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WO2010068999A1 - Procédé pour identifier un animal convenant à l'élevage - Google Patents

Procédé pour identifier un animal convenant à l'élevage Download PDF

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Publication number
WO2010068999A1
WO2010068999A1 PCT/AU2009/001651 AU2009001651W WO2010068999A1 WO 2010068999 A1 WO2010068999 A1 WO 2010068999A1 AU 2009001651 W AU2009001651 W AU 2009001651W WO 2010068999 A1 WO2010068999 A1 WO 2010068999A1
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Prior art keywords
bull
dairy
abv
cow
select customer
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Paul Douglas
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GENETYSIS Pty Ltd
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GENETYSIS Pty Ltd
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    • 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

Definitions

  • the present invention is directed to the field of animal breeding, including the breeding of commercially important animals such as cattle, sheep and fish.
  • the methods are useful for selecting animals suitable for breeding among a population of animals, such as a herd.
  • the methods involve analysis of trait information from ancestors of a candidate breeding animal and evaluating the genetic worth of that animal.
  • a cow that consistently provides higher than expected volumes of milk is selected for breeding on the expectation that a progeny animal will have an increased likelihood of having that same positive trait. While these simple methods may be effective, with the complexity of animal genetics the outcome is often significantly removed from that as expected. Furthermore, problems with inbreeding in a population can arise in the pursuit of mating animals having the same desirable traits.
  • phenotypic selection Whilst phenotypic selection has proven to be a useful tool, it is time consuming and expensive.
  • artificial selection based on phenotype may use progeny testing wherein the estimated breeding value of an individual is determined by performing multiple matings of the individual and determining the performance of the progeny for a particular trait or phenotypic character. It is estimated that the time taken to prove one Holstein bull takes approximately 64 months from conception to first proof, assuming a 9 month gestation period and that young bulls are test mated at one year of age and females are mated at 15 months of age. In this example, the total cost of proving one bull is about USD40,000, including the cost of housing and feeding the bull, collection and storage of semen, test matings and classification of daughters.
  • the present invention is directed to methods for identifying animals that a suitable or unsuitable for breeding.
  • the methods are based at least in part on a consideration of a trait exhibited in a maternal ancestor of the animal under scrutiny.
  • the present invention provides a method for evaluating the genetic worth of a candidate breeding animal (typically a female animal), the method comprising the steps of: obtaining information on a trait from at least one maternal ancestor of the candidate breeding animal, and analyzing the trait information to provide a probability that the trait will be found in the offspring of the candidate breeding animal.
  • the maternal ancestor is a male maternal ancestor of the candidate breeding animal, such as a male maternal grand parent.
  • the male maternal ancestor is one or more of the following: the male maternal grant parent of the candidate breeding animal, the male maternal great grand parent of the candidate breeding animal, the male maternal great great grand parent of the candidate breeding animal, the male maternal great great great grandparent of the candidate breeding animal, and the male maternal great great great great grand parent of the candidate breeding animal.
  • the method may include the further step of obtaining information on a trait of the male parent of the candidate breeding animal, and analyzing the trait of the male parent together with a trait of a maternal ancestor of the candidate breeding animal to provide a probability that the trait will be found in the offspring of the candidate breeding animal.
  • the following weights may be accorded to the trait information: the male parent: about or exactly one half, the male maternal grant parent: about or exactly one quarter, the male maternal great grand parent: about or exactly one eighth, the male maternal great great grand parent: about or exactly one sixteenth, the male maternal great great great grandparent: about or exactly one thirty-second, the male maternal great great great great grand parent: about or exactly one sixty-fourth.
  • the invention provides a method for producing a male animal for breeding, the method comprising the steps of evaluating the genetic worth of a female candidate breeding animal according to a method described herein, and inseminating the female candidate breeding animal to produce the male animal for breeding.
  • an animal that has a low genetic worth is excluded from the mating analysis.
  • the present invention further provides a method for evaluating the suitability of a first animal to mate with a second animal, the method comprising the step of evaluating the genetic worth of the first animal by a method as described herein.
  • the present invention provides a method for monitoring the genetic progress of an animal or a group of animals, the method comprising the steps of evaluating the genetic worth of the animal or each member of the group of animals by a method as described herein at a first time, .evaluating the genetic worth of the animal or each member of the group of animals by a method as described herein at a second time, and comparing the genetic worth of the animal or group of animals at the first and second times.
  • a further aspect of the invention provides a method for obtaining reproductive or regenerative material from an animal comprising evaluating the genetic worth of an animal by a method as described herein and obtaining a reproductive or regenerative material from the animal.
  • a reproductive or regenerative material obtain by that method is also provided.
  • a method for producing an animal comprising use of the reproductive or regenerative material is provided.
  • the invention further provides a computer executable code capable executing a method as described herein.
  • Figure 1 shows a mating analysis (purebred/crossbred) scheme utilising the predicted genotype of an animal identified to be mated.
  • the scheme incorporates maternal genetic contribution to the predicted animal genotype for genetic, genomic or variation values and incorporates this into a predicted genotype picture. Additional information regarding the animal to be mated may be incorporated, including visual/phenotype data, actual animal genomic value, as well variation/consistency analysis to further enhance the animal to be analysed.
  • the predicted animal's composite is then compared to the variation in population of these traits as based on normal distribution of population average and standard deviation values. Potential mating sires that have identified Genetic, Genomic and Consistency/Variation values are then excluded if they reinforce non preferred genotype traits in comparison to the average and standard deviation limit values as identified in the population.
  • Figure 2 shows a genetic prediction analysis utilising the predicted genotype of a nominated high genetic merit animal identified to be mated. Potential mating sires that have identified genetic, genomic and consistency/variation values are incorporated into the maternal pedigree line of nominated elite genetic merit animals. A predicted genotype picture for genetic, genomic or variation outcome values is generated. Additional information may be incorporated, including visual/phenotype data, actual animal genomic value, as well variation/consistency analysis to further enhance the predicted animal genotype picture. The predicted animal's composite is then compared to the variation in population of these traits as based on normal distribution of population average and standard deviation values.
  • Identified genetic, genomic and consistency/variation values are highlighted and analysed if they reinforce non preferred genotype traits in comparison to the average and standard deviation limit values as identified in the population. Potential mating sires are potentially allocated to the elite animals if they compliment, in comparison to the average and standard deviation limit values as identified in the population.
  • Figure 3 shows a maternal line prediction analysis.
  • This prediction scheme analyses the predicted genetic, genomic or variation values of an animals genotype and compares this to its actual genetic, genomic or variation values. This analysis is completed for the maternal pedigree of an animal. The identification of high difference to prediction animals within the pedigree reinforces superior and consistent genotypes from within the whole population. This identifies new genetic lines to develop and introduce into the population.
  • the present invention provides a method for evaluating the genetic worth of a candidate breeding animal, the method comprising the steps of: obtaining information on a trait of the male parent of the candidate breeding animal, obtaining information on the trait from at least one maternal ancestor of the candidate breeding animal, and analyzing the trait information to provide a probability that the trait will be found in the offspring of the candidate breeding animal.
  • the present invention therefore also provides a method for producing a male animal for breeding, the method comprising the steps of evaluating the genetic worth of a female candidate breeding animal as described herein, and inseminating the female candidate breeding animal to produce the male animal for breeding.
  • the method is capable of evaluating the "genetic worth" of a candidate breeding animal.
  • this term means the worth of the animal as a source of genetic material for breeding.
  • the method is not necessarily for the identification of high worth candidate breeding animals, but may also be used to identify moderate or low worth animals that could be excluded from a breeding program.
  • the worth may relate to a certain production characteristic that is readily translatable to a monetary value, however it will be understood that the worth may be non-monetary. For example, the worth may be simply of an aesthetic nature.
  • the present methods require the selection of maternal ancestors, and obtaining trait information from those ancestors.
  • the term "ancestor” refers to an individual having a genetic contribution to the candidate animal under consideration.
  • the term “ancestor” is thus a function of pedigree, the determination of which does not require prior knowledge of a particular trait or combination of traits present in the candidate animal.
  • Genotype information for an ancestor may be incomplete as a consequence of poor record keeping and the absence of reproductive or regenerative material e.g., semen, from the ancestor to permit genotyping, such that missing genotypes of the ancestral population may be inferred to complete a genotype analysis.
  • Ancestors in a pedigree may be overlapping, e.g., a sire and one of his sons, by virtue of contributing common reproductive or regenerative material to the current population notwithstanding any genes contributed independently by one or the other ancestor.
  • the term "ancestor” also includes a founder animal. Founder information may be used in the method described herein where the known pedigree is incomplete and/or the genotypes of the ancestors are not known or able to be derived. By “founder” is meant an individual in a pedigree for which both parents are not known. The present invention has utility where genotypes of a founder population are used to infer the genotypes of animals however this is less preferred than using actual genotypes of the animals.
  • ancestors may be characterized by obtaining and/or providing their genotypes e.g., for useful markers, a large number of useful markers or most markers using standard procedures for doing so. Genotypes can also be inferred from data on their relatives e.g., using statistical means such as MCMV modeling to predict missing values.
  • the ancestors are characterized by providing and/or obtaining known genotypes and/or by inferring their genotypes.
  • the information is obtained directly from the animal (or a product of the animal), it is anticipated that information obtained previously, or by another party, and stored in electronic or paper form may be used.
  • the term "maternal ancestor” is intended to mean any ancestor on the maternal side of the pedigree of the candidate breeding animal, and includes a male or female maternal grand parent, male or female maternal great grand parent, male or female maternal great great grand parent, ad nauseum. It is to be understood that the present methods do not exclude a consideration of animals on the paternal side of the pedigree. For example, a paternal great grand father may be analyzed by comparing its' genetic worth to a maternal ancestry prediction.
  • the number of ancestors is at least 1 , 2, 3, 4, or 5. Typically, better performance is seen where a greater number of ancestors are used. In one embodiment, the method at least 3 ancestors are used. Furthermore, any number of generations may be used in the method. In one embodiment, the number of generations is 1 , 2, 3, 4, or 5. Again, better performance is generally noted where a greater number of generations is used. In one embodiment of the method, 3 generations are used.
  • the maternal ancestor is a male maternal ancestor of the candidate breeding animal including any one or more of the male maternal grant parent, the male maternal great grand parent, the male maternal great great grand parent, the male maternal great great great grandparent, and the male maternal great great great grand parent.
  • the skilled artisan understands that trait information from ancestors of even earlier generations may provide useful trait information in the context of the invention..
  • the maternal ancestor(s) from which trait information is obtained and analyzed are one or more of the male maternal grant parent of the candidate breeding animal, the male maternal great grand parent of the candidate breeding animal, the male maternal great great grand parent of the candidate breeding animal, the male maternal great great great grandparent of the candidate breeding animal, and the male maternal great great great great grand parent of the candidate breeding animal.
  • Any number of ancestors, and in addition any combination of ancestors mat be used in the present methods.
  • Improvements to the performance of the method may be obtained whereby trait information from the male parent of the candidate breeding animal is analyzed with that of a maternal ancestor.
  • the male parent about or exactly one half
  • the male maternal grant parent about or exactly one quarter
  • the male maternal great grand parent about or exactly one eighth
  • the male maternal great great grand parent about or exactly one sixteenth
  • the male maternal great great great grandparent about or exactly one thirty-second
  • the male maternal great great great great grand parent about or exactly one sixty-fourth.
  • the term "animal” is intended to include all members of the Kingdom Animalia.
  • the skilled person understands that the methods are operable for any animal so long as a maternal ancestor may be identified (or even putatively identified), and that trait information is obtainable from the ancestor.
  • the methods operate at least in part on the well accepted dogma that traits are passed from one generation to the next by way of DNA, the genetic material found in virtually all animal cells. This mode of trait transmission is implemented in all members of the Kingdom Animalia, and so broad applicability of the present methods may be presumed.
  • the methods may also be applied in maternal line analysis of animals that are negative to prediction, and maintain this negative to prediction status in the offspring produced. These animals are often identified as cull or terminal breed mating animals to be removed from the population being examined. The present methods may be used to exclude negative difference to prediction animals from a mating population.
  • the trait information is phenotypic information.
  • the phenotypic information will typically relate to the animal's fitness and well being, to be productive, or to have the ability to efficiently and effectively reproduce a productive offspring.
  • the phenotypic information may also relate to the animal's productive output (such as form, composition, or presentation).
  • performance data is any data relating to an economically important trait in an animal, such as weight, body composition, fertility, energy efficiency, the ability to utilize certain feeds, muscling, growth rate, disease resistance, leg alignment, scrotal circumference, longevity and the like.
  • Phenotypic trait information may also relate to a product of the animal such as colostrum, milk, meat, or wool.
  • the phenotype may relate to a parameter selected from the group consisting of volume, protein composition and/or concentration, fat composition and/or concentration, growth factor composition and/or concentration, salt composition and/or concentration, or the consistency of any of these parameters over time.
  • the phenotype may relate to a parameter selected from the group consisting of protein composition and/or percentage, fat composition and/or percentage, tenderness, or the consistency of any of these parameters over time.
  • the phenotype may relate to a parameter selected from the group consisting of fibre diameter, strength or colour.
  • the type(s) of performance data useful in the context of the method will vary according to the candidate breeding animal under consideration.
  • the following phenotypic trait information may be relevant: ABV Cow Milk, ABV Cow Protein, ABV Cow Protein %, ABV Cow Fat, ABV Cow Fat %, Milking Speed, Temperament, Likeability, Fertility, Somatic Cell, Survival, Milk Protein, Protein %, Fat, Fat %, Udder Depth, Centre Ligament, Teat Placement, Rear Attachment Height, Fore Attachment, Rear Attachment Width, Teat Length, Teat, Length High, Pin Set High, Pin Set Low, Rear Set of Leg Straight, Rear Set of Leg Curved, Foot Angle, Foot Angle High, Pin Width, Pin Width High, Chest Width, Chest Width High, Body Depth, Body Depth High, Angularity, Angularity High, Muzzle Width, Rear Leg Rear View Out, Rear Leg Rear View Parallel, Calving Ease, Calving Ease Plus, Udder Texture,
  • Trait information relevant to beef cattle includes Milking Ability, birth Weight, 200 Day Growth, 400 Day Weight, 600 Day Weight, Mature Cow Liveweight, Weaning Liveweight, Yearling Liveweight, Gestation Length, Calving Ease, Scrotal Size, Carcase Weight, Eye Muscle Area, Rib and Rump Fat Depth, Intramuscular Fat, Retail Beef Yield %, Feed Conversion, and Disease & Parasite resistance.
  • Trait information suitable for sheep and goat breeding includes Fleece Weight, , Feed conversion, Fibre Diameter, Staple Strength, Feed Conversion, Disease & Parasite resistance.
  • racing animals such as horses, greyhounds
  • race time and rank hurdles, flat track, steeple chase, cross-country
  • monetary earnings annual and per race
  • body conformation physical traits desirable dressage traits age to puberty Mature Liveweight Weaning Liveweight Yearling Liveweight Gestation Length Litter size
  • fertility rates endurance/stamina parameters disease and parasite resistance
  • Performance data that is contemplated to be relevant to the breeding of fish includes spawning rate, egg (caviar) production & rate, reproduction rate, fingerlings produced, hatching rate, growth rate to market size, growth rate to maturity, liveweight at specified age, weight gain over specified time, body size, weight, length, metabolic rate, meat yield, dressing percentage, meat colour, meat odour, body colour, feed intake, feed conversion efficiency, feed conversion ratio, survival rate, mortality rate, disease resistance, parasite resistance, economic return).
  • Performance data exist for other animals of economic importance such as hogs (e.g. 21 day litter weight, number born alive, backfat, days to 230. Data used for swine include Terminal Sire Index (TSI), and Sow Productivity Index (SPI).
  • TTI Terminal Sire Index
  • SPI Sow Productivity Index
  • Data useful in sheep breeding includes birth/Rearing, Actual weights (adjusted for 60, 90, 120 days), No. Lambs Born, Units of lamb per lambing, Weight. Lamb Weaned, Units of Weight of lambs weaned, 60 day weight, 90 day weight, 120 day weight, Wool Grease Weight, and Pounds of grease fleece weight
  • the performance data includes known traits, and also traits that may be routinely used in the future such as methane production, grazing pattern analysis, grazing/feeding habit analysis, and oestrus activity.
  • Phenotype trait information may be captured by an automated or semi-automated system, including pressure sensor mats (gait analysis), infrared (mastitis, lameness/injury detection), gait analysis, image analysis (size, dimension, visual trait e.g. stature, bare area etc), sensor (animal detection, size, dimension analysis, flight time), weight (value and change versus production versus reproduction), pedometers (animal activity), feed conversion efficiency (individual feed management systems), in gate RFID systems.
  • pressure sensor mats gait analysis
  • infrared mastitis, lameness/injury detection
  • gait analysis image analysis
  • image analysis size, dimension, visual trait e.g. stature, bare area etc
  • sensor animal detection, size, dimension analysis, flight time
  • weight value and change versus production versus reproduction
  • pedometers animal activity
  • feed conversion efficiency individual feed management systems
  • the methods include the step of analyzing the trait information to provide a probability that the trait will be found in the offspring of the candidate breeding animal.
  • analyzing includes any qualitative, non-qualitative, quantitative, non-quantitative, comparative, non-comparative, statistical, non-statistical, numerical, or non-numerical consideration of the trait information for the purpose of providing a probability that the trait will be found in an offspring.
  • probability is intended to include an assessment or estimate of the likelihood or possibility that an offspring animal will exhibit the trait.
  • the term is not intended to be restricted to a mathematical probability, but may also encompass a qualitative probability.
  • the step of analyzing includes the identification of high positive difference to prediction animals over one generation, or a number of generations. This repetition of high performance linkages to the animal analysed indicates a higher reliability of this indicator through a reduced possibility of selectively controlled production bias of all individual animals within the maternal pedigree.
  • the step of analyzing is performed by the sire pathway method. Sire pathway is a reducing additive process of the individual sire traits, as genetically assessed by the productivity of their respective offspring within the population, relative to that population.
  • genetic prediction may be performed by adding half the sires genotype for the trait analyzed, plus a quarter of the maternal grand sire's genotyope value for the same trait, plus an eighth of the maternal great grand sires genotype value for the same trait.
  • the sire pathway method ignores or places less emphasis on the actual dam's performance through the pedigree as this may be separately and selectively biased.
  • breeding value is intended to mean the value of an individual animal as a genetic parent.
  • the value may be related to the ability of the parent to transmit a desirable trait to a progeny animal, or the inability to transmit an undesirable trait to a progeny animal.
  • the breeding value may be a genetic breeding value or a genomic breeding value. Breeding value is typically generated through the analysis of the expression of the genotype by an animal and/or its relative. Determination of the genomic breeding value involves the identification of key genes which provides a predictability of an animal's performance, or a prediction of an animal's ability to pass on these desirable genes to derived relatives. Breeding values may be used to develop optimal breeding strategies for review of herds and prediction of the outcome of a mating. It can also be used to develop benchmarks for comparisons between animals and groups of animals, or to access offspring performance and target focus genotypes.
  • the analysis step may include a consistency or variation analysis.
  • this analysis involves the analysis of the genotype/phenotype/genomic performance of a genetic line (related line) of animals.
  • the genetic analysis of these animals may identify an average genetic merit value which is represented by a breeding value.
  • Consistency/Variation analysis evaluates the variation around the average, with some genetic lines having a greater standard deviation or normal distribution around the average value, while other genetic lines have a narrow or more consistent variation around the average value.
  • the analysis of the standard deviation levels provides a genetic "handle" on consistency requirements for different breeding purposes. E.g. more consistent lower standard deviation values are potentially desirable for maternal breeding strategies; a higher more variable standard deviation value represents the opportunity for a paternal genetic strategy - i.e.
  • a further aspect of the invention is directed to a method for monitoring the genetic progress of an animal or a group of animals, the method comprising the steps of evaluating the genetic worth of the animal or each member of the group of animals by a method described herein at a first time, .and evaluating the genetic worth of the animal or each member of the group of animals by a method described herein at a second time, and comparing the genetic worth of the animal or group of animals at the first and second times.
  • the methods described herein also provide means to select a breeding animal from a herd of animals.
  • a breeder will have a finite number of animals from which to breed, and in choosing animals to parent the next generation of animals a decision is made at to which of those animals is better suited as compared with others in the population.
  • the invention further provides a method for comparing the genetic worth of at least two animals, the method comprising the step of evaluating the genetic worth of each of the at least two animals according to the methods described herein.
  • candidate animals will be all those animals (or reproductive or regenerative material of those animals) that are available to the breeder for breeding.
  • the number of candidate animals may be a few as two, or as many as hundreds, or even thousands.
  • the group of candidate animals to which the present method is applied may include only a subset of available animals. For example, if a dairy farmer practices "split-calving" only about half of the dams will be candidate animals.
  • the candidate animals may not necessarily be owned by the breeder, but may otherwise be available to him or her for breeding purposes.
  • a regenerative or reproductive material such as a spermatozoa or an ovum may be available to the breeder.
  • trait information relating to a maternal ancestor of the candidate animal is obtained.
  • This information may be any information useful in determining the genetic worth of an animal.
  • the trait information is genetic information.
  • Many types of genetic information will find use in the present methods, such as those obtained by analysis of genetic markers e.g., alleles, haplotypes, haplogroups, loci, quantitative trait loci, or DNA polymorphisms, restriction fragment length polymorphisms(RFLPs), amplified fragment length polymorphisms (AFLPs), single nuclear polymorphisms (SNPs), indels, short tandem repeats (STRs).
  • RFLPs restriction fragment length polymorphisms
  • AFLPs amplified fragment length polymorphisms
  • SNPs single nuclear polymorphisms
  • STRs short tandem repeats
  • Genotypic information may be provided by detecting one or more markers of interest (e.g. SNPs) in a sample from a candidate animal, and analysing the results obtained.
  • the markers of interest may be identified using a high- throughput system comprising a solid support having bound nucleic acid molecules of different sequence. Each nucleic acid of different sequence comprises a polymorphic genetic marker that is potentially informative.
  • Suitable samples for providing genotypic information include a nucleic acid molecule (e.g., RNA or genomic DNA) Genetic testing of animals may be performed using a hair follicle, for example, isolated from the tail of an animal to be tested.
  • Other examples of readily accessible samples include, for example, skin or a bodily fluid or an extract thereof or a fraction thereof.
  • a readily accessible bodily fluid includes, for example, whole blood, saliva, semen or urine.
  • Exemplary whole blood fractions are selected from the group consisting of buffy-coat fraction obtainable by ethanol fractionation
  • the sample may be prepared on a solid matrix for histological analyses, or alternatively, in a suitable solution such as, for example, an extraction buffer or suspension buffer, and the present invention clearly extends to the testing of biological solutions thus prepared.
  • a suitable solution such as, for example, an extraction buffer or suspension buffer
  • the high-throughput system of the present invention is employed using samples in solution.
  • the presence or absence of informative genetic markers may be determined by reactivity of a nucleic acid molecule to a hybridization probe or PCR primer.
  • a suitable probe or primer i.e., one capable of specifically detecting a marker, will specifically hybridize to a region of the genome in genomic DNA from the individual being tested that comprises the marker.
  • selective hybridizes means that the polynucleotide used as a probe is used under conditions where a target polynucleotide is found to hybridize to the probe at a level significantly above background. The background hybridization may occur because of other polynucleotides present, for example, in genomic
  • a probe or primer comprises nucleic acid and may consist of synthetic oligonucleotides up to about 100-300 nucleotides in length and more preferably of about 50-100 nucleotides in length and still more preferably at least about 8-100 or 8-50 nucleotides in length.
  • LNA locked nucleic acid
  • PNA protein-nucleic acid
  • probes or molecular beacons for the detection of one or more SNPs are generally at least about 8 to 12 nucleotides in length.
  • Longer nucleic acid fragments up to several kilobases in length can also be used, e.g., derived from genomic DNA that has been sheared or digested with one or more restriction endonucleases.
  • probes/primers can comprise RNA.
  • probes or primers for use in the present invention will be compatible with high- throughput systems.
  • exemplary probes and primers include locked nucleic acid (LNA) or protein-nucleic acid (PNA) probes or molecular beacons, preferably bound to a solid phase.
  • LNA or PNA probes bound to a solid support are used, wherein the probes each comprise an SNP and sufficient probes are bound to the solid support to span the genome of the species to which an individual being tested belongs.
  • Specificity of probes or primers may depend upon the format of hybridization or amplification reaction employed for genotyping.
  • sequence(s) of any particular probe(s) or primer(s) used in the method for the present invention will depend upon the marker to be detected.
  • the present invention may be generally applied to any marker for which a sequence is known.
  • Standard methods may be employed for designing probes and/or primers e.g., as described by Dveksler (Eds) (In: PCR Primer: A Laboratory Manual, Cold Spring Harbour Laboratories,
  • Probes and/or primers are preferably assessed to determine those that do not form hairpins, self-prime, or form primer dimers (e.g. with another probe or primer used in a detection assay). Furthermore, a probe or primer (or the sequence thereof) is preferably assessed to determine the temperature at which it denatures from a target nucleic acid (i.e. the melting temperature of the probe or primer, or Tm). Methods of determining Tm are known in the art and described, for example, in Santa Lucia, Proc. Natl.
  • the probe or molecular beacon it is particularly preferred for the probe or molecular beacon to be at least about 8 to 12 nucleotides in length and more preferably, for the SNP to be positioned at approximately the centre of the probe, thereby facilitating selective hybridization and accurate detection.
  • the probe/primer is generally designed such that the 3' terminal nucleotide hybridizes to the site of the SNP.
  • the 3' terminal nucleotide may be complementary to any of the nucleotides known to be present at the site of the SNP.
  • complementary nucleotides occur in both the probe/primer and at the site of the polymorphism, the 3' end of the probe or primer hybridizes completely to the marker of interest and facilitates, for example, PCR amplification or ligation to another nucleic acid. Accordingly, a probe or primer that completely hybridizes to the target nucleic acid produces a positive result in an assay.
  • the probe/primer is generally designed such that it specifically hybridizes to a region adjacent to a specific nucleotide of interest, e.g., an SNP. While the specific hybridization of a probe or primer may be estimated by determining the degree of homology of the probe or primer to any nucleic acid using software, such as, for example, BLAST, the specificity of a probe or primer is generally determined empirically using methods known in the art.
  • oligonucleotide synthesis is described, in Gait (Ed) (In: Oligonucleotide Synthesis: A Practical Approach, IRL Press, Oxford, 1984); LNA synthesis is described, for example, in Nielsen et al, J. Chem. Soc. Perkin Trans., 1 : 3423, 1997; Singh and Wengel, Chem. Commun. 1247, 1998; and PNA synthesis is described, for example, in Egholm et al., Am. Chem. Soc, 1 14: 1895, 1992; Egholm et al, Nature, 365: 566, 1993; and Orum et al., Nucl. Acids Res., 21 : 5332, 1993.
  • a marker may be detected using a probe or primer that selectively hybridizes to said marker in a sample from an individual under moderate stringency, and preferably, high stringency conditions.
  • a probe or primer is detectably labeled with a suitable reporter molecule, e.g., a chemiluminescent label, fluorescent label, radiolabel, enzyme, hapten, or unique oligonucleotide sequence etc, then the hybridization may be detected directly by determining binding of reporter molecule.
  • hybridized probe or primer may be detected by performing an amplification reaction such as polymerase chain reaction (PCR) or similar format, and detecting the amplified nucleic acid.
  • PCR polymerase chain reaction
  • the probe or primer is bound to solid support e.g., in the high-throughput system of the present invention.
  • a low stringency is defined herein as hybridization and/or a wash step(s) carried out in 2- 6 x SSC buffer, 0.1 % (w/v) SDS at 28 °C, or equivalent conditions.
  • a moderate stringency is defined herein as hybridization and/or a wash step(s) carried out in 0.2-2 x SSC buffer, 0.1% (w/v) SDS at a temperature in the range 45 °C to 65 °C, or equivalent conditions.
  • a high stringency is defined herein as hybridization and/or a wash step(s) carried out in 0.1 x SSC buffer, 0.1% (w/v) SDS, or lower salt concentration, and at a temperature of at least 65 °C, or equivalent conditions.
  • Reference herein to a particular level of stringency encompasses equivalent conditions using wash/hybridization solutions other than SSC known to those skilled in the art.
  • the stringency is increased by reducing the concentration of SSC buffer, and/or increasing the concentration of SDS and/or increasing the temperature of the hybridization and/or wash.
  • concentration of SSC buffer and/or increasing the concentration of SDS and/or increasing the temperature of the hybridization and/or wash.
  • the conditions for hybridization and/or wash may vary depending upon the nature of the hybridization matrix used to support the sample DNA, or the type of hybridization probe used.
  • Progressively higher stringency conditions can also be employed wherein the stringency is increased stepwise from lower to higher stringency conditions.
  • Exemplary progressive stringency conditions are as follows: 2 x SSC/0.1% SDS at about room temperature (hybridization conditions); 0.2 x SSC/0.1 % SDS at about room temperature (low stringency conditions); 0.2 x SSC/0.1 % SDS at about 420°C (moderate stringency conditions); and 0.1 x SSC at about 68 9 C (high stringency conditions). Washing may be carried out using only one of these conditions, e.g., high stringency conditions, or each of the conditions may be used, e.g., for 10-15 minutes each, in the order listed above, repeating any or all of the steps listed. However, as mentioned above, optimal conditions will vary, depending on the particular hybridization reaction involved, and may be determined empirically.
  • a change in the sequence of a region of the genome or an expression product thereof is detected using a method, such as, for example, an insertion, a deletion, a transversion, a transition.
  • a method such as, polymerase chain reaction (PCR), strand displacement amplification, ligase chain reaction, cycling probe technology or a DNA microarray chip amongst others.
  • Methods of PCR are known in the art and described, for example, in Dieffenbach (ed) and Dveksler (ed) (In: PCR Primer: A Laboratory Manual, Cold Spring Harbour Laboratories, NY, 1995).
  • PCR products may be detected using electrophoresis and detection with a detectable marker that binds nucleic acids.
  • a detectable marker e.g. a fluorophore
  • the amplification product detected using, for example, a lightcycler (Perkin Elmer, Wellesley, MA, USA).
  • the present invention also encompasses quantitative forms of PCR, such as, for example, Taqman assays.
  • Strand displacement amplification utilizes oligonucleotides, a DNA polymerase and a restriction endonuclease to amplify a target sequence.
  • the oligonucleotides are hybridized to a target nucleic acid and the polymerase used to produce a copy of this region.
  • the duplexes of copied nucleic acid and target nucleic acid are then nicked with an endonuclease that specifically recognizes a sequence at the beginning of the copied nucleic acid.
  • the DNA polymerase recognizes the nicked DNA and produces another copy of the target region at the same time displacing the previously generated nucleic acid.
  • SDA Strand displacement amplification
  • Ligase chain reaction uses at least two oligonucleotides that bind to a target nucleic acid in such a way that they are adjacent. A ligase enzyme is then used to link the oligonucleotides. Using thermocycling the ligated oligonucleotides then become a target for further oligonucleotides. The ligated fragments are then detected, for example, using electrophoresis, or MALDI-TOF. Alternatively, or in addition, one or more of the probes is labeled with a detectable marker, thereby facilitating rapid detection.
  • RNA-DNA duplex formed is a target for RNase H thereby cleaving the probe.
  • the cleaved probe is then detected using, for example, electrophoresis or MALDI-TOF.
  • SNPs SNPs that introduces or alters a sequence that is a recognition sequence for a restriction endonuclease is detected by digesting DNA with the endonuclease and detecting the fragment of interest using, for example, Southern blotting (described in Ausubel et al (In: Current Protocols in Molecular Biology. Wiley Interscience, ISBN 047 150338, 1987) and Sambrook et al (In: Molecular Cloning: Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratories, New York, Third Edition 2001 )).
  • nucleic acid amplification method described supra is used to amplify the region surrounding the SNP.
  • the amplification product is then incubated with the endonuclease and any resulting fragments detected, for example, by electrophoresis, MALDI-TOF or PCR.
  • the direct analysis of the sequence of polymorphisms of the present invention may be accomplished using either the dideoxy chain termination method or the Maxam-Gilbert method (see Sambrook et al, Molecular Cloning, A Laboratory Manual (2nd Ed., CSHP, New York 1989); Zyskind et al, Recombinant DNA Laboratory Manual, (Acad. Press, 1988)).
  • a region of genomic DNA comprising one or more markers is amplified using an amplification reaction, e.g., PCR, and following purification of the amplification product, the amplified nucleic acid is used in a sequencing reaction to determine the sequence of one or both alleles at the site of an SNP of interest.
  • one or more SNPs is/are detected using single stranded conformational polymorphism (SSCP).
  • SSCP relies upon the formation of secondary structures in nucleic acids and the sequence dependent nature of these secondary structures.
  • an amplification method such as, for example, a method described supra, is used to amplify a nucleic acid that comprises an SNP.
  • the amplified nucleic acids are then denatured, cooled and analyzed using, for example, non-denaturing polyacrylamide gel electrophoresis, mass spectrometry, or liquid chromatography (e.g., HPLC or dHPLC).
  • Regions that comprise different sequences form different secondary structures, and as a consequence migrate at different rates through, for example, a gel and/or a charged field.
  • a detectable marker may be incorporated into a probe/primer useful in SSCP analysis to facilitate rapid marker detection.
  • any nucleotide changes may be detected using, for example, mass spectrometry or capillary electrophoresis.
  • amplified products of a region of DNA comprising an SNP from a test sample are mixed with amplified products from an individual having a known genotype at the site of the SNP. The products are denatured and allowed to re-anneal. Those samples that comprise a different nucleotide at the position of the SNP will not completely anneal to a nucleic acid molecule from the control sample thereby changing the charge and/or conformation of the nucleic acid, when compared to a completely annealed nucleic acid.
  • Such incorrect base pairing is detectable using, for example, mass spectrometry.
  • Allele-specific PCR (as described, for example, In Liu et al, Genome Research, 7: 389- 398, 1997) is also useful for determining the presence of one or other allele of an SNP.
  • An oligonucleotide is designed, in which the most 3' base of the oligonucleotide hybridizes to a specific form of an SNP of interest (i.e., allele). During a PCR reaction, the 3' end of the oligonucleotide does not hybridize to a target sequence that does not comprise the particular form of the SNP detected.
  • PCR products are then detected using, for example, gel or capillary electrophoresis or mass spectrometry.
  • Primer extension methods are also useful for the detection of an SNP.
  • An oligonucleotide is used that hybridizes to the region of a nucleic acid adjacent to the SNP.
  • This oligonucleotide is used in a primer extension protocol with a polymerase and a free nucleotide diphosphate that corresponds to either or any of the possible bases that occur at the site of the SNP.
  • the nucleotide-diphosphate is labeled with a detectable marker (e.g. a fluorophore).
  • primer extension products are detected using mass spectrometry (e.g., MALDI-TOF).
  • the present invention extends to high-throughput forms of primer extension analysis, such as, for example, minisequencing (Sy Vamen et al, Genomics 9: 341 -342, 1995) wherein a probe or primer or multiple probes or primers is/are immobilized on a solid support (e.g. a glass slide), a sample comprising nucleic acid is brought into contact with the probe(s) or primer(s), a primer extension reaction is performed wherein each of the free nucleotide bases A, C, G, T is labeled with a different detectable marker and the presence or absence of one or more SNPs is determined by determining the detectable marker bound to each probe and/or primer.
  • minisequencing Sy Vamen et al, Genomics 9: 341 -342, 1995
  • a probe or primer or multiple probes or primers is/are immobilized on a solid support (e.g. a glass slide)
  • a sample comprising nucleic acid is brought into contact with the probe
  • LNA locked nucleic acid
  • PNA fluorescently labeled protein- nucleic acid
  • Flurophores conjugated to the LNA or PNA probe fluoresce at a significantly greater level upon hybridization of the probe to target nucleic acid compared to a probe that has not hybridized to a target nucleic acid.
  • the level of increase of fluorescence is not enhanced to the same level when even a single nucleotide mismatch occurs.
  • the degree of fluorescence detected in a sample is indicative of the presence of a mismatch between the LNA or PNA probe and the target nucleic acid, such as, in the presence of an SNP.
  • fluorescently labeled LNA or PNA technology is used to detect a single base change in a nucleic acid that has been previously amplified using, for example, an amplification method described supra.
  • LNA or PNA detection technology is amenable to a high-throughput detection of one or more markers immobilizing an LNA or PNA probe to a solid support, as described in Oram et al, Clin. Chem. 45: 1898- 1905, 1999.
  • Molecular Beacons are useful for detecting SNPs directly in a sample or in an amplified product (see, for example, Mhlang and Malmberg, Methods 25: 463-471 , 2001 ).
  • Molecular beacons are single stranded nucleic acid molecules with a stem-and- loop structure.
  • the loop structure is complementary to the region surrounding the SNP of interest.
  • the stem structure is formed by annealing two "arms" complementary to each other on either side of the probe (loop).
  • a fluorescent moiety is bound to one arm and a quenching moiety that suppresses any detectable fluorescence when the molecular beacon is not bound to a target sequence bound to the other arm.
  • the arms Upon binding of the loop region to its target nucleic acid the arms are separated and fluorescence is detectable. However, even a single base mismatch significantly alters the level of fluorescence detected in a sample. Accordingly, the presence or absence of a particular base at the site of an SNP is determined by the level of fluorescence detected.
  • the present invention encompasses other methods of detecting an SNP that is , such as, for example, SNP microarrays (available from Affymetrix, or described, for example, in US 6,468,743 or Hacia et al, Nature Genetics, 14: 441 , 1996), Taqman assays (as described in Livak et al, Nature Genetics, 9: 341 -342, 1995), solid phase minisequencing (as described in Syvamen et al, Genomics, 13: 1008-1017, 1992), minisequencing with FRET (as described in Chen and Kwok , Nucleic Acids Res. 25: 347-353, 1997) or pyrominisequencing (as reviewed in Landegren et al., Genome Res., 8(8): 769-776, 1998).
  • SNP microarrays available from Affymetrix, or described, for example, in US 6,468,743 or Hacia et al, Nature Genetics, 14: 4
  • polymorphism or marker occurs in a region of nucleic acid that encodes RNA
  • said polymorphism or marker is detected using a method such as, for example, RT-PCR, NASBA or TMA.
  • RT-PCR Methods of RT-PCR are known in the art and described, for example, in Dieffenbach (ed) and Dveksler (ed) (In: PCR Primer: A Laboratory Manual, Cold Spring Harbour Laboratories, NY, 1995).
  • Methods of TMA or self-sustained sequence replication use two or more oligonucleotides that flank a target sequence, a RNA polymerase, RNase H and a reverse transcriptase.
  • One oligonucleotide (that also comprises a RNA polymerase binding site) hybridizes to an RNA molecule that comprises the target sequence and the reverse transcriptase produces cDNA copy of this region.
  • RNase H is used to digest the RNA in the RNA-DNA complex, and the second oligonucleotide used to produce a copy of the cDNA.
  • the RNA polymerase is then used to produce a RNA copy of the cDNA, and the process repeated.
  • NASBA systems relies on the simultaneous activity of three enzymes (a reverse transcriptase, RNase H and RNA polymerase) to selectively amplify target mRNA sequences.
  • the mRNA template is transcribed to cDNA by reverse transcription using an oligonucleotide that hybridizes to the target sequence and comprises a RNA polymerase binding site at its 5' end.
  • the template RNA is digested with RNase H and double stranded DNA is synthesized.
  • the RNA polymerase then produces multiple RNA copies of the cDNA and the process is repeated.
  • the hybridization to and/or amplification of a marker is detectable using, for example, electrophoresis and/or mass spectrometry.
  • one or more of the probes/primers and/or one or more of the nucleotides used in an amplification reactions may be labeled with a detectable marker to facilitate rapid detection of a marker, for example, a fluorescent label (e.g. Cy5 or Cy3) or a radioisotope (e.g. 32P).
  • amplification of a nucleic acid may be continuously monitored using a melting curve analysis method, such as that described in, for example, US 6,174,670.
  • a melting curve analysis method such as that described in, for example, US 6,174,670.
  • Methods of the invention can identify nucleotide occurrences at SNPs using genome- wide sequencing or "microsequencing" methods. Whole-genome sequencing of individuals identifies all SNP genotypes in a single analysis. Microsequencing methods determine the identity of only a single nucleotide at a "predetermined" site. Such methods have particular utility in determining the presence and identity of polymorphisms in a target polynucleotide.
  • microsequencing methods as well as other methods for determining the nucleotide occurrence at SNP loci are discussed in Boyce-Jacino, et al, U.S. Pat. No. 6,294,336, incorporated herein by reference.
  • Microsequencing methods include the Genetic Bit Analysis method disclosed by Goelet, P. et al. (WO 92/15712, herein incorporated by reference). Additional, primer- guided, nucleotide incorporation procedures for assaying polymorphic sites in DNA have also been described (Komher et al, Nucl. Acids. Res. 17, 7779-7784, 1989; Sokolov, Nucl. Acids Res. 18, 3671 (1990); Syvanen et al, Genomics 8, 684-692, 1990; Kuppuswamy et al, Proc. Natl. Acad. Sci. (U.S.A.) 88, 1 143-1 147, 1991 ; Prezant et al, Hum. Mutat.
  • 6,294,336 provide a solid phase sequencing method for determining the sequence of nucleic acid molecules (either DNA or RNA) by utilizing a primer that selectively binds a polynucleotide target at a site wherein the SNP is the most 31 nucleotide selectively bound to the target.
  • nucleotide occurrences for SNPs may be determined using a DNAMassARRAY system (Sequenom, San Diego, Calif.) is used, which system combines SpectroChipsTM, microfiuidics, nanodispensing, biochemistry, and MALDI- TOF MS (matrix-assisted laser desorption ionization time of flight mass spectrometry).
  • DNAMassARRAY Sequenom, San Diego, Calif.
  • MALDI- TOF MS matrix-assisted laser desorption ionization time of flight mass spectrometry
  • High-throughput systems for analyzing markers, especially SNPs can include, for example, a platform such as the UHT SNP-ITTM platform (Orchid Biosciences, Princeton, N.J., USA) MassArrayTM system (Sequenom, San Diego, Calif., USA), the integrated SNP genotyping system (lllumina, San Diego, Calif, USA), TaqManTM (ABI, Foster City, Calif, USA), Rolling circle amplification, fluorescent polarization, amongst others described herein above.
  • SNP-ITTM is a 3-step primer extension reaction.
  • a target polynucleotide is isolated from a sample by hybridization to a capture primer, which provides a first level of specificity.
  • the capture primer is extended from a terminating nucleotide trisphosphate at the target SNP site, which provides a second level of specificity.
  • the extended nucleotide trisphosphate may be detected using a variety of known formats, including: direct fluorescence, indirect fluorescence, an indirect colorimetric assay, mass spectrometry, fluorescence polarization, etc. Reactions may be processed in 384 well format in an automated format using an SNPstreamTM instrument (Orchid BioSciences, Inc., Princeton, N. J.).
  • Such systems typically comprise a solid support having nucleic acids of different sequence bound directly or indirectly thereto, wherein each nucleic acid of different sequence comprises a polymorphic genetic marker.
  • Exemplary high-throughput systems are hybridization mediums e.g., a microfluidic device or homogenous assay medium.
  • a microfluidic device or homogenous assay medium.
  • Numerous microfluidic devices are known that include solid supports with microchannels (See e.g., U.S. Pat. Nos. 5,304,487, 5,1 10,745, 5,681 ,484, and 5,593,838).
  • the high throughput system comprises an SNP chip comprising 10,000-100,000 oligonucleotides each of which consists of a sequence comprising an SNP.
  • Each of these hybridization mediums is suitable for determining the presence or absence of a marker associated with a trait.
  • the nucleic acids are typically oligonucleotides, attached directly or indirectly to the solid support. Accordingly, the oligonucleotides are used to determine the nucleotide occurrence of a marker associated with a trait, by virtue of the hybridization of nucleic acid from the subject being tested to an oligonucleotide of a series of oligonucleotides bound to the solid support being affected by the nucleotide occurrence of the marker in question e.g., by the presence or absence of an SNP in the subject's nucleic acid. Accordingly, oligonucleotides may be selected that bind at or near a genomic location of each marker. Such oligonucleotides can include forward and reverse oligonucleotides that can support amplification of a particular polymorphic marker present in template nucleic acid obtained from the subject being tested.
  • the oligonucleotides can include extension primer sequences that hybridize in proximity to a marker to thereby support extension to the marker for the purposes of identification.
  • a suitable detection method will detect binding or tagging of the oligonucleotides e.g., in a genotyping method described herein.
  • U.S. Patent No. 5,837,832 describes an improved method for producing DNA arrays immobilised to silicon substrates based on very large scale integration technology.
  • U.S. Patent No. 5,837,832 describes a strategy called "tiling" to synthesize specific sets of probes at spatially-defined locations on a substrate which are used to produce the immobilised DNA array.
  • U.S. Patent No. 5,837,832 also provides references for earlier techniques that may also be used.
  • DNA may be synthesised in situ on the surface of the substrate. However, DNA may also be printed directly onto the substrate using for example robotic devices equipped with either pins or piezo electric devices.
  • Microarrays are generally produced stepwise, by the in situ synthesis of the target directly onto the support, or alternatively, by exogenous deposition of pre-prepared targets. Photolithography, mechanical microspotting, and ink jet technology are generally employed for producing microarrays.
  • a glass wafer, modified with photolabile protecting groups is selectively activated e.g., for DNA synthesis, by shining light through a photomask. Repeated deprotection and coupling cycles enable the preparation of high-density oligonucleotide microarrays (see for example, U.S. Pat. No. 5,744,305, issued Apr. 28, 1998).
  • Microspotting encompasses deposition technologies that enable automated microarray production, by printing small quantities of pre-made target substances onto solid surfaces. Printing is accomplished by direct surface contact between the printing substrate and a delivery mechanism, such as a pin or a capillary. Robotic control systems and multiplexed print heads allow automated microarray fabrication.
  • Ink jet technologies utilize piezoelectric and other forms of propulsion to transfer biochemical substances from miniature nozzles to solid surfaces. Using piezoelectricity, the target sample is expelled by passing an electric current through a piezoelectric crystal which expands to expel the sample. Piezoelectric propulsion technologies include continuous and drop-on- demand devices. In addition to piezoelectric ink jets, heat may be used to form and propel drops of fluid using bubble- jet or thermal ink jet heads; however, such thermal ink jets are typically not suitable for the transfer of biological materials due to the heat which is often stressful on biological samples. Examples of the use of ink jet technology include U.S. Pat. No. 5,658,802 (issued Aug. 19, 1997).
  • a plurality of nucleic acids is typically immobilised onto or in discrete regions of a solid substrate.
  • the substrate is porous to allow immobilisation within the substrate, or substantially non-porous to permit surface immobilization.
  • the solid substrate may be made of any material to which polypeptides can bind, either directly or indirectly.
  • suitable solid substrates include flat glass, silicon wafers, mica, ceramics and organic polymers such as plastics, including polystyrene and polymethacrylate.
  • semi-permeable membranes such as nitrocellulose or nylon membranes, which are widely available.
  • the semi-permeable membranes are mounted on a more robust solid surface such as glass.
  • the surfaces may optionally be coated with a layer of metal, such as gold, platinum or other transition metal.
  • the solid substrate is generally a material having a rigid or semi-rigid surface.
  • at least one surface of the substrate will be substantially flat, although in some embodiments it are desirable to physically separate synthesis regions for different polymers with, for example, raised regions or etched trenches.
  • the solid substrate is suitable for the high density application of DNA sequences in discrete areas of typically from 50 to 100 ⁇ m, giving a density of 10,000 to 40,000 cm "2 .
  • Attachment of the nucleic acids to the substrate may be covalent or non-covalent, generally via a layer of molecules to which the nucleic acids bind.
  • the nucleic acid probes/primers may be labeled with biotin and the substrate coated with avidin and/or streptavidin.
  • biotinylated probes/primers A convenient feature of using biotinylated probes/primers is that the efficiency of coupling to the solid substrate is determined easily.
  • a chemical interface may be provided between the solid substrate e.g., in the case of glass, and the probes/primers.
  • suitable chemical interfaces include hexaethylene glycol, polylysine.
  • polylysine may be chemically modified using standard procedures to introduce an affinity ligand.
  • the high-throughput system of the present invention is designed to determine nucleotide occurrences of one SNP or a series of SNPs.
  • the systems can determine nucleotide occurrences of an entire genome- wide high-density SNP map.
  • High-throughput systems for analyzing markers, especially SNPs can include, for example, a platform such as the UHT SNP-IT platform (Orchid Biosciences, Princeton, NJ. , USA) MassArrayTM system (Sequenom, San Diego, Calif., USA), the integrated SNP genotyping system (lllumina, San Diego, Calif., USA), TaqManTM (ABI, Foster City, Calif, USA).
  • Exemplary nucleic acid arrays are of the type described in WO 95/1 1995.
  • WO 95/1 1995 also describes sub-arrays optimized for detection of a variant form of a pre-characterized polymorphism. Such a sub-array contains probes designed to be complementary to a second reference sequence, which is an allelic variant of the first reference sequence.
  • the high throughput system comprises a SNP microarray such as those available from Affymetrix or described, for example, in US 6,468,743 or Hacia et al, Nature Genetics, 14: 441 , 1996.
  • DNA arrays are typically read at the same time by charged coupled device (CCD) camera or confocal imaging system.
  • the DNA array may be placed for detection in a suitable apparatus that can move in an x-y direction, such as a plate reader. In this way, the change in characteristics for each discrete position are measured automatically by computer controlled movement of the array to place each discrete element in turn in line with the detection means.
  • CCD charged coupled device
  • the detection means is capable of interrogating each position in the library array optically or electrically.
  • suitable detection means include CCD cameras or confocal imaging systems.
  • the system can further include a detection mechanism for detecting binding the series of oligonucleotides to the series of SNPs.
  • detection mechanisms are known in the art.
  • the high-throughput system of the present invention can include a reagent handling mechanism that may be used to apply a reagent, typically a liquid, to the solid support.
  • the high-throughput system can also include a mechanism effective for moving a solid support and a detection mechanism.
  • the problem in the sheep industry is that a recessive alternative of the ASIP gene may be carried by white sheep and cause black lambs when mated with another carrier sheep.
  • the exact genetic differences at the ASIP position have been determined to allow a genetic test that can identify the carriers of the problem variant of the gene.
  • a step in the present method may require the assembly of trait information for all candidate animals and ancestors to provide a pedigree dataset.
  • This step requires that separate items of information are brought together in physical or logical proximity, such that the information may be manipulated as a dataset according to the steps of the present method.
  • trait information for all candidate animals may be stored across a number of remote computers, yet all information being logically connected by way of local area network, or wide area network.
  • the dataset may be in paper, electronic or any other form. It may be assembled manually or by computer- or machine-assisted means.
  • the sire pathway method is a reducing additive process of the individual sires traits from the maternal pedigree (as genetically assessed by the productivity of their respective offspring within the total population, relative to the population). Therefore the genetic prediction for the respective female to be analysed is by adding half the sires genotype value for trait analysed, plus a quarter of the maternal grand sires genotype value for the same trait, plus an eighth of the maternal great grand sires genotype value for the same trait.
  • the sire pathway method ignores the actual dam's performance through the pedigree as this may be separately and selectively biased.
  • One embodiment of the method requires the generational identification of high positive difference to prediction animals over a number of generations. This repetition of high performance linkages to the animal analysed indicates a higher reliability of this indicator (through a reduced possibility of selectively controlled production bias of all individual animals within the maternal pedigree).
  • a candidate breeding animal may be ranked as having a higher genetic worth (as compared with another candidate animal) on the basis of a greater difference between the predicted genotype and the trait information.
  • the step of analyzing may require that the presence and/or absence of difference(s) between the candidate animals trait information and the predicted trait.
  • the trait may be predicted according to a herd database, or an industry-wide database.
  • the number of values compared is only limited by the genetic values that are available for the animal analysed, including the maternal pedigree, and the linkage to the genetic merit of the same traits that are available for the sires within the maternal pedigree.
  • the more relevant traits are those of higher economic value.
  • a consideration of the heritability of these traits also adds to the importance, as reflected by the ability for each generation to influence a trait.
  • the trait information is obtained from at least 1 generation of ancestors. In another embodiment of the method the trait information is obtained from at least 2 generations of ancestors. In a further embodiment of the method the trait information is obtained from at least 3 generations of ancestors. In another embodiment of the method the trait information is obtained from at least 4 generations of ancestors. A further embodiment of the method provides that the trait information is obtained from at least 5 generations of ancestors. In many circumstances, the accuracy of the genetic worth will be increased by the use of larger numbers of ancestors.
  • the present invention is useful in selecting both male and female animals for breeding, however, the invention is more applicable to female animal analysis. With further analysis in genomic analysis systems, the application of the invention to male animals will become more important. This is due to the reduced time line in generating actual or higher reliability of prediction of genetic performance, and the availability of these values to be compared to their genetic prediction.
  • the method is used in the context of a mating analysis.
  • the present invention further provides a method for evaluating the suitability of a first animal to mate with a second animal, the method comprising the step of evaluating the genetic worth of the first animal by a method as described herein.
  • the step of evaluating the genetic worth of the second animal may be further included in the method.
  • the second animal may or may not be an animal from the group of candidate animals under analysis by the present method
  • Useful information may be identified for potential mating candidates by analyzing key traits and comparing their values against the average and standard deviation levels for these traits. In specific predictor matings, potential sires are screened prior to the genetic prediction analysis. Potential sires with a significantly positive trait (based on standard deviation based difference to average) are considered, but if they contain a significantly negative trait (based on standard deviation based difference to average), they are excluded from the analysis.
  • an exclusion step is included. According to this step in the method, if a genotype trait is identified for protection, any potential mating sire that is less than average for that trait is excluded. To the best of the Applicant's knowledge this approach has not been disclosed on or before the priority date of this application. The skilled person will understand that varying levels of exclusion (and therefore acceptance) may be applied, again based on the statistical application of average and standard deviation levels
  • mating methodologies may be predicated on identifying a suggested mating nomination in order to correct a weakness.
  • the weakness identified in most mating packages may be based on visual, non genetic assessments. Visual assessment may be used with the mating methodologies described herein, as a secondary level of analysis in support of genotype prediction. It is proposed that the ability to exclude negative traits will find use in the breeding of companion animals, such as dogs. Many breeds have certain traits that can contribute to morbidity or even mortality in a dog. Such traits include anatomical defects such as hip dysplasia that can cause excessive wear of hip. Other undesirable traits include eye abnormalities, heart conditions, and deafness.
  • the mating analysis utilises the predicted genotype of an animal identified to be mated. This may incorporate maternal genetic contribution to the predicted animal genotype for genetic, genomic or variation values and incorporates this into a predicted genotype picture. Additional information regarding the animal to be mated can also be incorporated, including visual/phenotype data, actual animal genomic value, as well variation/consistency analysis to further enhance the animal to be analysed. The predicted animal's composite is then compared to the variation in population of these traits as based on normal distribution of population average and standard deviation values.
  • the method utilizes the predicted genotype of a nominated high genetic merit animal identified to be mated. Potential mating sires that have identified genetic, genomic and consistency/variation values are incorporated into the maternal pedigree line of nominated elite genetic merit animals. A predicted genotype picture for genetic, genomic or variation outcome values is generated. Additional information may be incorporated, including visual/phenotype data, actual animal genomic value, as well variation/consistency analysis to further enhance the predicted animal genotype picture.
  • the predicted animal's composite may then be compared to the variation in population of these traits as based on normal distribution of population average and standard deviation values. Identified genetic, genomic and consistency/variation values are highlighted and analysed if they reinforce undesirable genotype traits in comparison to the average and standard deviation limit values as identified in the population. In this way, the likelihood that a progeny animal displays undesirable traits is lessened.
  • Potential mating sires are potentially allocated to the elite animals if they compliment, in comparison to the average and standard deviation limit values as identified in the population.
  • any candidate animal or mating pair identified for breeding by the present methods does not necessarily assure the production of a progeny animal with a given phenotype.
  • the aim of the present method is to increase the likelihood that a desirable progeny animal is produced, as compared to a situation where the method is not used.
  • outlier animals are introduced into the mating analysis.
  • the use of outlier animals increases diversity and reduces problems of inbreeding.
  • the term "outlier animal” refers to an animal that has a maternal pedigree that is represented by animals with genetic breeding values at a defined standard deviation value different to their predicted values. These animals can occur through out the total population of animals with genetic values.
  • Such animals are a useful genetic resource to breed diverse pedigree lines of offspring, that may be developed by breeding new progeny lines. These new progeny lines may be resourced as potential candidates for future genetic advancement through the new and diverse maternal and paternal lines that are developed. Animals with high negative to prediction outliers are a potential resource for gene discovery and reinforcement of genomic marker identification.
  • the present invention also provides a method for obtaining a reproductive or regenerative material from an animal comprising evaluating the genetic worth of an animal by a method as described herein and obtaining the reproductive or regenerative material from the animal.
  • Such materials include gametes (sperm or ovum), as well as somatic cells that may be used for cloning an animal.
  • the reproductive or regenerative material so obtained may in turn be used for producing an animal.
  • the present invention also provides a process for producing genetic gain in a population comprising performing a method for the present invention according to any embodiment described herein; obtaining reproductive or regenerative material from a selected individual; and producing one or more individuals or one or more generations of individuals from the reproductive or regenerative material.
  • the present invention clearly extends to any individuals or generations of individuals produced by performing the process of the present invention.
  • the skilled artisan will be aware that the genetic contribution of the reproductive or regenerative material may not be carried forward to all generations beyond an initial progeny generation. Accordingly, when generations of individuals beyond the initial progeny generation are produced from the reproductive or regenerative material, the present invention encompasses any individual of those generations to the extent that the individual contains in its genome a chromosome segment derived from the reproductive or regenerative material that would explain the expected genetic gain or actual genetic gain from the reproductive or regenerative material.
  • Exemplary animals include (but are not limited to) cattle (e.g., Holstein, Jersey, Friesan, Australian Red, Hereford, Poll Hereford, Brahman, Angus, Santa Gertrudis, Murray Grey, Charolais, Limousin, Brown Swiss, Bos Indicus, Droughtmaster, Brangus, Australian Milking Zebu, Ayrshire, Braford, lllawarra, Red Angus, Simmental, Zebu, Braunvieh, Danish Red, Aberdeen Angus), sheep (e.g., Meatlinc, Dorset, Rambouillet.
  • cattle e.g., Holstein, Jersey, Friesan, Australian Red, Hereford, Poll Hereford, Brahman, Angus, Santa Gertrudis, Murray Grey, Charolais, Limousin, Brown Swiss, Bos Indicus, Droughtmaster, Brangus, Australian Milking Zebu, Ayrshire, Braford, lllawarra, Red Angus, Simmental, Zebu, Braunvieh, Danish Red, Aberdeen
  • the candidate breeding animal is not a human animal.
  • databases comprise data such as breeding values for one or more individuals of a population, data on ancestors (including founders) for individuals, including data on linkages between marker genotype(s) and phenotypes, data on reproductive or regenerative material, data on pedigree and phenotype e.g., obtained from one or more record(s) of pedigree and/or phenotype.
  • a database of the present invention comprises information regarding the location and nucleotide occurrences of genetic markers e.g, SNPs for significant ancestors or breeding individuals in a population and, more preferably, information pertaining to genetic markers used in the high-throughput system of the present invention or data pertaining to sufficient markers to be representative of a genome of a population i.e., spanning the genome and comprising sufficient polymorphisms to be useful for genome-wide screening.
  • the data may be arrayed in linkage groups, optionally according to a chromosome segment with which they are in linkage disequilibrium.
  • Information regarding genomic location of a marker may be provided for example by including sequence information of consecutive sequences surrounding a polymorphism, or by providing a position number for the polymorphism with respect to an available sequence entry, such as a Genbank sequence entry, or a sequence entry for a private database, or a commercially- licensed database of DNA sequences.
  • the database can also include information regarding nucleotide occurrences of polymorphic markers.
  • a database of the present invention can include other information regarding markers or haplotypes, such as information regarding frequency of occurrence in a population.
  • a database may also contain records representing additional information about a marker, for example information identifying the genome in which a particular marker is found, or nucleotide occurrence frequency data, or characteristics of a library or clone or individual which generated the DNA sequence, or the relationship of the sequence surrounding a polymorphic marker to similar DNA sequences in other species.
  • a database of the present invention may be a flat file database or a relational database or an object-oriented database.
  • the database may be internal i.e., a private database not accessible to external users, and typically maintained behind a firewall, by an enterprise.
  • the database may be external i.e., accessible to external users by virtue of being located outside an internal database, and typically maintained by a different entity than an internal database.
  • SNP databases A number of external public biological sequence databases, particularly SNP databases, are available and may be used with the current invention.
  • the dbSNP database available from the National Center for Biological Information (NCBI), part of the National Library of Medicine, USA may be used with the current invention to provide comparative genomic information to assist in identifying SNPs from a wide variety of different breeding populations.
  • NCBI National Center for Biological Information
  • the database comprises a population of information that may be modified by users to include new information e.g., actual breeding values from artificial selection or breeding programs, newly-identified markers, haplotypes, traits, chromosome segments, and their associations.
  • the population of information is typically included within a database, and may be identified using the methods of the current invention.
  • a population of information can include all of the SNPs and/or haplotypes of a genome-wide SNP map for a particular set of ancestors and/or individuals in a population having a small effective population size.
  • the present invention also provides a computer-readable medium for use in breeding comprising trait information useful as input data in the present methods and/or output data obtained from the present methods.
  • the present invention provides software or a computer system capable of executing a method described herein and/or holding a database described herein.
  • a computer system of the present invention may comprise a database as described herein and a user interface capable of receiving entry of data e.g., for querying the database and displaying results of a database query.
  • the interface may also permit population of one or more fields of data in the database where a user has authority to populate information.
  • the interface may be a graphic user interface where entries and selections are made e.g., using a series of menus, dialog boxes, and/or selectable buttons.
  • the interface typically takes a user through a series of screens beginning with a main menu.
  • the user interface can include links to access additional information, including information from other external or internal databases.
  • a computer system of the present invention that processes input data and displays the results of a database query will typically comprise a processing unit that executes a computer program, such as, for example, a computer program comprising a computer- readable program code embodied on a computer-usable medium and present in a memory function connected to the processing unit.
  • the memory function may be ROM or RAM.
  • the computer program is typically read and executed by the processing unit.
  • the computer-readable program code relates to a plurality of data files stored in a database.
  • the computer program can also comprise a computer-readable program code for providing a user interface capable of allowing a user to input nucleotide occurrences of the series of SNPs, locating data corresponding to the entered query information, and displaying the data corresponding to the entered query.
  • Data corresponding to the entered query information is typically located by querying a database as described above.
  • the computer system and computer program are used to perform a method for the present invention, such as a method for estimating the genetic worth of an individual.
  • a computer system of the present invention may be a stand-alone computer, a conventional network system including a client/server environment and one or more database servers, and/or a handheld device.
  • a number of conventional network systems including a local area network (LAN) or a wide area network (WAN), are known in the art.
  • client/server environments, database servers, and networks are well documented in the technical, trade, and patent literature.
  • the database server can run on an operating system such as UNIX, running a relational database management system, a World Wide Web application, and a World Wide Web Server.
  • PDA personal digital assistant
  • another type of handheld device of which many are known.
  • the present invention provides computer executable code capable of performing the method as described herein.
  • the code is typically stored in a computer- readable medium, the computer executable code adapted, when running on a computer system to execute the methods of the present invention and to direct a processing means to produce output signals that are representative for the relevance of a genetic worth.
  • EXAMPLE 1 Obtaining pedigree data of candidate breeding animal (dairy sire) A requirement of some aspects of the invention is the sire identification of the maternal line i.e., the sire of the animal of interest, her link to her dam and her dam's sire, and her link to her maternal grand dam and her maternal grand dams sire. This information is used to establish the animal's genetic profile.
  • trait information is obtained from the Australian Dairy Herd Improvement Orgnaizations (ADHIS Pty Ltd). This database uses a standard data interchange format, allowing for the downloading of significant quantities of trait data
  • EXAMPLE 2 Mating analysis for dairy cattle. From the maternal line of the animals pedigree, sire, maternal grand sire and maternal great grand sire's breeding value information for each genetic trait was obtained from the ADHIS database. The predicted genotype was established for each female by adding half of her sires genetic breeding values (for all traits recorded), plus a quarter of the maternal grand sires genetic breeding values, plus an eighth of the maternal great grand sires genetic breeding value (see Fig 1 ).
  • the predicted genotype values for all traits were compared against the industry normal distribution values for each breeding value analysed.
  • An element of the genotype mating strategy is in "excluding" potential sires that would compound any identified genotype trait that requires genetic protection by the mating strategy. (I.e. the identification of sires that fail the screening process as their genotype weakness would add to the genotype weakness identified through the construction of the maternal genotype picture).
  • any identified genetic recessives between potential mating sires and the pedigree of each animal were evaluated in order to exclude the potential of genetic recessives being brought together within the managed mating strategy.
  • the outcome is an analysis of the individual genotype of each animal, based on the maternal pedigree, the predicted genotype weaknesses of the whole group of animals analysed, and the nominated exclusion of potential sires against each individual animal's genotype and pedigree. This leaves either the remaining sires that have got through the screening process, or a resource of suggested sires that would not fail the exclusion process.
  • the present methods may be used in specialised mating situations whereby potential candidate sires are evaluated against a maternal pedigree to generate a predicted genotype picture for each sire/maternal line mating (see Fig 2). This is achieved by adding half a potential sires genetic breeding values (for all traits recorded), plus a quarter of the females sires genetic breeding values, plus an eighth of the maternal grand sires genetic breeding value, plus a sixteenth of the maternal great grand sires genetic breeding value.
  • a trait that is identified at a negative level relevant to the average value for that trait, based on a nominated standard deviation difference level, is itemised as a trait for genotype protection. Value-based genetic decisions are then made considering inbreeding levels and identified negative traits against the population reference values.
  • EXAMPLE 4 Genetic profile analysis The same predictive methodologies are utilised as in the genetic mating and genetic prediction process. The sire, maternal grand sire and maternal great grand sire's breeding value information were obtained for the genetic traits for the animal to be evaluated.
  • the predicted genotype is established for each female by adding half of her sires genetic breeding values (for all trait values in common), plus a quarter of the maternal grand sires genetic breeding values, plus an eighth of the maternal great grand sires genetic breeding value (see Fig. 3)
  • This value is then compared against the female's actual genetic value and identify the difference in value (i.e. the difference to prediction).
  • the same methodology was also applied to the female's dam and great grand dam to identify animals that demonstrate high levels of difference to prediction. These values may be extremely high, or even growing in magnitude. In contrast, some values may be consistently low, or even decreasing.
  • EXAMPLE 5 Genetic benchmarking analysis Genetic benchmarking is achieved by analysing individual and population sub groups against the total population for key performance genetic traits.
  • Genetic progress weights the average breeding value for a production trait within a sub population against the population average (or benchmark) for the same trait, as identified by the progress analysis of the whole population. Year of birth is the key reference point for comparison. This identifies the rate of progress for the specified trait against the rate of progress of the whole population.
  • Genetic progress predictions weights the number of offspring relative to the genetic merit of their sires as a reflection of influence of the sire groups average genetic merit and the potential for genetic progress of this sire groups progeny.
  • Year of birth is the key reference point for comparison.
  • Genetic merit versus profitability examines a full productive year of a group of animals. The animals are ordered in their genetic merit value, and then sub grouped into five equal groups, ranging from the bottom 0% to 20 % group, 21 % to 40% group, 41% to 60% group, 61 % to 80% group and 81% to 100% group.
  • Each animal's actual production performance relative to their genetic merit groups is calculated based on the current economic values for the production components analysed.
  • a benchmark reference is then established based of the analysis of the 5 genetic merit groups, and the financial return and profitability benchmark achieved from each group.
  • Genetic survival benchmarking is achieved by analysing the terminated animals within a sub population data set, based on both grouping their productive index during their first year of production, or grouping the genetic merit levels (evaluated by the sire pathways as described herein) of animals by year of birth, and comparing the total number of days producing i.e. a calculation of total number of days that the animal was producing within the sub population data set, prior to termination from the sub population data set.
  • the terminated animal sub set is ordered into their productive index or genetic merit values, and then sub grouped into five equal groups, ranging from the bottom 0% to 20 % group, 21 % to 40% group, 41% to 60% group, 61% to 80% group and 81% to 100% group. Year of birth is the key reference point for comparison.
  • a genetic trend analysis calculates a weighted average (weighted daughter number by sire) for sire genetic traits that are not calculated for the sub population offspring. Key traits are then averaged (weighted) by year of birth and trends for these sire based genetic values are referenced and benchmarked against the average and standard deviation values of all sires for that trait.
  • Examples 6 to 10 disclose exemplary SQL code for the execution of certain embodiments of the invention.
  • This code is the key analysis section of defining the paternal genetic merit levels against the whole population genetic and standard deviation values. This specifies the key criteria for analysis of each sire against the genotype picture of the maternal lines being analysed.
  • This code is the key analysis section of generating the cow's genotype picture by applying the reducing additive effect of the contribution of each sires genetic values in the maternal pedigree.
  • [ABV Survival] [Update Aust Type SD]I[ABV Survival]+(([Bull lnterpret]![ABV Survival]-[Update Aust Type SD]I[ABV Survival])/2)+(([Bull lnterpret_1 ]![ABV Survival]-[Update Aust Type SD]I[ABV Survival])/4)+(([Bull lnterpret_2]![ABV Survival]- [Update Aust Type SD]I[ABV Survival])/8), [Cow Pedigree Evaluation - Bull Interpret].
  • [ABV for Calving Ease] [Update Aust Type SD]I[ABV Calving Ease]+(([Bull Interpret] ![ABV for
  • [ABV Overall Type] [Update Aust Type SD]I[ABV Overall Type]+(([Bull Interpret] ![ABV Overall Type]-[Update Aust Type SD]I[ABV Overall Type])/2)+(([Bull lnterpret_1]![ABV Overall Type]-[Update Aust Type SD]I[ABV Overall Type])/4)+(([Bull lnterpret_2]![ABV Overall Type]-[Update Aust Type SD]I[ABV Overall Type])/8), [Cow Pedigree Evaluation - Bull Interpret].
  • [ABV Chest Width] [Update Aust Type SD]I[ABV Chest Width]+(([Bull Interpret] ![ABV Chest Width]-[Update Aust Type SD]I[ABV Chest Width])/2)+(([Bull lnterpret_1 ]![ABV Chest Width]-[Update Aust Type SD]I[ABV Chest Width])/4)+(([Bull lnterpret_2]![ABV Chest Width]-[Update Aust Type SD]I[ABV Chest Width])/8), [Cow Pedigree Evaluation - Bull Interpret].
  • [ABV Rear Set of Leg] [Update Aust Type SD]I[ABV Rear Set of Leg]+(([Bull Interpret] ![ABV Rear Set of Leg]-[Update Aust Type SD]I[ABV Rear Set of Leg])/2)+(([Bull lnterpret_1 ]![ABV Rear Set of Leg]-[Update Aust Type SD]I[ABV Rear Set of Leg])/4)+(([Bull lnterpret_2]![ABV Rear Set of Leg]-[Update Aust Type SD]I[ABV Rear Set of Leg])/8), [Cow Pedigree Evaluation - Bull Interpret].
  • [ABV Rear Leg Rear View] [Update Aust Type SD]I[ABV Rear Set Rear View]+(([Bull Interpret] ![ABV Rear Set Rear View]-[Update Aust Type SD]I[ABV Rear Set Rear View])/2)+(([Bull lnterpret_1 ]![ABV Rear Set Rear View]-[Update Aust Type SD]I[ABV Rear Set Rear View])/4)+(([Bull lnterpret_2]![ABV Rear Set Rear View]-[Update Aust Type SD]I[ABV Rear Set Rear View])/8), [Cow Pedigree Evaluation - Bull Interpret].
  • [ABV Fore Attachment] [Update Aust Type SD]I[ABV Fore Attachment]+(([Bull lnterpret]![ABV Fore Attachment]-[Update Aust Type SD]I[ABV Fore Attachment])/2)+(([Bull lnterpret_1 ]![ABV Fore Attachment]-[Update Aust Type SD]I[ABV Fore Attachment])/4)+(([Bull lnterpret_2]![ABV Fore Attachment]-[Update Aust Type SD]I[ABV Fore Attachment])/8), [Cow Pedigree Evaluation - Bull Interpret].
  • [AB V Rear Attachment Height] [Update Aust Type SD]I[ABV Rear Attachment Height]+(([Bull Interpret] ![ABV Rear Attachment Height]-[Update Aust Type SD]I[ABV Rear Attachment Height])/2)+(([Bull lnterpret_1 ]![ABV Rear Attachment Height]-[Update Aust Type SD]I[ABV Rear Attachment Height])/4)+(([Bull lnterpret_2]![ABV Rear Attachment Height]-[Update Aust Type SD]I[ABV Rear Attachment Height])/8), [Cow Pedigree Evaluation - Bull Interpret].
  • [ABV Rear Attachment Width] [Update Aust Type SD]I[ABV Rear Attachment Width]+(([Bull Interpret] ![ABV Rear Attachment Width]-[Update Aust Type SD]I[ABV Rear Attachment Width])/2)+(([Bull lnterpret_1 ]![ABV Rear Attachment Width]-[Update Aust Type SD]I[ABV Rear Attachment Width])/4)+(([Bull lnterpret_2]![ABV Rear Attachment Width]-[Update Aust Type SD]I[ABV Rear Attachment Width])/8), [Cow Pedigree Evaluation - Bull Interpret].
  • [ABV Centre Ligament] [Update Aust Type SD]I[ABV Centre Ligament]+(([Bull Interpret] ![ABV Centre Ligament]-[Update Aust Type SD]I[ABV Centre Ligament])/2)+(([Bull lnterpret_1 ]![ABV Centre Ligament]-[Update Aust Type SD]I[ABV Centre Ligament])/4)+(([Bull lnterpret_2]![ABV Centre Ligament]-[Update Aust Type SD]I[ABV Centre Ligament])/8), [Cow Pedigree Evaluation - Bull Interpret].
  • [AB V Loin Strength] [Update Aust Type SD]I[ABV Loin Strength]+(([Bull lnterpret]![ABV Loin Strength]-[Update Aust Type SD]I[ABV Loin Strength])/2)+(([Bull lnterpret_1]![ABV Loin Strength]-[Update Aust Type SD]I[ABV Loin Strength])/4)+(([Bull lnterpret_2]![ABV Loin Strength]-[Update Aust Type SD]I[ABV Loin Strength])/8)
  • This code is the key analysis section of excluding potential sires from a cow genotype that exhibits identified genotype traits that require protection.
  • This code is the key analysis section of defining each individual candidates difference to prediction between the animals predicted genotype versus actual genetic value.
  • Termination AS [Dam Termination], [ABVCow Pedigree Input]. APRPredicted, [ABVCow Pedigree lnput].ASIPredicted, [Excel Abv].ASI, [Excel Abv]![ASI]-[ABVCow Pedigree lnput]![ASIPredicted] AS Difference, [Bull Interpret]. [Secondary ID], [Bull Interpret]. Name, [Bull Interpret]. [Breed Code] AS [Sire Breed], [Bull I nterpreM]. [Secondary ID], [Bull lnterpret_1 ].Name, [Bull Interpret ⁇ ].
  • This code is the key analysis section of defining each maternal pedigree and identifying their difference to prediction status
  • PreparationABV5eSearch2. [Cow ID], LactationPILast.LastOfPI AS Pl, PreparationABV5eSearch2. [Positive Family], PreparationABV5eSearch2. [Breed Code], PreparationABV5eSearch2.BirthYear, PreparationABV5eSearch2.[Last Calving Year], PreparationABV5eSearch2.APRPredicted, PreparationABV5eSearch2.ASIPredicted, PreparationABV5eSearch2.ASI, PreparationABV5eSearch2.[Cow ASI Diff], PreparationABV5eSearch2.[Dam ASI Diff], PreparationABV5eSearch2.[GDam ASI Diff], PreparationABV5eSearch2.[GGDam ASI Diff], PreparationABV5eSearch2.[GGGDam ASI Diff], PreparationABV5eSearch2.[GGGDam ASI Diff], PreparationABV5eSearch2.[GG
  • This code is one genetic analysis component (which represents the same methodology for all benchmark trait and performance analysis) that groups the animal groups into comparative analysis sub sets for comparison
  • Lactation Protein aEHMPDProductionAgeFactor.factM, aEHMPDProductionAgeFactor.factF, aEHMPDProductionAgeFactor.factP, [aEHMPDQuartileProgressb] ![LactationMilk] * [aEHMPDProductionAgeFactor]![factM] AS FactorAgelactationMilk, [aEHMPDQuartileProgressb]![LactationFat] * [aEHMPDProductionAgeFactor]![factF] AS FactorAgelactationFat,
  • [Cow ID] aEHMPDQuartilePrep2FFABV.[Cow lD]) WHERE (((aEHMPDQuartileProgressb.LactationDaysCalvingDatetoLactTermDate)>249) AND ((aEHMPDQuartileProgressb.[Excel Abv_ASI]) Is Not Null) AND ((aEHMPDQuartileProgressb.[Secondary ID]) Is Not Null) AND ((aEHMPDQuartileProgressb.LactationMilk) Is Not Null)) ORDER BY aEHMPDQuartileProgressb.[Excel Abv_ASI] DESC , aEHMPDQuartileProgressb.CalvingDate DESC;
  • This code is the key analysis section of defining each individual candidate that has been terminated from the analysis group and examining their genetic merit, pedigree and production levels for comparison against lifetime survival days and lifetime contribution to production and profitability.
  • [Secondary ID] AS MGSireSec, [Bull InterpreM ]. Name AS MGSireName, [Bull InterpreM ].ASI AS MGSireASI, [Bull InterpreM]. AP R AS MGSireAPR, [Bull InterpreM].
  • [AB V Overall Type] AS [MGSireABV Overall Type], [Bull InterpreM].
  • [AB V Mammary System] AS [MGSireABV Mammary System], [Bull InterpreM ].
  • ABVSomaticCell AS MGSireSCC, [Bull InterpreM ].
  • ABVFertility AS MGSireFertility, [Bull InterpreM ].
  • [ABV Survival] AS MGSireSurvivallndex, [Bull InterpreM ].
  • This code is one survival analysis component (which represents the same methodology for all survival trait and performance analysis) that groups the animal groups into comparative analysis sub sets for survival comparison.
  • SPABVSomaticCell SPABVFertility, SPSurvivallndex, LactationMilk, LactationFat, LactationProtein, LactationASI, PIMiIk, PIFat, PIProtein, Pl, PIAnalysis, [aEHMPDSurvivalb8dLifetime_Cow ID], SumOfLactationMilk, SumOf Lactation Fat, SumOfLactationProtein, [CountOfCow ID] ) SELECT aEHMPDSurvivalb8eAnalysis.[Cow No], aEHMPDSurvivalb8eAnalysis.[aEHMPDSurvivalb8c2yo_Cow ID], aEHMPDSurvivalb ⁇ eAnalysis.
  • aEHMPDSurvivalb ⁇ eAnalysis.DateOfBirth aEHMPDSurvivalb ⁇ eAnalysis.CalvingDate, aEHMPDSurvivalb ⁇ eAnalysis. LactTermDate, aEHMPDSurvivalb ⁇ eAnalysis. birthYear, aEHMPDSurvivalb ⁇ eAnalysis. TerminationYear, aEHMPDSurvivalb ⁇ eAnalysis.TerminationDate, aEHMPDSurvivalb ⁇ eAnalysis.[Calving Year], aEHMPDSurvivalb ⁇ eAnalysis.
  • MGSireSec aEHMPDSurvivalb ⁇ eAnalysis.
  • MGSireName aEHMPDSurvivalb ⁇ eAnalysis.
  • MGSireASI aEHMPDSurvivalb ⁇ eAnalysis.
  • MGSireAPR aEHMPDSurvivalb ⁇ eAnalysis.
  • MGSireABV Overall Type aEHMPDSurvivalb ⁇ eAnalysis.
  • MGSireABV Mammary System aEHMPDSurvivalb ⁇ eAnalysis.
  • MGSireSCC aEHMPDSurvivalb ⁇ eAnalysis.
  • MGSireFertility aEHMPDSurvivalb ⁇ eAnalysis.
  • MGSireSurvivallndex aEHMPDSurvivalb ⁇ eAnalysis.
  • [SPABV Overall Type] aEHMPDSurvivalb ⁇ eAnalysis.
  • [SPABV Mammary System] aEHMPDSurvivalb ⁇ eAnalysis.
  • SPABVSomaticCell aEHMPDSurvivalb ⁇ eAnalysis.
  • LactationFat (0.04 ⁇ * [aEHMPDSurvivalb ⁇ eAnalysis]![l_actationMilk])
  • AS LactationASI aEHMPDSurvivalb ⁇ eAnalysis.
  • PIMiIk aEHMPDSurvivalb ⁇ eAnalysis.
  • PIFat aEHMPDSurvivalb ⁇ eAnalysis.
  • PIProtein aEHMPDSurvivalb ⁇ eAnalysis.
  • Pl aEHMPDSurvivalb ⁇ eAnalysis.
  • PIAnalysis aEHMPDSurvivalb ⁇ eAnalysis.
  • This code is the key analysis section of analysing sires used within a genetic group and to trace the genotype progress for each trait by year of birth
  • This code is the key analysis section of analysing offspring of genetic groups defining each groups differences to dams, the average of the difference and the standard deviation levels that define the groups into their variation/consistency status.
  • This code is the key analysis section of analysing offspring of genetic groups defining each groups phenotype average and standard deviation levels that define the groups into their variation/consistency status.
  • Avg(LTEImport.OT) AS AvgOfOT, Avg(LTEImport.Mam) AS AvgOfMam, StDev(LTEImport.OT) AS StDevOfOT, StDev(LTEImport.Mam) AS StDevOfMam

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Abstract

La présente invention porte sur des procédés pour identifier des animaux qui conviennent ou non à l'élevage. Les procédés sont effectués sur la base, au moins en partie, d'une considération d'une caractéristique présentée chez un ancêtre maternel de l'animal examiné. Par conséquent, selon un aspect, la présente invention porte sur un procédé pour évaluer la valeur génétique d'un animal d'élevage candidat (typiquement un animal femelle), le procédé consistant : à obtenir des informations concernant une caractéristique d'au moins un ancêtre maternel de l'animal d'élevage candidat, et à analyser les informations de la caractéristique afin de fournir la probabilité selon laquelle la caractéristique se retrouvera dans la descendance de l'animal d'élevage candidat.
PCT/AU2009/001651 2008-12-19 2009-12-18 Procédé pour identifier un animal convenant à l'élevage Ceased WO2010068999A1 (fr)

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WO2016077693A1 (fr) * 2014-11-14 2016-05-19 Genus Plc Bovins laitiers hybrides et systèmes permettant de maximiser l'avantage hybride
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CN113678767A (zh) * 2021-08-10 2021-11-23 中国水产科学研究院黄海水产研究所 一种对虾抗病性状的选育方法
CN113678767B (zh) * 2021-08-10 2022-08-23 中国水产科学研究院黄海水产研究所 一种对虾抗病性状的选育方法
CN114304057A (zh) * 2021-12-23 2022-04-12 深圳市金新农科技股份有限公司 一种针对体尺性状的分子选育方法及其应用
CN114793964A (zh) * 2022-03-07 2022-07-29 江苏中水东泽农业发展股份有限公司 一种红螯螯虾的离体孵化系统和方法
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CN117502372A (zh) * 2023-12-06 2024-02-06 北京沃德辰龙生物科技股份有限公司 基于父系和母系饲料转化效率的肉种鸡选育方法

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