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WO1999008507A1 - Technique de reproduction dirigee permettant de restreindre le developpement de l'appareil genital - Google Patents

Technique de reproduction dirigee permettant de restreindre le developpement de l'appareil genital Download PDF

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Publication number
WO1999008507A1
WO1999008507A1 PCT/AU1998/000646 AU9800646W WO9908507A1 WO 1999008507 A1 WO1999008507 A1 WO 1999008507A1 AU 9800646 W AU9800646 W AU 9800646W WO 9908507 A1 WO9908507 A1 WO 9908507A1
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WO
WIPO (PCT)
Prior art keywords
qtl
organisms according
selecting organisms
selecting
parent
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Ceased
Application number
PCT/AU1998/000646
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English (en)
Inventor
Robert Dixon Teasdale
Chen-Hung Kao
Karen Aitken
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Forbio Pty Ltd
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Forbio Pty Ltd
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Filing date
Publication date
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Priority to AU87207/98A priority Critical patent/AU8720798A/en
Publication of WO1999008507A1 publication Critical patent/WO1999008507A1/fr
Anticipated expiration legal-status Critical
Ceased legal-status Critical Current

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Classifications

    • A—HUMAN NECESSITIES
    • A01—AGRICULTURE; FORESTRY; ANIMAL HUSBANDRY; HUNTING; TRAPPING; FISHING
    • A01K—ANIMAL HUSBANDRY; AVICULTURE; APICULTURE; PISCICULTURE; FISHING; REARING OR BREEDING ANIMALS, NOT OTHERWISE PROVIDED FOR; NEW BREEDS OF ANIMALS
    • A01K67/00—Rearing or breeding animals, not otherwise provided for; New or modified breeds of animals
    • A01K67/02—Breeding vertebrates
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6813—Hybridisation assays
    • C12Q1/6827—Hybridisation assays for detection of mutation or polymorphism
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6888—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms
    • C12Q1/6895—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms for plants, fungi or algae
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/13—Plant traits
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/156—Polymorphic or mutational markers

Definitions

  • This invention relates to a method of directed breeding of organisms.
  • This invention has particular but not exclusive application to a method of directed breeding for reduced reproductive structure development in plants, and for illustrative purposes reference will be made to such application. However, it is to be understood that this invention could be used in other applications, such as methods of directed breeding of traits of other plants and animals.
  • Organisms including plants, animals and lower organisms such as yeasts, may benefit commercially from reducing the development of reproductive structures or organs.
  • the complete inhibition of flowering, by reducing the development of reproductive structures would be particularly beneficial to the forest industry, in particularly conifers.
  • Flowering is a costly process to a plant, taking about 16% (over 30% in some cases) of photosynthate each year. Thus if flowering could be prevented extra photosynthate would be diverted by the plant into making more biomass.
  • non-flowering in forest species would save expense involved in removing seedlings that arise in plantations following sexual maturity of the trees.
  • avoidance of the development of reproductive structures will save damage to valuable timber that may arise from cone indentations to trunks and to cone stems which penetrate the trunk.
  • Sterility is an apparent side effect from reduced reproductive development. Although sterility does occur in nature, it is selected against and therefore is of a very low and unusable frequency. There are no reports of directed breeding for sterility in the literature.
  • pines require more than five years to mature to flowering stage.
  • the estimated level of genetic diversity in the Australian breeding material is lower than in other conifer breeding programs (Moran and Bell 1987, Theoretical and Applied Genetics 73:616-612).
  • this invention in one aspect resides in a method of selecting organisms for directed breeding for reduced reproductive development including the steps of: scoring members of a set of progeny, of which at least one parent is known, for the quantitative trait of reproductive structure development; determining the genotype of each member of said set and parent/s; performing quantitative trait loci analysis to identify one or more loci relating to said quantitative trait, and screening individuals for the presence of markers associated with said identified quantitative trait loci.
  • a reduced number or lack of reproductive structures or organs may indicate reduced reproductive development.
  • the reproductive structures may be cones, seeds, flowers or parts thereof.
  • the selected organism is a plant that has ornamental foliage, it may be desired to select an individual with very few flowers.
  • the selected organism is used in forestry, such as conifers, it may be desire to select an individual with few or no cones.
  • the reproductive development may be reduced to insignificant levels such as to cause sterility.
  • the flowering propensity may be reduced such as to prevent seed or cone formation.
  • the reduced reproductive development trait may be scored in any suitable manner appropriate to the trait and the organism. For example, scoring may involve counting the total number of reproductive structures, such as cones or flowers, on the progeny.
  • the progeny may be selected from a full-sib or half-sib family. Any number of progeny may be used to enable linkage analysis.
  • the progeny may be derived from one known parent that has been exposed to open pollination. This may be particularly applicable for gymnosperms, where the megagmetophyte is haploid and independent of paternal genotype.
  • the progeny may be derived from any generation of a known parental cross. It is preferred that the progeny are representative of a two- generation pedigree derived from known parents of elite quality. One or both parents may be indicative of the desired trait of reduced reproductive development, such as being inclined towards low flowering propensity or low seed or cone production.
  • the parent/s may also be selected based on factors such as population size, a high level of variance or good performances in relation to height, diameter, volume, branching traits, straightness and the like.
  • any art-recognised genotyping techniques may be utilised to determine the molecular genotype of the individuals of the family.
  • linkage maps may be constructed using molecular marker methods such as Restriction Fragment Length polymorphism (RFLP) mapping, Random Amplification Polymorphic DNA (RAPD) mapping, Amplified Fragment Length Polymorphism (AFLP) mapping, microsatellite mapping, and the like.
  • the mapping may use any suitable primers or molecular markers appropriate to the mapping method to be used.
  • the linkage maps of markers may identify individual loci that code for the desired quantitative trait of reduced reproductive development.
  • Several methods may be used to locate QTL and to estimate the effects of QTLs. This involves searching for associations that may exist between the mapped molecular markers and the desirable quantitative trait.
  • QTL analysis may treat the identified molecular markers on the linkage maps as "signals" which may "tag" QTLs of interest.
  • the markers associated with particular linkage groups may further define the identified QTL. Any program or scheme well known in the art that performs QTL analysis may be suitable.
  • QTL analysis may be performed by interval mapping (IM) or by single marker T-tests.
  • QTL analysis is performed by multiple interval mapping (MIM).
  • QTLs through their association with genetic markers, may be used to screen individuals for favourable alleles. This may allow more precise identification of organisms suitable for breeding or propagation in comparison to phenotypic selection. Progeny from selected or random new crosses or from further crosses from one or more of the original parents may be screened for the presence in individuals of genetic markers associated with one or more of the identified QTLs. This may be achieved by marker-assisted selection (MAS) according to any recognised method suitable to the selected organism. For example, plant material may be collected and genetically analysed to identify progeny expressing the molecular markers predicted to phenotypically correlate to desired trait of reduced reproductive ability. It is to be appreciated that a person skilled in the art would be able to identify markers in a population for the selected quantitative trait chosen using an art-recognised genotyping method.
  • MAS marker-assisted selection
  • the organisms selected and identified for the presence of desired QTLs are preferably used in a breeding and/or propagation program.
  • the identified individuals may be bred or propagated in any suitable manner appropriate to the organism of interest.
  • the selected individual/s may be clonally propagated or used in any stage of the development of a population, including a two parent population, a multiple parent population or backcross population.
  • FIG 1 is the linkage map of linkage group 2 of the A1 parent
  • FIG 2 is the linkage map of linkage group 5 of the A1 parent
  • FIG 3 is the linkage map of linkage group 6 of the A1 parent
  • FIG 4 is the linkage map of linkage group 10 of the A1 parent
  • FIG 5 is the linkage map of linkage group 12 of the A1 parent
  • FIG 6 is the linkage map of linkage group 2 of the A2 parent
  • FIG 7 is the linkage map of linkage group 13 of the A2 parent
  • the population consisted of 134 progeny from a control cross between two elite parents of Pinus radiata (Victoria, Australia) The progeny were grown in a replicated trial over nine sites in southern Australia The trait measured was total brown cone number (CN) The data were corrected for trial variation The flowering data were transformed to improve normality using a square root transformation The mean cone number was 9 62 with a standard deviation of 9 55 for the family studied
  • RAPD polymorphic DNA
  • LOD odds
  • Map distances in centimorgans were calculated using the Haldane mapping function. Error detection functions of Mapmaker were employed to check potential genotyping errors in the marker orders.
  • RFLP restriction fragment length polymorphism
  • RAPD resistance fragment length polymorphism
  • MIM multi-marker intervals simultaneously to fit multiple QTL in the model, enabling epistasis to be detected.
  • Epistatic effects were detected between QTL located on linkage groups 2 and 5, and 5 and 12 (Table 1).
  • the IM analysis detected QTL with large effects, but was unable to detect QTL of smaller effect or marked by epistasis. By fixing the QTL of large effect the MIM analysis is able to identify further QTL of small effect. For all the traits MIM analysis also enables the estimation of the QTL position and effect to be improved.
  • the MIM analysis unlike the IM method, also allows closely linked QTL to be separated, as in the QTL located on chromosome 10 which are in adjacent intervals (Table 1). These QTL have opposite effects and using the IM analysis were not detected.
  • Table 2 shows the primers used during linkage map construction which were successful in locating the QTLs identified using MIM analysis Table 2
  • Marker assisted selection (MAS) Mapping markers linked to QTLs may identify regions of the genome that may contain gene/ ⁇ or individual chromosomal segments, involved in the expression of the quantitative trait, even if the effect is responsible only for a small fraction of the total phenotypic variance. Genetic markers, by association with QTLs, may be used to screen individuals for favourable alleles with more precise identification, rather than by phenotypic selection.
  • the original 134 progeny were screened for selection of four of the six QTL detected in parent A1 identified in Table 1. This resulted in the reduction of cone number of the selected individuals from an average of 9.62 to 0.83 (Table 3). Selection for the two QTL detected in the A2 parent reduced the cone number for 9.62 to 2.3.
  • the effect of MAS on increasing the accuracy of evaluation has particular application to low heritability traits such as reduced reproductive development.
  • MAS can be conducted at any age, including seedlings still in the nursery. MAS of seedlings is also not affected by environmental variance that can bias conclusions that may be based on morphological characters.
  • MAS allows the prediction of future performance of seedlings, which enables selection of elite material for clonal propagation during the juvenile stage.
  • pine trees may be MAS as juveniles, predicting for low or no cone number prior to the five years or more required for maturation to the stage of cone development
  • woody plants, in particularly conifers and specifically pine tress significantly decrease their ability to be clonally propagated in tissue culture during the later mature stages of development Clonal propagation not only expands the elite material directly intended for the market, but also expands the amount of elite plant material for targeting transgene expression and other manipulations
  • the selected individual/s may be clonally propagated or used in any stage of a population development in a two parent population, a multiple parent population, a backcross population or bred for introgression of the genomic segments that may contain the identified QTLs
  • molecular markers and QTL information is valuable in directing the future breeding of trees for desired combination of traits
  • a tree expressing identified markers for low cone number and other valuable wood quality traits may be crossed with another tree expressing similar or distinct set of markers
  • the progeny thereof may contain a combination of markers such that the cone number is substantially reduced, perhaps to the statistical level approaching zero for a given tree in a large population Such progeny is then selected and propagated for commercial gains

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  • Life Sciences & Earth Sciences (AREA)
  • Chemical & Material Sciences (AREA)
  • Organic Chemistry (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Engineering & Computer Science (AREA)
  • Zoology (AREA)
  • Analytical Chemistry (AREA)
  • Wood Science & Technology (AREA)
  • Health & Medical Sciences (AREA)
  • Biotechnology (AREA)
  • Genetics & Genomics (AREA)
  • General Engineering & Computer Science (AREA)
  • General Health & Medical Sciences (AREA)
  • Physics & Mathematics (AREA)
  • Biophysics (AREA)
  • Biochemistry (AREA)
  • Immunology (AREA)
  • Microbiology (AREA)
  • Molecular Biology (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Environmental Sciences (AREA)
  • Mycology (AREA)
  • Animal Behavior & Ethology (AREA)
  • Animal Husbandry (AREA)
  • Biodiversity & Conservation Biology (AREA)
  • Botany (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)

Abstract

L'invention a trait à la reproduction de végétaux et d'animaux à appareil génital diminué par utilisation de loci de caractère quantitatif (QTL). La floraison constitue pour les plantes un mécanisme épuisant, consommant aux environ de 16 à 30 % de photosynthétat chaque année, de ce fait, l'inhibition de la floraison et un développement restreint de l'appareil génital se soldent par un accroissement de la production d'arbres, la diminution les dommages occasionnés aux arbres par les cônes, etc., et permettent de réduire les coûts liés à l'enlèvement des jeunes plants. Il a été identifié par cartographie par intervalles deux QTL permettant de réduire le nombre des cônes tandis que des analyses par cartographie par intervalles multiples ont permis de déceler huit QTL. Le choix de quatre QTL a débouché sur une réduction de 92 % du nombre des cônes.
PCT/AU1998/000646 1997-08-15 1998-08-14 Technique de reproduction dirigee permettant de restreindre le developpement de l'appareil genital Ceased WO1999008507A1 (fr)

Priority Applications (1)

Application Number Priority Date Filing Date Title
AU87207/98A AU8720798A (en) 1997-08-15 1998-08-14 Method of directed breeding for reduced reproductive development

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
AUPO8635A AUPO863597A0 (en) 1997-08-15 1997-08-15 Method of directed breeding of organisms
AUPO8635 1997-08-15

Publications (1)

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WO1999008507A1 true WO1999008507A1 (fr) 1999-02-25

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PCT/AU1998/000646 Ceased WO1999008507A1 (fr) 1997-08-15 1998-08-14 Technique de reproduction dirigee permettant de restreindre le developpement de l'appareil genital

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AU (1) AUPO863597A0 (fr)
WO (1) WO1999008507A1 (fr)
ZA (1) ZA987274B (fr)

Citations (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO1990004651A1 (fr) * 1988-10-19 1990-05-03 Whitehead Institute For Biomedical Research Topographie de traits quantitatifs en utilisant des marqueurs genetiques
WO1995019697A1 (fr) * 1994-01-21 1995-07-27 North Carolina State University Procede de selection de plantes dans des familles de plantes ligneuses vivaces au moyen de marqueurs genetiques
US5492547A (en) * 1993-09-14 1996-02-20 Dekalb Genetics Corp. Process for predicting the phenotypic trait of yield in maize

Patent Citations (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO1990004651A1 (fr) * 1988-10-19 1990-05-03 Whitehead Institute For Biomedical Research Topographie de traits quantitatifs en utilisant des marqueurs genetiques
US5492547A (en) * 1993-09-14 1996-02-20 Dekalb Genetics Corp. Process for predicting the phenotypic trait of yield in maize
US5492547B1 (en) * 1993-09-14 1998-06-30 Dekalb Genetics Corp Process for predicting the phenotypic trait of yield in maize
WO1995019697A1 (fr) * 1994-01-21 1995-07-27 North Carolina State University Procede de selection de plantes dans des familles de plantes ligneuses vivaces au moyen de marqueurs genetiques

Non-Patent Citations (4)

* Cited by examiner, † Cited by third party
Title
GENETICS, Volume 132, 1992, G. STUBER et al., "Identification of Genetic Factors Contributing to Heterosis in a Hybrid from Two Elite Maize Inbred Lines Using Molecular Markers", pages 823-839. *
GENETICS, Volume 141, 1995, Y. ESHED and D. ZAMIR, "An Intregression Line Population of Lycopersican Pannellii in the kkCultivated Tomato Enables the Identification and Fine Mapping of Yield-Associated QTL", pages 1147-1162. *
J. GENET. L. BREED, Volume 49, 1995, M. TAHIR and F. MUCHLBAUER, "Association of Quantitative Trait Loci with Isozymemarkers in Lentil (Lens Culinaris L.)", pages 145-150. *
SYMPOSIA OF THE SOCIETY FOR EXPERIMENTAL BIOLOGY, Volume 50, 1996, M. LEE, "Comparative Genetic and QTL Mapping in Sorghun and Maize", pages 31-38. *

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AUPO863597A0 (en) 1997-09-11
ZA987274B (en) 1999-02-15

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