, this is taken to mean the information contained within the nucleus, but also includes the organelles.

As used herein, the term "higher eukaryote" means a multicellular eukaryote, typically characterized by its greater complex physiological mechanisms and relatively large size. Generally, complex organisms such as plants and animals are included in this category. Preferred higher eukaryotes to be transformed by the present invention include, for example, monocot and dicot angiosperm species, gymnosperm species, fern species, plant tissue culture cells of these species, animal cells and algal cells. It will of course be understood that prokaryotes and eukaryotes alike may be transformed by the methods of this invention.

As used herein, the term "host" refers to any organism that is the recipient of a replicable plasmid. or expression vector comprising a plant chromosome. Ideally, host strains used for cloning experiments should be free of any restriction enzyme activity that might degrade the foreign DNA used. Preferred examples of host cells for cloning, useful in the present invention, are bacteria such as Escherichia coli. Bacillus subtilis, Pseiidomonas, Streptomxces. Salmonella, and yeast cells such as S. cerevisiae. Host cells which can be targeted for expression of a minichromosome may be plant cells of any source and specifically include Arabidopsis. maize, rice, sugarcane, sorghum, barley. soybeans, tobacco, wheat, tomato, potato, citrus, or any other agronomically or scientifically important species.

As used herein, the term "hybridization" refers to the pairing of complementary RNA and DNA strands to produce an RNA-DNA hybrid, or alternatively, the pairing of two DNA single strands from genetically different or the same sources to produce a double stranded DNA molecule.

As used herein, the term "linker" refers to a DNA molecule, generally up to 50 or 60 nucleotides long and synthesized chemically, or cloned from other vectors. In a preferred embodiment, this fragment contains one, or preferably more than one, restriction enzyme site for a blunt-cutting enzyme and a staggered-cutting enzyme, such as BainWl. One end of the linker fragment is adapted to be ligatable to one end of the linear molecule and the other end is adapted to be ligatable to the other end of the linear molecule.

As used herein, a "library" is a pool of random DNA fragments which are cloned. In principle, any gene can be isolated by screening the library with a specific hybridization probe (see, for example, Young et al, 1977). Each library may contain the DNA of a given organism inserted as discrete restriction enzyme-generated fragments or as randomly sheered fragments into many thousands of plasmid vectors. For puφoses of the present invention, E. coli, yeast, and Salmonella plasmids are particularly useful when the genome inserts come from other organisms.

As used herein, the term "lower eukaryote" refers to a eukaryote characterized by a comparatively simple physiology and composition, and most often unicellularity. Examples of lower eukaryotes include flagellates, ciliates, and yeast.

As used herein, a "minichromosome" is a recombinant DNA construct including a centromere and capable of transmission to daughter cells. The stability of this construct through cell division could range between from about 1 % to about 100%. including about 5%, 10%, 20%. 30%>, 40%, 50%, 60%, 70%, 80%, 90% and about 95%. The minichromosome construct may be a circular or linear molecule. It may include elements such as one or more telomeres, ARS sequences, and genes. The number of^" such sequences included is only limited by the physical size limitations of the construct itself^". It could contain DNA derived from a natural centromere, although it may be preferable to limit the amount of^" DNA to the minimal amount required to obtain a segregation efficiency in the range of 1- 100%. The minichromosome may be inherited through mitosis or meiosis, or through both meiosis and mitosis. As used herein, the term minichromosome specifically encompasses and includes the terms "plant artificial chromosome^" or "PLAC," and all teachings relevant to a PLAC or plant artificial chromosome specifically apply to constructs within the meaning of the term minichromosome.

As used herein, by "minichromosome-encoded protein" it is meant a polypeptide which is encoded by a sequence of a minichromosome of the current invention. This includes sequences such as selectable markers, telomeres, etc.. as well as those proteins encoded by any other selected functional genes on the minichromosome.

A " 180 base pair repeat^" is defined as any one of the specific repeats disclosed in SEQ ID NOS: 184-212, or a "consensus" sequence derived therefrom. Thus, a given "180 base pair repeat" may include more or less than 180 base pairs, and may reflect a sequence not represented by any of the specific sequences provided herein. As used herein, the term "plant" includes plant cells, plant protoplasts, plant calh. and the like, as well as whole plants regenerated therefrom

As used herein, the term "plasmid ^' oi "cloning vectoi " refeis to a closed covalently circular extrachromosomal DNA or linear DNA which is able to autonomously replicate in a host cell and which is normally nonessential to the survival of the cell A wide variety of plasmids and other vectors are known and commonly used in the art (see, for example. Cohen et al, U.S. Patent No. 4.468.464. which discloses examples of DNA plasmids, and which is specifically incoφorated herein by reference).

As used herein, a "probe" is any biochemical reagent (usually tagged in some way for ease of identification), used to identify or isolate a gene, a gene product, a DNA segment or a protein

As used herein, the term "recombination" refers to any genetic exchange that involves breaking and rejoining of DNA strands.

As used herein the term "regulatory sequence'^" refers to any DNA sequence that influences the efficiency of transcription or translation of any gene. The term includes, but is not limited to. sequences comprising promoters, enhancers and terminators.

As used herein, a "selectable marker" is a gene whose presence results in a clear phenotype, and most often a growth advantage for cells that contain the marker This growth advantage may be present under standard conditions, altered conditions such as elevated temperatuie. or in the presence of^" certain chemicals such as herbicides or antibiotics Use of selectable markers is described, for example, in Broach et al ( 1979) Examples of selectable markers include the thymidine kinase gene, the cellular adenine-phosphonbosyltransferase gene and the dihydrylfolate reductase gene. hygromycin phosphotransferase genes, the bar gene and neomycin phosphotransferase genes, among othei s Prefened selectable markers in the present invention include genes whose expression confer antibiotic or herbicide resistance to the host cell, sufficient to enable the maintenance of a vector within the host cell, and which facilitate the manipulation of the plasmid into new host cells Of^" particular interest in the present invention are proteins conferring cellular resistance to ampicillin. chloramphenicol. tetracychne. G-418. bialaphos. and glyphosate for example

As used herein, a "screenable marker" is a gene whose presence results in an identifiable phenotype This phenotype may be observable under standard conditions, altered conditions such as elevated temperature, or in the presence of certain chemicals used to detect the phenotype.

As used herein, the term "site-specific recombination" refers to any genetic exchange that involves breaking and rejoining of DNA strands at a specific DNA sequence

As used herein, a "structural gene" is a sequence which codes for a polypeptide or

RNA and includes 5' and 3' ends. The structural gene may be from the host into which the structural gene is transformed or from another species. A structural gene will preferably, but not necessarily, include one or more regulatory sequences which modulate the expression of the structural gene, such as a promoter, terminator or enhancer. A structural gene will preferably, but not necessauly, confer some useful phenotype upon an organism comprising the structural gene, for example, herbicide resistance In one embodiment of the invention, a structural gene may encode an RNA sequence which is not translated into a protein, for example a tRNA or rRNA gene.

As used herein, the term "telomere" refers to a sequence capable of capping the ends of a chromosome, thereby preventing degradation of the chromosome end. ensuring replication and preventing fusion to other chromosome sequences.

As used herein, the terms "transformation" or "transfection" refer to the acquisition in cells of new DNA sequences through the chromosomal or extra- chromosomal addition of DNA This is the process by which naked DNA DNA coated with protein, or whole minichromosomes are introduced into a cell, resulting in a potentially heritable change

XII. Examples

The following examples are included to demonstrate preferred embodiments of the invention It should be appreciated by those of skilled the art that the techniques disclosed in the examples which follow represent techniques discovered by the inventors to function well in the practice of the invention and thus can be considered to constitute preferred modes for its practice However, those of skill in the art should, in light of the present disclosure, appreciate that many changes can be made in the specific embodiments which are disclosed and still obtain a like or similar result without departing from the concept spirit and scope ot the invention More specifically it will be apparent that certain agents which are both chemically and physiologically related may be substituted for the agents described herein while the same or similar results would be achieved All such similar substitutes and modifications apparent to those skilled in the art are deemed to be within the spirit, scope and concept of the invention as defined by the appended claims

EXAMPLE 1

Generation of an Arabidopsis thaliana Mapping Population

To generate a pollen donor plant, two parental lines carrying qitl were crossed to one another The qitl I allele was in the Landsberg ecotype background and the qιtl-2 allele was in the Columbia ecotype background The Landsberg ecotype was readily discernible from the Columbia ecotype because it carries a recessive mutation eiecta, which causes the stems to thicken, lnfloresences to be more compact, and the leaves to be more rounded and small than wildtype To utilize this as a marker of a donor plant qi tl 2 pollen was crossed onto a qrtl-I female stigma The F| progeny were heterozygous at all molecular markers yet the progeny retain the quaitet phenotype ot a tetrad of fused pollen grains In addition, progeny display the ERECTA phenotype of the Columbia plant This visible marker serves as an indication that the crossing was successful in generating plants segregating ecotype specific markers Further testing was done to the donor plants by performing PCR analysis to insure that progeny were heterozygous at molecular loci

Due to the fact that the pollen grains cannot be directly assayed for marker segregation and because of the desire to create a long-term resource available for multiple marker assays, it was necessary to cross individual tetrads generated by the donor plant This created sets of progeny plants which yielded both large quantities of tissue and seed These crosses were accomplished efficiently by generating a recipient plant homozygous for male sterility (msl) The recessive mutant nisi was chosen to guard against the possibility of the recipient plant self-fertilizing and the progeny being mistaken for tetrad plants. Due to the fact that the homozygous plant does not self, a stock seed generated by a heterozygous male sterilirs I plant needs to be maintained from which sterile recipient plants can be selected

EXAMPLE 2 Tetrad Pollinations Tetrad pollinations were carried out as follows A mature flower was removed from the donor plant and tapped upon a glass microscope slide to release mature tetrad pollen grains This slide was then placed under a 20-40x Zeiss dissecting microscope To isolate individual tetrad pollen grains, a small wooden dowel was used to which an eyebrow hair with rubber cement was mounted Using the light microscope, a tetrad pollen unit was chosen and touched to the eyebrow hair The tetrad preferentially adhered to the eyebrow hair and was thus lifted from the microscope slide and transported the recipient plant stigmatic surface The transfer was carried out without the use of the microscope, and the eyebrow hair with adhering tetrad was then placed against the recipient stigmatic surface and the hair was manually dragged across the stigma surface The tetrad then preferentially adhered to the stigma of the recipient and the cross pollination was completed Initially. 57 tetrad seed sets consisting of 3-4 seeds each, were collected Plants were grown from these tetrad seed sets, and tissue was collected DNA was extracted from a small portion of the stored tissue foi PCR based segregation analysis Additionally the segregation of the visible eiecta phenotype was scored When the plants set seed, the seed was collected as a source for the larger amounts of DNA required to analyze RFLP segregation by Southern blotting

EXAMPLE 3 Preparation and Analysis of Centromere-Spanning Contigs Previously. DNA fingeφnnt and hybridization analysis of two bacterial artificial chromosome (BAC) libraries led to the assembly of physical maps covering nearly all single-copy portions of the Arabidopsis genome (Marra et al , 1999) However, the presence of repetitive DNA near the Aiabidopsis centromeres, including 180 bp repeats retroelements. and middle repetitive sequences complicated efforts to anchor centromeric BAC contigs to particular chromosomes (Murata et «/ , 1997, Heslop-Harnson et al , 1999 Brandes et al , 1997, Franz et al 1998. Wright et al , 1996, Komecznyet al , 1991 , Pehssier et al , 1995, Voytas and Ausubel. 1988, Chye et al , 1997, Tsay et al , 1993, Richards et al , 1991. Simoens et al 1988 Thompson et al 1996, Pehssier et al , 1996) The inventors used genetic mapping to unambiguously assign these unanchored contigs to specific centromeres, scoring polymoφhic markers in 48 plants with crossovers informative for the entire genome (Copenhaver et al 1998) In this manner several centromeric contigs were connected to the physical maps ot the chromosome arms (see EXAMPLE 6 and Table 4), and a large set of DNA markers defining centromere boundaries were generated DNA sequence analysis confirmed the structure of the contigs for chromosomes II and IV (Lin et al . 1999)

CEN2 and CEN4 were selected in particular for analysis Both reside on structurally similar chromosomes with a 3 5 Mb rDNA arrays on their distal tips, with regions measuring 3 and 2 Mb, respectively between the rDNA and centromeres, and 16 and 13 Mb regions on their long arms (Copenhaver and Pikaard, 1996) The virtually complete and annotated sequence of chromosomes II and IV was used to conduct an analysis of centromeres at the nucleotide level (http //www ncbi nlm nih gov/Entrez/nucleotide html) The sequence composition was analyzed within the genetically-defined centromere boundaries and compared to the adjacent pencentromenc regions (FIGs 12A-T) Analysis of the two centromeres facilitated comparisons of sequence patterns and identification of conserved sequence elements

The centromere sequences were found to harbour 180 bp repeat sequences These sequences were found to reside in the gaps of each centromeric contig (FIG 3, FIGs 12B, 12L). with few repeats and no long arrays elsewhere in the genome BAC clones near these gaps have end sequences corresponding to repetitive elements that likely constitute the bulk of the DNA between the contigs, including 180 bp repeats, 5S rDNa oi 160-bp repeats (FIG 3) Fluorescent in situ hybridization has shown these repetitive sequences are abundant components of Arabidopsis centromeres (Murata et al , 1997, Heslop-Hamson et al , 1999, Brandes et al , 1997) Genetic mapping and pulsed-field gel electrophoresis indicate that many 180 bp repeats reside in long arrays measuring between 0 4 and 1 4 Mb in the centromeric regions (Round et al , 1997). sequence analysis revealed additional interspersed copies near the gaps The inventors specifically contemplate the use of such 180 bp repeats for the construction of minichromosomes The annotated sequence of chromosomes II and IV identified regions with homology to middle repetitive DNA, both within the functional centromeres and in the adjacent regions (FIGs 12B- 12E and 12L- 120)

In a 4 3 Mb sequenced region that includes CEN2 and a 2 8 Mb sequenced region that includes CEN4, retrotransposon homology was found to account for > 10% of the DNA sequence, with a maximum of 62% and 70% respectively (FIGs 12C. 12M) Sequences with similarity to transposons or middle repetitive elements were found to occupy a similar zone, but were less common (29% and 1 1 % maximum density for chromosomes II and IV respectively (FIGs. 12D-12E and FIG. 12N- 120). Finally, unlike in the case of^" Drosophila and Neurospora centromeres (Sun et al, 1997; Cambareri et al. 1998) low complexity DNA, including microsatellites. homopolymer tracts, and AT rich isochores, were not found to be enriched in the centromeres of Arabidopsis. Near CEN2. simple repeat sequence densities were comparable to those on the distal chromosome arms, occupying 1.5% of the sequence within the centromere, 3.2% in the flanking regions, and ranging from 20 to 319 bp in length (71 bp on average). Except for an insertion of mitochondrial DNA at CEN2 the DNA in and around the centromeres did not contain any large regions that deviated significantly from the genomic average of - 64% A + T (FIGs. 12F, 12P) (Bevan et al, 1999).

Unlike the 180 bp repeats, all other repetitive elements near CEN2 and CEN4 were less abundant within the genetically-defined centromeres than in the flanking regions. The high concentration of repetitive elements outside of the functional centromere domain suggest they may be insufficient for centromere activity. Thus, identifying segments of the Arabidopsis genome that are enriched in these repetitive sequences does not pinpoint the regions that provide centromere function; a similar situation may occur in the genomes of other higher eukaryotes.

The repetitive DNA flanking the centromeres may play an important role, forming an altered chromatin conformation that serves to nucleate or stabilize centromere structure. Alternatively, other mechanisms could result in the accumulation of repetitive elements near centromeres. Though evolutionary models predict repetitive DNA accumulates in regions of low recombination (Charlesworth et al, 1986:. Charlesworth et al, 1994), many Arabidopsis repetitive elements are more abundant in the recombinationally active pericentromeric regions than in the centromeres themselves. Instead, retroelements and other transposons may preferentially insert into regions flanking the centromeres or be eliminated from the rest of^" the genome at a higher rate. EXAMPLE 4 Genetic Mapping of Centromeres

To map centromeres. F| plants which were heterozygous for hundreds of polymoφhic DNA markers were generated by crossing quartet mutants from the Landsberg and Columbia ecotypes (Chang et al 1988. Ecker, 1994, Konieczy and Ausubel, 1993) In tetrads from these plants, genetic markers segregate in a 2 2 ratio (FIG 6, Preuss et al 1994) The segregation of markers was then determined in plants which were generated by crossing pollen tetrads from the Fi plants onto a Landsberg homozygote The genotype of the pollen grains within a tetrad was inferred from the genotype of the progeny Initially, seeds were generated from greater than 100 successful tetrad pollinations, and tissue and seeds were collected from 57 of these. This provided sufficient material for PCR, as well as seeds necessary for producing the large quantities of tissue required for Southern hybridization and RFLP mapping In order to obtain a more precise localization of the centromeres the original tetrad population was increased from 57 tetrads to over > 1 ,000 tetrads

PCR analysis was performed to determine marker segregation To account for the contribution of the Landsberg background from the female parent, one Landsberg complement from each of the four tetrad plants was subtracted As shown in FIG 5, markers from sites spanning the entire genome were used for pair-wise comparisons of all other markers Tetratypes indicate a crossover between one or both markers and their centromeres where as ditypes indicate the absence of crossovers (or presence of a double crossover)

Thus, at every genetic locus, the resulting diploid progeny was either L/C or C/C

The map generated with these plants is based solely on male meioses, unlike the existing map, which represents an average of recombination's in both males and females Therefore, several well-established genetic distances were recalculated and thus will determine whether recombination frequencies are significantly altered The large quantities of genetic data generated by the analysis must be compared pair-wise to perform tetrad analysis All of the data was managed in a Microsoft Excel spread-sheet format, assigning Landsberg alleles a value of " 1 ^" and Columbia alleles a value of "0"' Within a tetrad, the segregation of markers on one chromosome was compared to centromere-linked reference loci on a different chromosome (see Table 2 below) Multiplying the values of each locus by an appropriate reference, and adding the results for each tetrad easily distinguished PD, NPD, and TT tetrads with values of 2. 0, and 1 , respectively

Monitoring the position of crossovers in this population identified chromosomal regions that could be separated by recombination from centromeres (tetratype). as well as regions that always cosegregated with centromeres (ditype) (Copenhaver et al , 1998, Copenhaver et al 1999) Tetratype frequencies decrease to zero at the centromere, consequently, centromere boundaries were defined as the positions that exhibited small but detectable numbers of tetratype patterns By scoring the segregation of centromere linked markers in approximately 400 tetrads, centromeres 1-5 were localized to regions on the physical map corresponding to contigs of 550, 1445, 1600, 1790 and 1770 kb, respectively (FIG 3) Additionally, for each centromeric interval, a number of useful recombtnants were identified The results of the analysis indicated that centromeres reside within large domains that restrict recombination machinery activity and that the transition between these domains and the surrounding recombination-proficient DNA is markedly abrupt

Table 2: Scoring protocol for tetratypes.

Individual members Reference Reference Reference of a tetrad Locus 1 Locus Locus 2 Locus Locus 3 Locus

A 1 x 1 = 1 0 x 1 = 0 0 x 1 = 0

B 1 x 1 = 1 0 x 0 1 x 1 = 1

C 0 x 0 = 0 1 x 0 = 0 0 x 0 - 0

D 0 λ 0 = 0 1 x 0 = 0 1 x 0 = 0

2 0 1 I PD I NPD I TT

Analysis of polymoφhisms corresponding to 180 bp repeats (RCEN markers. Round et al, 1997) confirmed that these iepeats map within the genetically-defined centromeres Polymoφhisms associated with the 180 bp repeats were analyzed by pulsed field gel electrophoresis as described previously (Round et al, 1997) Segregation of these polymoφhisms in tetrads with informative crossovers confirmed complete linkage of a 180 bp repeat array at each centromere In genetic units, the centromere intervals averaged 0.44 cM, (% recombination = 1/2 tetratype frequency), reflecting recombination rates at least 10-30 fold below the genomic average of 221 kb/cM (Somerville and Somerville, 1999; http. //nasc. nott.ac.uk/new_n_map. html).

The low recombination frequencies typically observed near higher eukaryotic centromeres may be due to DNA modifications or unusual chromatin states (Choo. 1998. Puechberty, 1999, Mahtani and Willard, 1998, Charlesworth et al , 1986, Charlesworth et al, 1994) To modify these states, and thus improve centromere mapping resolution by raising recombination frequencies. FI Landsberg/Columbia plants were treated with one of a series of compounds known to cause DNA damage, modify chromatin structure, or alter DNA modifications. FI Landsberg qitl I Columbia qrtl plants were grown under 24 hour light in 1" square pots and treated with methanesulfonic acid ethyl ester (0 05%)), 5-aza-2'-deoxycytιdιne (25 or 100 mg/1), Zeocin ( lug/ml), methanesulfonic acid methyl ester (75 ppm). cis-diamminedichloro-platinum (20 ug/ml), mitomycin C ( lOmg/1), n-nitroso-n-ethylurea ( 100 uM), n-butync acid (20 uM), tπchostatin A ( 10 uM), or 3-methoxybenzamιde (2 mM) Plants were watered and flower-bearing stems were immersed in these solutions Alternatively, plants were exposed to 350 nm UV (7 or 10 seconds), or heat shock (38 or 42°C for 2 hours) Pollen tetrads from these plants were used to pollinate Landsberg stigmas 3-5 days after each treatment: the FI plants were subsequently subjected to additional treatments (up to 5 times per plant, every 3-5 days) Tetrads from treated plants were crossed to Landsberg stigmas, and progeny from 8- 107 tetrads subjected to each treatment were recovered and analyzed, yielding >600 additional tetrads These tetrads exhibited higher recombination in iegions immediately flanking the centromeres ( 1 6 vs 3 4% recombination in untreated and treated plants. respectively), although the sample size was insufficient to determine if any individual tieatment had a profound affect The map locations of centromeres were refined on chromosomes 2 to 5 (FIG 1 ), yielding intervals spanned by contigs of 880. 1 150. 1260. and 1070 kb. respectively, with all tetrads consistently localizing centromere functions to the same region (Copenhaver et al , 1999)

Efforts to increase recombination yielded a large number of tetrads with crossovers near the centromeres, these crossoveis clustered within a narrow region at the centromere boundaries Five crossovers occurred over a 70 kb region near CEN2, and 7 over a 200 kb region near CEN1, yet no crossovers were detected in the adjacent centromeric intervals of 880 and 550 kb respectively (FIG 3) Thus, the centromeres were found within large domains that restrict recombination machinery activity, the transition between these domains and surrounding, recombination-proficient DNA is remarkably abrupt (FIG 12A and K) Although analysis of more tetrads would yield additional recombination events, the observed distribution of crossovers indicate that centromere positions would not be significantly refined

EXAMPLE 5 Sequence Analysis of Arabidopsis Centromeres A. Abundance of genes in the centromeric regions Expressed genes are located within 1 kb of essential centromere sequences in 5 cerevisiae. and multiple copies of tRNA genes reside within an 80 kb fragment necessary for centromere function in S pombe (Kuhn et al , 1991) In contrast, genes are thought to be relatively rare in the centromeres of higher eukaryotes. though there are notable exceptions The Drosophila light, concertina, responder, and rolled loci all map to the centromeric region of chromosome 2. and translocations that remove light from its native heterochromatic context inhibit gene expression. In contrast, many Drosophila and human genes that normally reside in euchromatin become inactive when they are inserted near a centromere. Thus, genes that reside near centromeres likely have special control elements that allow expression (Karpen. 1994: Lohe and Hilliker, 1995). The sequences of Arabidopsis CEN2 and CEN4, provided herein, provide a powerful resource for understanding how gene density and expression correlate with centromere position and associated chromatin.

Annotation of chromosome II and IV (http:// www.ncbi.nlm.nih.gov/Entrez/nucleotide.html) identified many genes within and adjacent to CEN2 and CEN4 (FIG. 8, FIGs. 12A- 12T). The density of predicted genes on Arabidopsis chromosome arms averages 25 per 100 kb, and in the repeat-rich regions flanking CEN2 and CEN4 this decreases to 9 and 7 genes per 100 kb. respectively (Bevan et al, 1999). Many predicted genes also reside within the recombination-deficient, genetically-defined centromeres. Within CEN2, there were 5 predicted genes per 100 kb; while CEN4 was strikingly different, with 12 genes per 100 kb.

There was strong evidence that several of the predicted centromeric genes are transcribed. The phosphoenolpyruvate gene (CUEl) defines one CEN 5 border; mutations in this gene cause defects in light-regulated gene expression (Li et al, 1995). Within the sequenced portions of CEN2 and CEN4, 17% (27/160) of the predicted genes shared

>95%> identity with cloned cDNAs (ESTs). with three-fold more matches in CEN4 than in

CEN2 (http://www.tigr.org/tdb/at/agad/). Twenty-four of these genes have multiple exons, and four correspond to single-copy genes with known functions. A list of the predicted genes identified is given in Table 3. below. A list of additional genes encoded within the boundaries of CEN4 are listed in Table 4. The identification of these genes is significant in that the genes may themselves contain unique regulatory elements or may reside in genomic locations flanking unique control or regulatory elements involved in centromere function or gene expression. In particular, the current inventors contemplate use of these genes, or DNA sequences 0 to 5 kb upstream or downstream of these sequences, for insertion into a gene of choice in a minichromosome It is expected that such elements could potentially yield beneficial regulatory controls of the expression of these genes, even when in the unique environment of a centromere

To investigate whether the remaining 23 genes were uniquely encoded at the centromere, a search was made in the database of annotated genomic Arabidopsis sequences With the exception ot two genes, no homologs with >95% identity were found elsewhere in the 80%) of the genome that has been sequenced The number of independent cDNA clones that correspond to a single-copy gene provides an estimate of the level of gene expression On chromosome II, predicted genes with high quality matches to the cDNA database (> 95% identity) match an average of four independent cDNA clones (range 1 -78) Within CEN2 and CEN4. 1 1/27 genes exceed this aveiage (Table 3) Finally, genes encoded at CEN2 and CEN4 are not members of a single gene family, nor do they correspond to genes predicted to play a role in centromere functions, but instead have diverse roles.

Many genes in the Arabidopsis centromeric regions are nonfunctional due to early stop codons or disrupted open reading frames, but few pseudogenes were found on the chromosome arms Though a large fraction of these pseudogenes have homology to mobile elements, many correspond to genes that are typically not mobile (FIGs 12I-J and FIGs 12S-T) Within the genetically-defined centromeres there were 1 0 (CEN2) and 0 7 (CEN4) of these nonmobile pseudogenes per 100 kb. the repeat-rich regions bordering the centromeres have 1 5 and 0 9 per 100 kb respectively The distributions of pseudogenes and transposable elements are overlapping, indicting that DNA insertions in these regions contributed to gene disruptions

Table 3: Predicted genes within CEN2 and CEN4 that correspond to the cDNA database.

Putative function GenBank piotein # of EST accession matches "

CEN2

Unknown AAC69124 1

SH3 domain protein AAD 15528 5

Unknown A AD 15529 1 unknownt AAD37022 1

RNA hehcase± AAC26676 2

40S nbosomal protein S 16 AAD22696 9 CEN4

Unknown AAD36948 1

Unknown AAD36947 4 leucyl tRNA synthetase AAD36946 4 aspartic protease AAD29758 6

Peroxisomal membrane protein (PPM2) 5} AAD29759 5

5 -adenylylsulfate reductase AAD29775 14 symbiosis-related protein AAD29776 3

ATP synthase gamma chain 1 (APCI) ^ AAD48955 3 protein kinase and EF hand AAD03453 3

ABC transporter AAD03441 1 Transcnptional regulatoi AAD03444 14

Unknown AAD03446 12 human PCF1 lp homolog AAD03447 6

NSF piotein A AD 17345 2

1.3-beta-glucan synthase AAD48971 2

pyndine nucleotide-disulphide oxidoreductase AAD48975 4

Polyubiquitin (UBQ11) 4? AAD48980 72 wound induced protein AAD48981 6 short chain dehydrogenase/reductase AAD48959 7

SL15t AAD48939 2

WD40-repeat protein AAD48948 0

* Independent cDNAs with >95% identity, t related gene present in non-centromenc DNA, z potentially associated with a mobile DNA element, ^ characterized gene (B Tugal. 1999, J F Gutierrez-Marcos, 1996, N Inohara, 1991 , J Callis, 1995)

Table 4: List of additional genes encoded within the boundaries of CEN4.

Putative Function GenBank Nucleotide accession Position

3'(2').5'-Bιsphosphate Nucleotidase ACO 12392 71298 -73681 Transcnptional regultor ACO 12392 8061 1 -81844 Equihbrative nucleoside transporter 1 ACO 12392 88570 -90739 Equihbrative nucleoside transporter 1 ACO 12392 94940 -96878 Equihbrative nucleoside transporter 1 AC012392 98929 - 101019 Equihbrative nucleoside tiansporter 1 ACO 12392 113069 -115262 unknow n AC012392 122486 -124729

4-coumarate-CoA hgase AC012392 126505 -128601 ethylene responsive protein ACO12392 130044 -131421

Oxygen-evolving enhancer protein precursor AC012392 134147 -135224

Kinesin ACO12392 137630 -141536 receptor-like protein kinase ACO12392 141847 -144363

LpxD-hke protein AC012392 144921 -146953 hypersensitivity induced protein ACO 12392 147158 -147838 ubiquitin ACO12392 149057 ^■ -149677 unknown ACO 12392 150254- -151072 ubiquitin-hke protein ACO12392 153514- -154470 ubiquitin-hke protein AC012392 155734- -156513 ubiquitin-hke protein ACO 12392 156993- •157382 unknown ACO12392 159635- -165559 unknown ACO 12392 166279- ^■166920 unknown ACO 12392 167724- ^■170212 ubiquitin-hke protein ACO12392 176819 - 178066 polyubiquitin (UBQ10) fc ACO12392 180613- 182007 phosphatιdylιnosιtol-3.4.5-tπphosphate binding ACO12477 89384 - 91291 protein

Mitochondπal ATPase ACO 12477 94302 -94677 RING-H2 finger protein ACO 12477 95522 96142 unknown ACO 12477 104747 - 105196

Mitochondnal ATPase ACO 12477 105758 - 106595 ferredoxin— NADP+ reductase ACO 12477 107451 - 109095 unknown ACO 12477 109868 - 1 10620

U3 snoRNP-associated protein ACO 12477 1 1 1841 -1 14133

UV-damaged DNA binding factor ACO 12477 1 14900 -121275

Glucan endo- 1.3-Beta-Glucosιdase precursoi AC012477 122194 - 122895

D123 -like protein ACO 12477 125886 - 126887

Adrenodoxin Precursoi ACO 12477 127660 - 129246

N7 like-protein ACO 12477 129718 - 131012

N7 like-protein ACO 12477 131868 -133963

N7 like-protein ACO 12477 134215 - 136569

N7 like-protein ACO 12477 139656 - 140864 fc characterized gene (J Calhs 1995)

B. Conser>ation of centromeric DNA

To investigate the conservation of CEN2 and CEN4 sequences PCR primer pairs were designed that correspond to unique regions in the Columbia sequence and used to survey the centromeric regions of Landsberg and Columbia at -20 kb intervals (FIGs 14A B) The primers used for the analysis are listed in FIGs 15A B Amplification products of the appropriate length were obtained in both ecotypes for most primer pairs (85%) indicating that the amplified regions were highly similar In the remaining cases primer pairs amplified Columbia but not Landsberg DNA even at very low stringencies In these regions additional primeis weie designed to determine the extent of nonhomology In addition to a laige insertion of mitochondnal DNA in CEΛ_ two othei non-conserv ed legions w ere identified (FIGs 14A B) Because this DNA is absent fiom Landsbeig centiomeres it is unlikely to be required for centiomere function consequently the lelev nt portion of the centiomenc sequence is icduced to 577 kb (CEN2) and 1250 kb (CEN4) The high degiee of sequence conseivation between Landsberg and Columbia centromeres indicated that the inhibition of recombination frequencies was not due to large regions of nonhomology but instead was a propeity ot the centiomeres themselves

C. Sequence similarity between CEN2 and CEN4 In order to discern centromere function a search was conducted for novel sequence motifs shared between CEN2 and CEN4, excluding from the comparison retroelements transposons characterized centromeric repeats and coding sequences resembling mobile genes After masking simple lepetitive sequences including homopolymer tracts and microsatellites contigs of unique sequence measuring 417 kb and 851 kb for CEN2 and CEN4, iespectively, were compared with BLAST (http //blast wustl edu)

The comparison showed that the complex DNA within the centromere regions was not homologous over the entne sequence length Howevei 16 DNA segments in CEN2 matched 1 1 regions in CEN4 with >60% identity (FIG 16) The sequences were grouped into families of related sequences and weie designated AtCCS l -7 (Aiabidopsis thaliana centromere conserved sequences 1-7) These sequences were not prev iously known to be repeated in the Aiabidopsis genome The sequences comprised a total of 17 kb (4%)) of CEN2 DNA had an average length of 1017 bp and had an A + T content of 65% Based on similarity the matching sequences were sorted into gioups including two families containing 8 sequences each (AtCCS l and AtCCS2 SEQ ID NOS 1 - 14) 3 sequences from a small family encoding a putative open reading frame (AtCCS3 SEQ ID NOS 21-22)). and 4 sequences found once within the centromeres (AtCCS4-AtCCS7 SEQ ID NOS 15-20) one ot which (AtCCS6 SEQ ID NO 17) corresponds to piedicted CEN2 and CEN4 proteins w ith similanty throughout their exons and introns (FIG 16) Searches of the Aiabidopsis genomic sequence database demonstrated that AtCCS l - AtCCSS were modeiately repeated sequences that appear in centromeric and peπcentiomeπc legions The lemaining sequences weie piesent only in the genetically-defined centiomeres Similar compai isons of all 16 S cerevisiae centromeres defined a consensus consisting of a conserved 8 bp CDEI motif, an AT-rich 85 bp CDEII element, and a 26 bp CDEII region with 7 highly conserved nucleotides (Fleig et c// , 1995) In contrast, surveys of the three S pombe centromeres revealed conservation of overall centromere structuie. but no univeisally conserved motifs (Clark. 1998)

EXAMPLE 6 Mapping Results: Arabidopsis Chromosomes 1-5 The centromere on chromosome 1 was mapped between mι342 (56 7 cM) and T27K12 (59 1 cM) A more refined position places the centromere between the marker T22C23-t7 (-58 5 cM) and T3P8-sp6 (-59 1 cM) Contained within this interval are the previously described markers EKRIV and RCEN 1

The centromere on chromosome 2 was mapped between mι310 ( 18 6 cM) and g4133 (23 8 cM) A moie refined position places the centromere between the markers F5J15-sp6 (- 19 1 cM) and T15D9 (- 19 3 cM) The following sequenced (http //www ncbi nlm nih gov/Entrez/nucleotide html ) BAC (bacterial artificial chromosome) clones aie known to span the region between the markers F5J 15-sp6 and T15D9 T13E1 1. F27C21. F9A 16. T5M2. T17H 1. T18C6. T5E7. T12J2 F27B22 T6C20, T14C8. F7B 19 and T15D9

There is a gap in BAC coverage between T 12J2 and F27B22 RARE cleavage pulse field gels or DNA sequence tiling will be used to isolate DNA in the gap for sequencing The centromere on chromosome 3 w as mapped between atpox (48 6 cM ) and ATA (53.8 cM). A more refined position places the centromere between the marker T9G9-sp6 (-53.1 cM) and T5M 14-sp6 (-53.3 cM). Contained within this interval is the previously described marker: RCEN3.

The centromere on chromosome 4 was mapped between mι233 ( 18 8 cM) and mi 167 (21.5 cM). A more refined position places the centromere between the markers T24H24.30k3 (-20.3 cM) and F13H 14-t7 (-21.0 cM). The following sequenced (http://www.ncbi.nlm.nih.gov/Entrez/nucleotide.html) BAC (bacterial artificial chromosome) clones are known to span the region between the markers F5J 15-sp6 and T6A13-sp6: T27D20, T19B 17, T26N6. F4H6. T19J18. T4B21 , T1J1 , T32N4. C 17L7. C6L9. F6H8. F2I 12. F14G16.and F28D6

There is a gap in BAC coverage between F2I 12 and F14G 16. RARE cleavage. pulse field gels or DNA sequence tiling will be used to isolate DNA in the gap for sequencing.

The centromere on chromosome 5 was mapped between nga76 (71 6 cM) and PhyC (74.3 cM). A more refined position places the centromere between the markers F13K20-t7 (-69.4 cM) and CUE l (-69 5 cM) Contained within this interval arc the publicly available markers: um579D. mι291 b. CMs l .

A table listing the BAC clones known to reside within the centromeres on chromosomes I-V given as well as Genbank Accession numbers for the sequences of these clones, is given below, in Table 5 and Table 6.

Genetic positions (/ e. cM values) correspond to the Lister and Dean Recombinant Inbred Genetic map. available on-line at http. //nasc. nott.ac.uk/new_n_map. html Markei s are available at http://genome-wvvw .stanford.edu/Arabidopsis/aboutcaps.html Table 5: BAC clones residing within A. thaliana centromeres and associated Genbank accession numbers

^■I 48-

Table 6: Fully sequenced BAC clones containing A. thaliana centromere sequences*

^■"^■ The sequences for clones from centromeres 1 3 and 5 are given in SEQ ID NOS 184- 208 Sequences foi contigs including the centiomere 2 and 4 clones are given by SEQ ID NOS 209-212 BAC clone number designations are given The centiomcie number origin of the clone is as indicated Where a second date is given the second date indicates the date for the lev ised sequence

EXAMPLE 7

Constructing BAC Vectors for Testing Centromere Function

A BAC clone may be retrofitting with one or more plant telomeres and selectable markers together with the DNA elements necessary for Agiobactermm transformation (FIG 9) This method ill provide a means to delivei any BAC clone into plant cells and to test it for centromere function

The method works in the following way The conversion vector contains a retrofitting cassette The retrofitting cassette is flanked by Tn 10 Tn5 Tn7 Mu or other transposable elements and contains an origin of replication and a selectable marker for Agiobactermm, a plant telomere array followed by T-DNA right and left borders followed by a second plant telomere array and a plant selectable marker (FIG 9) The conversion vector is transformed into an E coli strain carrying the target BAC The transposable elements flanking the retrofitting cassette then mediate transposition of the cassette iandomly into the BAC clone The retrofitted BAC clone can now be transformed into an appropriate stiain of Agi obaclei mm and then into plant cells vvheie it can be tested for high fidelity meiotic and mitotic transmission which would indicate that the clone contained a complete functional plant centromere

EXAMPLE 8 Construction of Plant Minichromosomes

Minichromosomes are constructed by combining the prev iously isolated essential chiomosomal elements Exemplary minichromosome vectors include those designed to be shuttle vectors ; e thev can be maintained in a convenient host (such as E coli A obacteuum or yeast) as well as plant cells

A. General Techniques for Minichromosome Construction

A minichromosome can be maintained in £ coli or other bacterial cells as a circulai molecule by placing a removable stuffer fragment between the telomeric sequence blocks The stuffer fragment is a dispensable DNA sequence bordered by unique restriction sites, which can be lemoved b> restriction digestion of the circular DNAs to create linear molecules with telomeric ends The linear minichromosome can then be isolated by for example, gel electrophoiesis In addition to the stuffer fragment and the plant telomeres. the minichromosome contains a replication origin and selectable marker that can function in plants to allow the circular molecules to be maintained in bacterial cells The minichromosomes also include a plant selectable marker a plant centromere, and a plant ARS to allow replication and maintenance of the DNA molecules in plant cells Finally, the minichromosome includes several unique restriction sites where additional DNA sequence inserts can be cloned The most expeditious method of physically constructing such a minichromosome * e hgating the various essential elements together for example, will be apparent to those of ordinary skill in this art

A number of minichromosome vectoi s have been designed by the current inventors and are disclosed herein for the purpose of illustration (FIGs 7A-7H) These vectors are not limiting however as it will be apparent to those of skill in the art that many changes and alterations may be made and still obtain a functional vector

B. Modified Technique for Minichromosome Construction A two step method was developed tor construction of minichromosomes which allows adding essential elements to BAC clones containing centromeric DNA These procedures can take place in vn o eliminating problems of chromosome breakage that often happen in the test tube The details and adv antages of the techniques are as follows 1.) One plasmid can be created that contains markers, origins and bordei sequences for Agrobacterium transfer, markers for selection and screening in plants, plant telomeres. and a loxP site 01 other site useful for site-specific recombination in vivo or //; i ttro The second plasmid can be an existing BAC clone, isolated from the available genomic libraries (FIG. 1 1 A).

2 ) The two plasmids are mixed, either within a single E. coli cell, or in a test tube, and the site-specific recombinase cre is introduced. This will cause the two plasmids to fuse at the loxP sites (FIG. 1 IB).

3.) If deemed necessary, useful restriction sites (Asel/Pacl or Not I) are included to remove excess material, (for example other selectable markers or replication origins)

4.) Variations include vectors with or without a Kan^R gene (FIGs 1 IB. 1 IC). with or without a LAT52 GUS gene, with a LAT52 GFP gene, and with a GUS gene under the control of other plant promoters (FIGs. 1 IC, 1 ID and 1 IE).

C. Method for Preparation of Stable Non-Integrated Minichromosomes A technique has been developed to ensure that minichromosomes do no integrate into the host genome (FIG. 1 IF). In particular, minichromosomes must be maintained as distinct elements separate from the host chromosomes To ensure that the introduced minichromosome does not integrate, the inventors envision a variety that would encode a lethal plant gene (such as dipthena toxin or any other gene product that, when expressed. causes lethality in plants). This gene could be located between the right Agrobactermm border and the telomere. Minichromosomes that enter a plant nucleus and integrate into a host chromosome would result in lethality However, if the minichromosome remains separate, and further, if the ends of this construct are degraded up to the telomeres, then the lethal gene would be removed and the cells would survive. EXAMPLE 9 In Vivo Screen of Centromere Activity by the Analysis of Dicentric Chromosomes

A method was designed for the screening of centromere activity (FIG 10) In the method plants are first transformed w ith binaiy BAC clones that contain DNA from the genetically-defined centromeric regions By allowing the DNA to integrate into the host chromosomes, it is expected that this integration will lesult in a chromosome with two centromeres This is an unstable situation which often leads to chromosome breakage, as single chromosomes harboring two or more functional centromeres will often times break at junctions between the two centromeres when pulled towards opposite poles during mitotic and meiotic events This can lead to severe growth defects and inviable progeny when genes important or essentially for cellular and developmental processes are disrupted by the breakage event Therefore regions having centromere function could be identified by looking for clones that exhibit upon introduction into a host plant any of the following predicted properties reduced efficiencies of transformation causation of genetic instability when integrated into natural chromosomes such that the transformed plants show aberrant sectors and increased lethality a difficulty to maintain particularly when the transformed plants are grown under conditions that do not select for maintenance of the transgenes a tendency to integrate into the genome at the distal tips ot chromosomes or at the centromeric regions In contrast, clones comprising non-centromenc DNA will be expected to integrate in a more random pattern Confirmation of a resulting distribution and pattern of integration can be determined by sequencing the ends of the inserted DNA

The screen is performed by identifying clones of greater than 100 kb that encode centromere DNA in a BiBAC library (binary bacterial artificial chromosomes) (Hamilton 1997) This is done by screening filters comprising a BiBAC genomic hbraiy for clones that encode DNA from the centromeres (FIG 10 step 1 ) The BiBAC v ector is used because it can contain large inserts of Arabidopsis genomic material and also encodes the binary sequences needed for Aςi obactenum-mediated transformation The centromere sequence containing BiBAC v ectors aie then directly integrated into chromosomes by Agrobactermm-mediated transformation (FIG. 10. step 2 ) As a control. BiBAC constructs containing non-centromenc DNA also are used for transformation BiBACs harboring sequences with centromere function will result in forming dicentπc chromosomes. Progeny from transformed plants will be analyzed for nonviabihty and gross morphological differences that can be attributed to chromosomal breaks due to the formation of dicentnc chromosomes (FIG. 10. step 3) Non-centromere sequences are expected to show little phenotypic differences from wildtype plants

EXAMPLE 10 Refined Centromere Mapping with Treatment for Increased Recombination

In order to achieve a more refined map position for the centromeres in Arabidopsis thaliana. various chemical and environmental treatments were used to stimulate recombination The treatments were used on pollen donors in crosses performed to create the tetrad sets of plants (see EXAMPLE 2). Pollen donor plants were planted individually in 1 inch square pots and grown undei 24 hr light in a growth room until flowering. Flowering plants were then dipped in one of the following solutions and watered with 50 ml of the same solution.

I

--•

I

I cπ oo

Following treatment, plants were then returned to the growth room and grown under standard conditions foi 2-5 days. Pollen was then collected from newly opened flowers and used to pollinate teceptive stigmas as described in Example 2 Then the pollen donor plants were again treated as described above and used in another round ot pollination. Pollen donor plants were typically subjected to 5-10 rounds of treatment and pollen collection.

Treatments were also performed using non-chemical agents As above, the treatments were used to achieve more refined map positions for the centromeres in Arabidopsis by stimulating recombination in additional pollen donor plants The treatments were as follows:

Table 8: Non-Chemical Treatment A ents.

Heat shock treatments were performed by placing the pot containing the pollen donor plants in shallow dishes filled with water (to prevent desiccation), and placing the plant-containing dishes in incubators of the appropriate temperature UV exposure was performed by placing the pollen donor plants in a BioRad UV chamber and illuminating the plants at the appropriate wave length for varying amounts of time. Both the UV and heat shock plants were subjected to several rounds of treatment and pollen collection Plants exposed to a gamma radiation source (Cobalt-60) were treated only once and then discarded to prevent the accumulation of deleterious chromosomal rearrangements. Following treatment, plants were then returned to the growth room and grown under standard conditions for 2-5 days. Pollen was then collected from newly opened floweis and used to pollinate receptive stigmas as described in Example 2 Then the pollen donor plants were again treated as described above and used in another round of pollination Pollen donor plants were typically subjected to 5- 10 rounds of treatment and pollen collection The results are shown at Table 9 below.

Table 9: Results of Recombination After Treatments

"* indicates significant by X^" (df=l )

EXAMPLE 11 Facilitation of Genetic Introgression

It is also contemplated by the inventors that one could employ techniques or treatments which stimulate recombination to facilitate introgression Introgression describes a breeding technique whereby one or more desired traits is transferred into one strain (A) from another (B). the trait is then isolated in the genetic background of the desired strain (A) by a series of backcrosses to the same strain (A). The number of backcrosses required to isolate the desired trait in the desired genetic background is dependent on the frequency of recombination in each backcross Backcrossing transfers a specific desirable trait from one source to an inbred or other plant that lacks that trait This can be accomplished, for example, by first crossing a supenoi inbred (A) (recurrent parent) to a donor inbred (non-iecurrent parent), which carries the appropriate gene(s) for the trait in question, for example, a construct prepared in accordance with the current invention The progeny of this cross first are selected in the resultant progeny for the desired trait to be transferred fiom the non-recurrent parent, then the selected progeny are mated back to the superior recurrent parent (A) After five or more backcross generations with selection for the desired trait, the progeny are hemizygous for loci controlling the characteristic being transferred, but are like the superior parent for most or almost all other genes The last backcross generation would be selfed to give progeny which are pure breeding for the gene(s) being transfened, e. one or more transformation events

Therefore, through a series a breeding manipulations, a selected transgene may be moved from one line into an entirely different line without the need for further recombinant manipulation. Transgenes are valuable in that they typically behave genetically as any other gene and can be manipulated by breeding techniques in a manner identical to any other corn gene Therefore, one may produce inbred plants which are true breeding for one or more transgenes. By crossing different inbred plants, one may produce a large number of different hybrids with different combinations of transgenes In this way. plants may be produced which have the desirable agronomic properties frequently associated with hybrids (^"hybrid vigor^*'), as well as the desirable characteristics imparted by one or more ιransgene(s).

Breeding also can be used to transfer an entire minichromosome from one plant to another plant For example, by crossing a first plant having a minichromosome to a second plant lacking the minichromosome. progeny of any generation of this cross may be obtained having the minichromosome. or any additional number of desired minichromosomes Through a series of backcrosses. a plant may be obtained that has the genetic background of the second plant but has the minichromosome from the first plant All of the compositions and methods disclosed and claimed herein can be made and executed without undue experimentation in light of the present disclosure While the compositions and methods of this invention have been descnbed in terms of preferred embodiments, it will be apparent to those of skill in the art that variations mav be applied to the compositions and methods and in the steps or in the sequence of steps of the method described herein without departing from the concept, spirit and scope of the invention More specifically, it will be apparent that certain agents which are both chemically and physiologically related may be substituted for the agents described herein while the same or similar results would be achieved All such similar substitutes and modifications apparent to those skilled in the art are deemed to be within the spirit, scope and concept of the invention as defined by the appended claims

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WHAT IS CLAIMED IS:

1 A lecombinant DNA constaict comprising a plant centromere

2 The lecombinant DNA constiuct of claim 1 which additionally compnses a telomere

3 The recombinant DNA construct of claim 2. wherein the telomere is a plant telomere

4 The recombinant DNA construct of claim 3. wherein the plant telomeie is an Arabidopsis thaliana telomere

5 The recombinant DNA construct of claim 2 wherein the telomere is a yeast telomere

6 The recombinant DNA construct of claim 1. which additionally comprises an autonomous replicating sequence (ARS)

7 The recombinant DNA construct of claim 6, wherein said ARS is a plant ARS

8 The recombinant DNA construct of claim 6 wherein said plant ARS is an Aiabidopsis thaliana ARS

9 The recombinant DNA construct of claim 1 which additionally compnses a structural gene

10 The recombinant DNA construct of claim 9, wherein the structuial gene comprises a selectable or screenable marker gene 1 1 The recombinant DNA construct of claim 9. which additionally comprises a second structural gene

12 The recombinant DNA construct ot claim 9. wheiein said structuial gene is selected from the group consisting of an antibiotic resistance gene, a herbicide lesistance gene, a nitiogen fixation gene, a plant pathogen defense gene, a plant stress-induced gene, a toxin gene, a receptoi gene, a ligand gene and a seed storage gene

13 The recombinant DNA construct of claim 12. wherein said construct is capable of expressing said structural gene.

14 The recombinant DNA construct of claim 13. wherein said construct is capable of expressing said structural gene in a prokaryote

15 The recombinant DNA construct of claim 13, wheiein said construct is capable ot expressing said structural gene in a eukaryote

16 The recombinant DNA construct of claim 15, wherein said eukaryote is a higher eukaryote

17 The recombinant DNA construct of claim 16. wherein said higher eukaiyote is a plant

18 The recombinant DNA construct of claim 9. wherein said structural gene is selected from the group consisting of a hormone gene, an enzyme gene, an interleukin gene, a clotting factor gene, a cytokine gene, an antibody gene, and a growth factor gene

19 The recombinant DNA construct of claim 18. wherein said construct is capable of expressing said structural gene 20 The lecombinant DNA construct ot claim 19. wherein said construct is capable of expressing said structural gene in a prokaryote.

21. The lecombinant DNA construct of claim 19. wherein said construct is capable of expressing said structural gene in a eukaryote

22 The recombinant DNA construct of claim 21. wherein said eukaryote is a higher eukaryote.

23 The recombinant DNA construct of^" claim 22. wherein said higher eukaryote is a plant.

24 The recombinant DNA construct of claim 1. further defined as a plasmid.

25. The recombinant DNA construct of claim 24. wherein the plasmid comprises an origin of replication.

26. The recombinant DNA construct of claim 25. wherein the origin of replication functions in bacteria.

27. The recombinant DNA construct of claim 26. wherein the origin of replication functions in E coli

28. The recombinant DNA construct of claim 26. wherein the origin of replication functions in Agrobacterium.

29 The recombinant DNA construct of claim 25. wherein the origin of replication functions in plants 30 The recombinant DNA construct of claim 25. wherein the origin of replication functions in yeast

3 1 The recombinant DNA construct of claim 30. wherein said yeast is 5 cerevisiae.

32. The recombinant DNA construct of claim 24. wherein the plasmid comprises a selection marker

33 The recombinant DNA construct of claim 32. wherein the selection marker functions in bacteria.

34. The recombinant DNA construct of claim 32. wherein the selection marker functions in E coli

35 The recombinant DNA construct of claim 32. wherein the selection marker functions in Agrobactermm.

36. The recombinant DNA construct of claim 32. wherein the selection marker functions in plants

37. The recombinant DNA construct of claim 32. wherein the selection marker functions in yeast

38. The recombinant DNA construct of claim 37, wherein said yeast is S. cerevisiae

39 The recombinant DNA construct of claim 1. which is capable of being maintained as a chromosome, wherein said chromosome is transmitted in dividing cells

40 The recombinant DNA construct of claim 1. wherein said plant centromere is an Arabidopsis thaliana centromere 41 The recombinant DNA construct of claim 40. wherein said plant centromere is an Aiabidopsis thaliana chromosome I centromeie

42 The recombinant DNA construct of claim 41. wherein said centromere is flanked by the genetic markers T22C23-T7 and T3P8-SP6.

43 The recombinant DNA construct of claim 42, wherein the centromere is further defined as flanked by the genetic markers T22C23-T7 and T5D 18. T22C23-T7 and T3L4, T5D18 and T3P8-SP6. T5D18 and T3L4, and T3L4 and T3P8-SP6

44 The recombinant DNA construct of claim 40, wherein said plant centromere comprises an Arabidopsis thaliana chromosome 2 centromere.

45 The recombinant DNA construct of claim 44. wherein said centromere comprises from about 100 to about 61 1.000 contiguous nucleotides of the nucleic acid sequence of SEQ ID NO:209.

46. The recombinant DNA construct of claim 44. wherein said centromere comprises from about 500 to about 61 1.000 contiguous nucleotides of the nucleic acid sequence of SEQ ID NO:209

47 The recombinant DNA construct of claim 44. wherein said centromere compnses from about 1 ,000 to about 61 1.000 contiguous nucleotides of the nucleic acid sequence of SEQ ID NO:209

48 The recombinant DNA construct of claim 44. wherein said centromere comprises from about 10.000 to about 61 1.000 contiguous nucleotides of the nucleic acid sequence of^" SEQ ID NO.209. 49 The recombinant DNA constiuct of claim 44 wherein said centiomere comprises from about 20 000 to about 61 1.000 contiguous nucleotides of the nucleic acid sequence of SEQ ID NO 209

50 The recombinant DNA construct of claim 44 wherein said centromere comprises from about 40.000 to about 61 1.000 contiguous nucleotides of the nucleic acid sequence of SEQ ID NO 209

51 The recombinant DNA construct of claim 44. wherein said centromere comprises from about 80,000 to about 611,000 contiguous nucleotides of the nucleic acid sequence of SEQ ID NO 209

52 The recombinant DNA construct of claim 44 wherein said centromeie comprises from about 150.000 to about 61 1.000 contiguous nucleotides of the nucleic acid sequence of SEQ ID NO 209

53 The recombinant DNA construct of claim 44 wheiein said centromere comprises from about 300.000 to about 61 1.000 contiguous nucleotides of the nucleic acid sequence of SEQ ID NO 209

54 The recombinant DNA construct of claim 44. w herein said centromere comprises the nucleic acid sequence of SEQ ID NO 209

55 The recombinant DNA construct of claim 44. wherein said centromere comprises from about 100 to about 50.959 contiguous nucleotides of the nucleic acid sequence of SEQ ID NO 210

56 The recombinant DNA construct of claim 44. wherein said centromere comprises from about 500 to about 50,959 contiguous nucleotides of the nucleic acid sequence of SEQ ID NO 210 57. The recombinant DNA construct of claim 44. wherein said centromere comprises from about 1.000 to about 50.959 contiguous nucleotides of the nucleic acid sequence of SEQ ID NO:210.

58. The recombinant DNA construct of claim 44. wherein said centromere comprises from about 5,000 to about 50,959 contiguous nucleotides of the nucleic acid sequence of SEQ ID NO:210.

59. The recombinant DNA construct of claim 44, wherein said centromere comprises from about 10,000 to about 50,959 contiguous nucleotides of the nucleic acid sequence of SEQ ID NO:210.

60. The recombinant DNA construct of claim 44. wherein said centromere comprises from about 20,000 to about 50,959 contiguous nucleotides of the nucleic acid sequence of SEQ ID NO:210.

61. The recombinant DNA construct of claim 44, wherein said centromere comprises from about 30,000 to about 50,959 contiguous nucleotides of the nucleic acid sequence of SEQ ID NO:210.

62. The recombinant DNA construct of claim 44. wherein said centromere comprises from about 40.000 to about 50.959 contiguous nucleotides of the nucleic acid sequence of SEQ ID NO:210.

63. The recombinant DNA construct of claim 44. wherein said centromere comprises the nucleic acid sequence of SEQ ID NO:210.

64. The recombinant DNA construct of claim 40. wherein said plant centromere is an Arabidopsis thaliana chromosome 3 centromere. 65 The recombinant DNA construct of claim 62. wherein centromere is further defined as flanked by the genetic markers T9G9-SP6 and T5M 14-SP6

66. The recombinant DNA construct of claim 65. wherein the centromere is still further defined as flanked by a pair of genetic markers selected from the group consisting of T9G9-SP6 and TI4H20. T9G9-SP6 and T7K14. T9G9-SP6 and T21 P20. T14H20 and T7K14, T14H20 and T21P20. T14H20 and T5M 14-SP6. T7K14 and T5M 14-SP6. T7K 14 and T21 P20, and T21 P20 and T5M 14-SP6.

67. The recombinant DNA construct of claim 40. wherein said plant centromere is an Arabidopsis thaliana chromosome 4 centromere.

68 The recombinant DNA construct of claim 67. wherein said centromere comprises from about 100 to about 1.082,000 contiguous nucleotides of the nucleic acid sequence of SEQ ID NO:21 1.

69. The recombinant DNA construct of claim 67. wherein said centromere comprises from about 500 to about 1 ,082,000 contiguous nucleotides of the nucleic acid sequence of SEQ ID NO-21 1.

70 The recombinant DNA construct of claim 67. wherein said centromere comprises from about 1 ,000 to about 1 ,082,000 contiguous nucleotides of the nucleic acid sequence of SEQ ID NO:21 1

71. The recombinant DNA construct of^" claim 67. wherein said centromere comprises from about 5.000 to about 1.082.000 contiguous nucleotides of the nucleic acid sequence of SEQ ID NO.21 1. 72. The recombinant DNA construct of claim 67, wherein said centromere comprises from about 10,000 to about 1.082.000 contiguous nucleotides of the nucleic acid sequence of SEQ ID NO:21 1.

73. The recombinant DNA construct of claim 67. wherein said centromere comprises from about 50,000 to about 1 ,082.000 contiguous nucleotides of the nucleic acid sequence of SEQ ID NO:21 1.

74. The recombinant DNA construct of claim 67, wherein said centromere comprises from about 100,000 to about 1 ,082,000 contiguous nucleotides of the nucleic acid sequence of SEQ ID NO:21 1.

75. The recombinant DNA construct of claim 67, wherein said centromere comprises from about 200,000 to about 1.082,000 contiguous nucleotides of the nucleic acid sequence of SEQ ID NO:21 1.

76. The recombinant DNA construct of claim 67, wherein said centromere comprises from about 400,000 to about 1 ,082,000 contiguous nucleotides of the nucleic acid sequence of SEQ ID NO:21 1.

77. The recombinant DNA construct of claim 67, wherein said centromere comprises from about 800.000 to about 1.082,000 contiguous nucleotides of the nucleic acid sequence of SEQ ID NO:21 1.

78. The recombinant DNA construct of claim 67, wherein said centromere comprises the nucleic acid sequence of SEQ ID NO:21 1.

79. The recombinant DNA construct of claim 67, wherein said centromere comprises from about 100 to about 163,317 contiguous nucleotides of the nucleic acid sequence of^" SEQ ID NO:212. 80 The recombinant DNA construct of claim 67 wherein said centromere comprises from about 500 to about 163 317 contiguous nucleotides of the nucleic acid sequence of SEQ ID NO 212

81 The recombinant DNA construct of claim 67 wherein said centromeie comprises from about 1 000 to about 163.317 contiguous nucleotides of the nucleic acid sequence of SEQ ID NO 212

82 The recombinant DNA construct of claim 67 wherein said centromere comprises from about 5 000 to about 163,317 contiguous nucleotides of the nucleic acid sequence of SEQ ID NO 212

83 The recombinant DNA construct of claim 67 wherein said centromere comprises from about 10.000 to about 163.317 contiguous nucleotides of the nucleic acid sequence of SEQ ID N0 212

84 The recombinant DNA construct of claim 67 wherein said centromere comprises from about 30.000 to about 163,317 contiguous nucleotides of the nucleic acid sequence of SEQ ID N0 212

85 The recombinant DNA construct of claim 67 wherein said centromeie compnses from about 50 000 to about 163.317 contiguous nucleotides of the nucleic acid sequence of SEQ ID N0 212

86 The recombinant DNA construct of claim 67 wherein said centromere comprises from about 80 000 to about 163,317 contiguous nucleotides of the nucleic acid sequence of SEQ ID NO 212 87 The recombinant DNA constiuct of claim 67 wheiein said centromere comprises from about 120 000 to about 163.317 contiguous nucleotides of the nucleic acid sequence ol SEQ ID NO 212

88 The recombinant DNA construct of claim 67 wherein said centromere compnses the nucleic acid sequence of SEQ ID NO 212

89 The recombinant DNA construct of claim 40. wherein said plant centromere is an Arabidopsis thaliana chiomosome 5 centromere

90 The recombinant DNA construct of claim 89. wherein said centromere is flanked by the genetic markers F13K20-T7 and CUE l

91 The recombinant DNA construct of claim 90. wherein said centromere is flanked by a pair of genetic markers selected from the group consisting of F13K20-T7 and T18M4, F13K20-T7 and T18F2. F13K20-T7 and T24I20. T18M4 and T 18F2. T 18M4 and T24I20. T18M4 and CUEl . T18F2 and T24I20. T18F2 and CUEl. and T24I20 and CUEl

92 The recombinant DNA construct of claim 1. compnsing n copies of a repeated nucleotide sequence, wherein n is at least 2

93 The recombinant DNA construct ot claim 92. wherein n is fiom about 5 to about 100.000

94 The recombinant DNA construct of claim 92, wherein n is from about 10 to about 80.000

95 The recombinant DNA construct of claim 92. wheiein n is from about 25 to about 60 000 96. The recombinant DNA construct of claim 92. wherein n is from about 100 to about 50.000.

97. The recombinant DNA construct of claim 92. wherein n is from about 200 to about 40,000.

98. The recombinant DNA construct of claim 92. wherein n is from about 400 to about 30.000.

99. The recombinant DNA construct of claim 92. wherein n is from about 1.000 to about 30,000.

100. The recombinant DNA construct of claim 92, wherein n is from about 5.000 to about 20.000.

101. The recombinant DNA construct of claim 92, wherein n is from about 10.000 to about 15,000.

102. The recombinant DNA construct of claim 92. wherein said repeated nucleotide sequence is isolatable from the nucleic acid sequence given by SEQ ID NO: 184, SEQ ID NO: 185. SEQ ID NO: 186. SEQ ID NO: 187. SEQ ID NO: 188. SEQ ID NO: 189. SEQ ID NO: 190. SEQ ID NO: 191 , SEQ ID NO: 192. SEQ ID NO: 193. SEQ ID NO: 194. SEQ ID NO: 195. SEQ ID NO: 196. SEQ ID NO: 197. SEQ ID NO: 198. SEQ ID NO: 199. SEQ ID NO:200. SEQ ID NO:201. SEQ ID NO:202. SEQ ID NO:203. SEQ ID NO:204. SEQ ID NO:205. SEQ ID NO:206. SEQ ID NO:207. SEQ ID NO:208. SEQ ID NO:209. SEQ ID NO:210. SEQ ID NO:21 1 or SEQ ID NO:212.

103. A minichromosome vector comprising a plant centromere and a telomere sequence. 104 The minichromosome vector of claim 103. comprising an autonomous replicating sequence

105 The minichromosome vector of claim 103. comprising a second telomere sequence.

106. The minichromosome vector of claim 103. comprising a structural gene.

107. The minichromosome vector of claim 103. further defined as comprising a second structural gene.

108. The minichromosome vector of claim 103. further defined as comprising a nucleic acid sequence selected from the group consisting of SEQ ID NO: l . SEQ ID NO:2. SEQ ID NO:3. SEQ ID NO:4. SEQ ID NO:5, SEQ ID NO:6. SEQ ID NO.7. SEQ ID NO:8, SEQ ID NO:9. SEQ ID NO: 10, SEQ ID NO: 1 1 , SEQ ID NO: 12. SEQ ID NO: 13. SEQ ID NO: 14. SEQ ID NO: 15. SEQ ID NO: 16, SEQ ID NO: 17. SEQ ID NO: 18. SEQ ID NO: 19. SEQ ID NO:20. and SEQ ID NO:21.

109. A cell transformed with a recombinant DNA construct comprising a plant centromere.

1 10. The cell of claim 109. wherein said cell is a prokaryotic cell.

1 1 1 The cell of claim 109. wherein said cell is a eukaryotic cell.

1 12. The cell of claim 1 1 1 , wherein said cell is a yeast cell.

1 13. The cell of claim 109. wherein said cell is a higher eukaryotic cell

1 14. The cell of claim 1 13. wherein said higher eukaryotic cell is a plant cell. 1 15. The cell of claim 1 14. wherein said plant cell is from a dicotyledonous plant.

1 16. The cell of claim 1 15, wherein said dicotyledonous plant is selected from the group consisting of group consisting of tobacco, tomato, potato, sugar beet, pea. carrot, cauliflower, broccoli, soybean, canola, sunflower, alfalfa, cotton and Arabidopsis:

117. The cell of claim 1 16, wherein said dicotyledonous plant is Arabidopsis thaliana.

1 18. The cell of claim 1 14, wherein said plant cell is from a monocotyledonous plant.

1 19. The cell of claim 1 18, wherein said monocotyledonous plant is selected from the group consisting of wheat, maize, rye, rice, turfgrass. oat, barley, sorghum, millet, and

120. The cell of claim 109. wherein the plant centromere is an Arabidopsis thaliana centromere.

121. The cell of claim 120, further defined as an Arabidopsis thaliana cell.

122. The cell of claim 109. wherein said recombinant DNA construct comprises a telomere.

123. The cell of claim 109. wherein said recombinant DNA construct comprises an autonomous replicating sequence (ARS).

124. The cell of claim 109. wherein said recombinant DNA construct comprises a structural gene. 125 The cell of claim 124. wherein the structural gene comprises a selectable or screenable marker gene.

126. The cell of claim 124, wherein said recombinant DNA construct comprises a second structural gene.

127. The cell of claim 124, further defined as capable of expressing said structural gene

128. A plant comprising the cell of claim 109.

129. A method of preparing a transgenic plant cell comprising contacting a starting plant cell with a recombinant DNA construct comprising a plant centromere, whereby said starting plant cell is transformed with said recombinant DNA construct.

130 The method of claim 129, wherein said recombinant DNA construct comprises a structural gene.

131. The method of claim 130. wherein the recombinant DNA construct comprises a second structural gene.

132 The method of claim 129. w herein the plant centromere is an Arabidopsis thaliana centromere

133. The method of claim 132. wherein said starting plant cell is an Arabidopsis thaliana cell.

134. A transgenic plant comprising a minichromosome vector, wherein said vector comprises a plant centromere and a telomere sequence 135 The transgenic plant of claim 134 wherein said minichromosome vectoi comprises an autonomous replicating sequence

136 The transgenic plant of claim 134 wherein said minichromosome vectoi comprises a second telomere sequence

137 The transgenic plant of claim 134 wherein said minichromosome vector comprises a structural gene

138 The transgenic plant of claim 137, wherein said structural gene is selected from the group consisting of an antibiotic resistance gene, a herbicide resistance gene, a nitrogen fixation gene, a plant pathogen defense gene, a plant stress-induced gene a toxin gene, a receptor gene, a ligand gene and a seed storage gene

139 The transgenic plant of claim 137. wherein said first exogenous structural gene is selected from the group consisting of a hormone gene, an enzyme gene, an interleukin gene a clotting factor gene a cytokine gene, an antibody gene, and a growth factor gene

140 The transgenic plant of claim 134 wherein said minichromosome vector comprises a second structural gene

141 The transgenic plant of claim 134 wherein said minichromosome vector comprises a nucleic acid sequence selected from the group consisting of SEQ ID NO 1 , SEQ ID NO 2, SEQ ID NO 3 SEQ ID NO 4 SEQ ID NO 5. SEQ ID NO 6. SEQ ID NO 7 SEQ ID NO 8. SEQ ID NO 9, SEQ ID NO 10, SEQ ID NO 1 1 SEQ ID NO 12. SEQ ID NO 13. SEQ ID NO 14 SEQ ID NO 15 SEQ ID NO 16. SEQ ID NO 17 SEQ ID NO 18. SEQ ID NO 19. SEQ ID NO 20 and SEQ ID NO 21

142 The transgenic plant of claim 134. further defined as a dicotyledonous plant 143 The transgenic plant of claim 143. wherein said dicotyledonous plant is selected from the group consisting of tobacco, tomato, potato, sugar beet. pea. canot. cauliflower, broccoli, soybean, canola. sunflowei . alfalfa, cotton and Arabidopsis

144 The transgenic plant of claim 143. wherein the dicotyledonous plant is Arabidopsis thaliana

145 The transgenic plant of claim 134, further defined as a monocotyledonous plant

146 The transgenic plant of claim 145. wherein said monocotyledonous plant is selected from the group consisting of wheat, maize, rye. rice, turfgrass. oat. barley, sorghum, millet, and sugarcane.

147. A method of producing a minichromosome vector comprising

(a) obtaining a first vector and a second vector, wherein said first vector or said second vector comprises a selectable or screenable markei. an origin of replication, a telomere. and a plant centromere, and wherein said first vector and said second vector comprises a site for site-specific recombination; and

(b) contacting said first vector with said second vector to allow site-specific recombination to occur between said site for site-specific iecombination on said first vector and said site for site-specific recombination on said second vector to create a minichromosome vector comprising said selectable or screenable marker, said origin of replication, said telomere and said plant centromere.

148 The method of claim 147. wherein said contacting is done ;// viti o

149 The method of claim 148. wherein said contacting is done /// vn o 150 The method of claim 149. wherein said contacting is carried out in a prokaryotic cell

151 The method of claim 150. wheiein said prokaryotic cell is an Agi obactei nun cell

152 The method of claim 150. wherein said prokaryotic cell is an E cob cell

153 The method of claim 149, wherein said contacting is carried out in lower eukaryotic cell

154 The method of claim 153. wherein said lower eukaryotic cell is a yeast cell

155 The method of claim 149. wherein said contacting is carried out in a higher eukaryotic cell

156 The method of claim 155. wherein said higher eukaryotic cell is a plant cell

157 The method of claim 156. wherein said plant cell is an Arabidopsis thaliana cell

158 The method of claim 147. wherein said contacting is done in the presence of a recombinase

159 The method of claim 158. wherein said recombinase is selected from the group consisting of Cre, Flp. Gin, Pin. Sre. pinD. Int-B 13. and R

160 The method of claim 147. wherein said first vector or said second vectoi comprises bordei sequences for Agrø/?<-/cre///</;;-medιated transformation 161. The method of claim 147. wherein said plant centromere is an Arabidopsis thaliana centromere.

162. The method of claim 147. wherein said telomere is a plant telomere.

163. The method of claim 147. wherein said plant selectable or screenable marker is selected from the group consisting of GFP, GUS, BAR, PAT, HPT or NPTII.

164. A method of screening a candidate centromere sequence for plant centromere activity, said method comprising the steps of:

(a) obtaining an isolated nucleic acid sequence comprising a candidate centromere sequence;

(b) integratively transforming plant cells with said isolated nucleic acid: and

(c) screening for centromere activity of said candidate centromere sequence.

165. The method of claim 164, wherein said screening comprises observing a phenotypic effect present in the integratively transformed plant cells or plants comprising said plant cells, wherein said phenotypic effect is absent in a control plant cell not integratively transformed with said isolated nucleic acid sequence, or a plant comprising said control plant cell.

166. The method of claim 165. wherein said phenotypic effect is selected from the group consisting of: reduced viability, reduced efficiency of^" said transforming, genetic instability in the integratively transformed nucleic acid, aberrant plant sectors, increased ploidy, aneuploidy, and increased integrative transformation in distal or centromeric chromosome regions.

167. The method of claim 164. wherein said isolated nucleic acid sequence comprises a bacterial artificial chromosome. 168 The method of claim 167 wherein said bacterial artificial chromosome is further defined as a binaiy bactenal artificial chromosome

169 The method of claim 164 w herein said integratively transforming compnses use of Agi obactermm-mediated transformation

170 The method of claim 164 wherein said contiol plant cell has been integratively transformed with a nucleic acid sequence other than a candidate centromere sequence

171 A recombinant DNA construct compnsmg an Arabidopsis polyubiquitin 1 1 promoter, wherein said promoter comprises from about 25 to about 2 000 contiguous nucleotides of the nucleic acid sequence of SEQ ID NO 180

172 The recombinant DNA construct of claim 171 wherein said wheiein said promoter comprises from about 75 to about 2 000 contiguous nucleotides ot the nucleic acid sequence of SEQ ID NO 180

173 The recombinant DNA construct of claim 171 , wherein said wherein said promoter comprises from about 125 to about 2,000 contiguous nucleotides of the nucleic acid sequence of SEQ ID NO 180

174 The recombinant DNA construct ot claim 171 wherein said wherein said promoter comprises from about 200 to about 2 000 contiguous nucleotides of the nucleic acid sequence of SEQ ID NO 180

175 The recombinant DNA construct of claim 171 , wherein said wherein said promoter comprises from about 400 to about 2 000 contiguous nucleotides of the nucleic acid sequence of SEQ ID NO 180 176 The recombinant DNA construct of claim 171 w herein said wherein said promoter comprises Irom about 800 to about 2 000 contiguous nucleotides ot the nucleic acid sequence of SEQ ID NO 180

177 The recombinant DNA constiuct of claim 171 w herein said wherein said promoter comprises from about 1 000 to about 2 000 contiguous nucleotides of the nucleic acid sequence of SEQ ID NO 180

178 The recombinant DNA construct of claim 171 wherein said promoter compnses the nucleic acid sequence of SEQ ID NO 180

179 The recombinant DNA construct of claim 171 further comprising an enhancer

180 The recombinant DNA construct ot claim 171 furthei comprising a telomeie sequence

181 The recombinant DNA construct of claim 171 further comprising a plant centromere sequence

182 The recombinant DNA construct of claim 171 , further comprising an ARS

183 The recombinant DNA construct of claim 171 wherein said promoter is operably linked to a structural gene

184 The recombinant DNA construct of claim 183 wherein said structural gene is selected from the group consisting of an antibiotic resistance gene, a herbicide resistance gene a nitrogen fixation gene a plant pathogen defense gene a plant sti ess-induced gene a toxin gene a receptor gene a ligand gene and a seed storage gene 185. The recombinant DNA construct of claim 183, wherein said structural gene is selected from the group consisting of a hormone gene, an enzyme gene, an interleukin gene, a clotting factor gene, a cytokine gene, an antibody gene, and a growth factor gene.

186. A recombinant DNA construct comprising an Arabidopsis 40S ribosomal protein S 16 promoter, wherein said promoter comprises from about 25 to about 2.000 contiguous nucleotides of the nucleic acid sequence of SEQ ID NO: 182.

187. The recombinant DNA construct of claim 186, wherein said wherein said promoter comprises from about 75 to about 2,000 contiguous nucleotides of the nucleic acid sequence of SEQ ID NO: 182.

188. The recombinant DNA construct of claim 186. wherein said wherein said promoter comprises from about 125 to about 2,000 contiguous nucleotides of the nucleic acid sequence of SEQ ID NO: 182.

189. The recombinant DNA construct of claim 186, wherein said wherein said promoter comprises from about 200 to about 2,000 contiguous nucleotides of the nucleic acid sequence of SEQ ID NO: 182.

190. The recombinant DNA construct of claim 186, wherein said wherein said promoter comprises from about 400 to about 2,000 contiguous nucleotides of the nucleic acid sequence of SEQ ID NO: 182.

191. The recombinant DNA construct of claim 186, wherein said wherein said promoter comprises from about 800 to about 2.000 contiguous nucleotides of the nucleic acid sequence of SEQ ID NO: 182.

192. The recombinant DNA construct of ciaim 186, wherein said wherein said promoter comprises from about 1 ,000 to about 2,000 contiguous nucleotides of the nucleic acid sequence of SEQ ID NO: 182. 193 The recombinant DNA construct of claim 186 wherein said promoter comprises the nucleic acid sequence of SEQ ID NO 182

194 The lecombinant DNA construct of claim 186 further comprising an enhancer

195 The recombinant DNA construct of claim 186. further comprising a telomere sequence

196 The recombinant DNA construct of claim 186. further comprising a plant centromere sequence

197 The recombinant DNA construct of claim 186, further comprising an ARS

198 The recombinant DNA construct of claim 186 wherein said promoter is operably linked to a structural gene

199 The recombinant DNA construct of claim 198, wherein said structural gene is selected from the group consisting of an antibiotic resistance gene, a herbicide resistance gene a nitrogen fixation gene, a plant pathogen defense gene, a plant stress-induced gene, a toxin gene, a receptor gene, a ligand gene and a seed storage gene

200 The recombinant DNA construct of claim 198 wherein said structural gene is selected from the group consisting of a hormone gene, an enzyme gene, an interleukin gene, a clotting factor gene, a c>tokιne gene, an antibody gene, and a growth factor gene

201 A recombinant DNA construct comprising an Aiabidopsis polyubiquitin 1 1 3 regulatory sequence, wherein said 3 regulatory sequence comprises from about 25 to about 2001 contiguous nucleotides of the nucleic acid sequence of SEQ ID NO 181 202 The recombinant DNA construct of claim 201. wherein said wherein said 3^' regulatory sequence compnses from about 75 to about 2001 contiguous nucleotides ot the nucleic acid sequence of SEQ ID NO 181

203 The recombinant DNA construct of claim 201. wherein said wherein said 3^" regulatory sequence comprises from about 125 to about 2001 contiguous nucleotides of the nucleic acid sequence of SEQ ID NO: 181

204 The recombinant DNA construct of claim 201. wherein said wherein said 3' regulatory sequence comprises from about 200 to about 2001 contiguous nucleotides of the nucleic acid sequence of SEQ ID NO.181.

205 The recombinant DNA construct ot claim 201. wherein said wherein said 3^' regulatory sequence comprises from about 400 to about 2001 contiguous nucleotides of the nucleic acid sequence of SEQ ID NO.181

206 The recombinant DNA construct of claim 201 , wherein said wherein said 3^' regulatory sequence comprises from about 800 to about 2001 contiguous nucleotides of the nucleic acid sequence of SEQ ID NO.181

207 The recombinant DNA construct of claim 201. wherein said wherein said 3^' regulatory sequence comprises from about 1.000 to about 2.001 contiguous nucleotides of the nucleic acid sequence of SEQ ID NO 181

208 The recombinant DNA construct of claim 201. wherein said 3^' regulatory sequence comprises the nucleic acid sequence of SEQ ID NO 181

209 The recombinant DNA construct of claim 201. further comprising an enhancer

210 The recombinant DNA construct of claim 201. further comprising a telomere sequence 21 1 The recombinant DNA construct of claim 201. further comprising a plant centromere sequence.

212. The recombinant DNA construct of claim 201. further comprising an ARS

213 The recombinant DNA construct of claim 201 , wherein said 3^' regulatory sequence is operably linked to a structural gene

214 The recombinant DNA construct of claim 213, wherein said structural gene is selected from the group consisting of an antibiotic resistance gene, a herbicide resistance gene, a nitrogen fixation gene, a plant pathogen defense gene, a plant stress-induced gene, a toxin gene, a receptor gene, a ligand gene and a seed storage gene.

215. The recombinant DNA construct of claim 213, wherein said structural gene is selected from the group consisting of a hormone gene, an enzyme gene, an interleukin gene, a clotting factor gene, a cytokine gene, an antibody gene, and a growth factor gene.

216. A recombinant DNA construct comprising an Arabidopsis 40S ribosomal protein S 16 3' regulatory sequence, wherein said 3' regulatory comprises from about 25 to about 2.000 contiguous nucleotides of the nucleic acid sequence of SEQ ID NO: 183.

217. The recombinant DNA construct of claim 216, wherein said wherein said 3' regulatory sequence comprises from about 75 to about 2.000 contiguous nucleotides of the nucleic acid sequence of SEQ ID NO: 183.

218. The recombinant DNA construct of^" claim 216. wherein said wherein said 3' regulatory sequence comprises from about 125 to about 2.000 contiguous nucleotides of the nucleic acid sequence of SEQ ID NO 183. 219 The recombinant DNA construct of claim 216 wherein said wherein said 3^' regulatory sequence comprises from about 200 to about 2,000 contiguous nucleotides of the nucleic acid sequence of SEQ ID NO 183

220 The recombinant DNA construct of claim 216, wherein said wherein said 3^' regulatory sequence comprises from about 400 to about 2 000 contiguous nucleotides of the nucleic acid sequence of SEQ ID NO 183

221 The recombinant DNA construct of claim 216. wherein said wherein said 3' regulatory sequence comprises from about 800 to about 2,000 contiguous nucleotides of the nucleic acid sequence of SEQ ID NO 183

222 The recombinant DNA construct of claim 216, wherein said wherein said 3' regulatory sequence comprises from about 1.000 to about 2.000 contiguous nucleotides of the nucleic acid sequence of SEQ ID NO 183

223 The recombinant DNA construct of claim 216. wherein said 3' regulatory sequence comprises the nucleic acid sequence of SEQ ID NO 183

224 The recombinant DNA construct of claim 216, further comprising an enhancer

225 The recombinant DNA construct of claim 216, further comprising a telomere sequence

226 The recombinant DNA construct ot claim 216, further comprising a plant centromere sequence

227 The recombinant DNA construct of claim 216. further comprising an ARS

228 The recombinant DNA construct of claim 216 wherein said 3 regulatory sequence is operably linked to a structural gene