WO2004072227A2 - Animal testing procedure - Google Patents
Animal testing procedure Download PDFInfo
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- WO2004072227A2 WO2004072227A2 PCT/NZ2004/000028 NZ2004000028W WO2004072227A2 WO 2004072227 A2 WO2004072227 A2 WO 2004072227A2 NZ 2004000028 W NZ2004000028 W NZ 2004000028W WO 2004072227 A2 WO2004072227 A2 WO 2004072227A2
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- progeny
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- breeding
- pedigree
- genetic markers
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- 241001465754 Metazoa Species 0.000 title claims abstract description 61
- 238000012956 testing procedure Methods 0.000 title description 3
- 238000000034 method Methods 0.000 claims abstract description 99
- 230000002068 genetic effect Effects 0.000 claims abstract description 71
- 238000009395 breeding Methods 0.000 claims abstract description 70
- 230000001488 breeding effect Effects 0.000 claims abstract description 70
- 238000003205 genotyping method Methods 0.000 claims abstract description 15
- 239000003550 marker Substances 0.000 claims description 18
- 238000004458 analytical method Methods 0.000 claims description 17
- 241001494479 Pecora Species 0.000 claims description 12
- 239000011159 matrix material Substances 0.000 claims description 9
- 238000005070 sampling Methods 0.000 claims description 9
- 230000000996 additive effect Effects 0.000 claims description 4
- 230000007717 exclusion Effects 0.000 claims description 4
- 239000000654 additive Substances 0.000 claims description 3
- 239000003181 biological factor Substances 0.000 claims description 2
- 108090000623 proteins and genes Proteins 0.000 claims description 2
- 108020004414 DNA Proteins 0.000 description 36
- 230000000384 rearing effect Effects 0.000 description 21
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- 238000012935 Averaging Methods 0.000 description 2
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- 238000009310 extensive farming Methods 0.000 description 2
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- 235000019688 fish Nutrition 0.000 description 2
- 238000012248 genetic selection Methods 0.000 description 2
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Classifications
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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
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- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
- C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
- C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
- C12Q1/6879—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for sex determination
-
- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q2600/00—Oligonucleotides characterized by their use
- C12Q2600/156—Polymorphic or mutational markers
Definitions
- This invention relates to an animal testing procedure. Specifically, this invention relates to a method of determining the genetic value of an animal during animal breeding.
- Species that are under some form of artificial genetic selection provide the majority of the world's food and natural fibres, companion animals and racing animals.
- single sire matings risk low pregnancy rates if the ram is not active or is infertile, while such extensive recording often causes stress to ewe flocks during lambing which may increase miss-mothering and lamb loss.
- DNA testing has been widely used in the breeding of high value animals such as horses to monitor the accuracy of pedigree records.
- Such parentage matching is typically very reliable and effective when there is a mother and progeny with two or more potential sires.
- the exclusion method tries to exclude all possibilities but the correct one, by excluding relationships with incompatible genotypes.
- a common way to cope with genotyping errors is to allow a discrepancy at one marker. This means that there must be at least two discrepant markers to exclude possible parents (as it is unlikely that two of the genotypes in the comparison will be in error).
- a small set of markers it is difficult to exclude all incorrect relationships, and if there need to be two out of a small number of markers showing an inconsistency this will exacerbate the problem.
- this method is used to determine the parentage of progeny produced in large scale animal breeding.
- breeding value should be taken to mean a measure of the genetic merit of an individual according to the mean of its progeny (and adjusted for the contributions of the other parent(s), for the trait or combination of traits of interest.
- breeding values may be determined for both parents and/or progeny.
- One or more breeding values may also be calculated for each individual, depending on the trait(s) of interest.
- Identification of possible parents preferably involves the accurate recording of the mating mob (groups of sires and mothers wh ch have the opportunity to mate) and the parturition mob (groups of mothers in def ned areas and the animals which are potentially their offspring). Such recordal s standard practice in conventional pedigree recording.
- Possible parents may also be identified by some form of objective measurement of specific traits or through other farm management practices.
- genetictyping should be taken to mean the analysis of the distribution of a number of polymorphic genetic markers.
- markers are analysed simultaneously using standard molecular biology techniques known in the art, such as multiplex or parallel analysis systems.
- DNA markers Such markers will herein be referred to as DNA markers, though this should not be seen as limiting.
- selected markers should be taken to mean a set of markers which together enable a cost-effective solution to parentage testing and genetic evaluation using the methods proposed here. Using current technology this would normally constitute four to ten microsatellite markers chosen to be highly polymorphic and able to be multiplexed (i.e. analysed together), but the proposed technology will make use of any marker information no matter how good or poor that information is.
- markers with lower probability of pedigree exclusion e.g. SNP markers
- SNP markers pedigree exclusion markers
- the key feature of the selected markers is that less markers are used than one would reasonably expect from simulation or know from experience to provide a perfect solution to parentage problem. Ideally between 50 and 90% of progeny would be matched to a single parent with high probability while the remainder would have multiple possible parents.
- the use of a selected number of DNA markers to generate DNA profiles does not enable the identification of the parents of all progeny. Instead, the partial parentage information provided by selected DNA marker information can be used to calculate the statistical probability for each possible parentage.
- the identification of possible parents creates a database of likely parents for each offspring. Having a finite number of potential parents then allows the statistical probabilities of each being the true parents to be calculated.
- the set of possibilities are more likely to contain relatives of the true parents than unrelated animals. In some cases incorrectly allowing these as possible parents may still be better than not assigning parents to a progeny.
- the parentage probabilities are then preferably used to calculate breeding values for each progeny, taking into account available biological information such as mating and lambing dates, pregnancy scanning data, specific trait records and so forth to modify the likelihood for each possible parentage.
- breeding values can be calculated by a number of techniques that involve either by taking into account all possible pedigree combinations weight/referenced by their probability and doing one analysis or by sampling possible pedigree combinations based on their probability and running multiple breeding value analyses and averaging the results.
- DNA testing has been widely used in the breeding of high value animals such as horses to monitor the accuracy of pedigree records.
- DNA parentage matching is very reliable and effective when matching a mother and progeny with two possible sires.
- the present invention utilises a set of DNA markers that do not identify the pedigree of all offspring. In comparison, the number of DNA markers used will only offer partial solutions to the pedigree of the offspring. While initially counter- intuitive, this offers a cost effective option to determining pedigrees in large-scale animal breeding using current DNA marker technology.
- the optimal number of markers for a given situation will vary with the number of animals involved and the accuracy with which breeding value are required.
- the breeding values data provided by the partial parentage solution of the present invention provides similar genetic progress to that achieved using traditional pedigree recording, but with greatly relaxed management constraints and half or less than half the number of DNA markers required for a near complete pedigree solution.
- the process makes genetic progress using DNA pedigrees feasible and cost effective even in large-scale farmed species such as sheep.
- the present invention also unexpectedly provides additional benefits that arise from the technology, including robustness to error rates in genotyping data, in addition to options for incorporating marked Quantitative Trait Loci (QTL) in the breeding DNA profile and breeding analysis.
- QTL marked Quantitative Trait Loci
- the marker information can be used in conjunction with knowledge of the characteristics of the QTL and of its status in the parents to undertake marker or gene assisted selection of progeny with only partially determined parentage, allowing the selection for favourable gene variants.
- the estimated breeding value for each offspring can be calculated.
- the present invention will provide a better solution, or at least a cost and labour effective alternative to traditional pedigree recording or to applications of DNA technology which aim to identify the exact parents of offspring in a breeding situation.
- the present invention is directed to determining a breeding value of progeny in large scale breeding situations.
- the invention is based upon the inventors investigations into the ability to use a selected number of DNA markers in conjunction with currently relaxed management restraints to achieve similar results to that achieved using traditional pedigree recordal or full DNA profiling.
- This example details a simulation model that has been developed to demonstrate how partial pedigree information can be used for the calculation of breeding values.
- the simulation used parameters that are typical for a prolific sheep breeding operation, and using DNA markers typical of those that could be used cost- effectively for this situation. Breeding values were calculated using an inverse additive relationship matrix incorporating the parental uncertainty in the genetic evaluation. Simulation Methods.
- a pedigree is simulated comprising three generations. This allowed some genetic similarities between the parents, as would normally be the case in practice.
- ⁇ Paternal line included 5 grand-sires and 20 grand-mothers.
- ° Maternal line included 10 grand-sires and 120 grand-mothers.
- the number of progeny produced from each mating was based on a distribution of 0.15, 0.45, 0.35, 0.04 and 0.01 for 1-5 lambs respectively.
- Generation III progeny o 10 animals were randomly selected for use as sires from the set of potential sires from generation II.
- the marker data was simulated for six markers, based on a set of markers currently being used by the applicants.
- the allele frequency data for these markers was calculated from a set of unrelated animals.
- Genotypes were assigned to generation I animals by randomly selecting alleles based on the allele frequency data.
- the likelihood of the data given a putative parentage is calculated relative to the likelihood of the data given no relationship.
- Genotype (g 0 ) Genotypes T(g P 1 g 0 ) P(9P)
- Genotype (g 0 ) Genotype or Or (8f or g m ) T(g m 1 g 0 ) P(9m)
- a probability is assigned to putative parentage in proportion to its likelihood, from the set of parentages which are more likely than a randomly chosen set of parents. o
- the rate of genotype errors was assumed to be 1 % when performing the likelihood calculations.
- Generation I animals were assigned genetic values for a trait with a known mean (40), residual standard deviation (8.4) and heritability (0.3). Genetic values determined for generation til and III animals using known pedigree relationships and quantitative genetics theory. Phenotypes for generation III animals were produced from their genetic values, a component that depended on their birth and rearing rank (see the following table), and a randomly sampled environmental component. Phenotypes were not modified according to sex.
- o BVs were estimated using ASREML (software that is able to produce estimated BVs by using a supplied inverse relationship matrix or by using a supplied pedigree) with known (generation III) phenotypic information.
- the model included fixed effects of sex and birth/rearing rank combination. o It was assumed that the litter size of each mother was known. In practice this may rely on pregnancy scanning information.
- TRUE True pedigrees
- Partial pedigrees - average relationship matrix method Pedigrees were assumed unknown and the relationship matrix was formed, using the partial pedigree probabilities, and inverted. birth ranks and rearing ranks were derived as the weighted (by the probabilities) means of the assigned mothers' litter sizes and rearing group sizes. Where a mother had a birth rank greater than 3 (5% of mothers had >3 progeny generated), the birth rank for this mother was set to 3. This reflects typical on-farm practice. Assigned rearing ranks were rounded to integer values, with a maximum of three, for the purposes of the genetic evaluation.
- Partial pedigrees - pedigree sampling method Pedigrees were assumed unknown. Sample sets of possible parentages according to their probabilities, analyse each sample, using standard genetic evaluation software, as if it contained true parentage information, and then average the estimated breeding values from each of these analyses. One hundred samples were used in this example.
- Each sampled parentage allows calculation of a birth rank (from collection and sampling of dead offspring if possible, or from litter size from pregnancy scan data), and a rearing rank. These data are of the types that are available with full parentage recording, and therefore can be handled by standard genetic evaluation software. Only birth rank and rearing rank calculations were included in the present example.
- BP Best pedigree
- Progeny that ranked below the dam's scanned litter size were downweighted - by a factor of 0.75 if the progeny had a check value of 0, and by 0.5 if it had a check value of 1.
- the new set of probabilities was then used to reassign parentage and the process iterated 15 times (which was found to be sufficient to ensure further reassignment was minimal).
- the FP method therefore, used a single pedigree for breeding value analysis, but one which gave family sizes that coincided more closely with prior expectations than the BP method.
- Simulation results are presented as the means (over replicates of the simulation) of the correlations between breeding values calculated using the true pedigree and by the other two methods (partial pedigrees or best pedigrees). Results are presented for three different groups of animals: sires, mothers and progeny. Each of these has substantially different amounts of information (number and type of close relatives with trait information) for estimating breeding values.
- FP Progeny 0.927 0.002 0.882 0.003 The table shows that the ARM and the PS methods are similar if birth and rearing ranks are known. Because ARM uses rounded average birth and rearing ranks, when these are estimated, it performs worse than the PS method (particularly for progeny). Further results are presented for PS in preference to ARM.
- the UQPS method gives similar results to the PS method. This indicates that the weighting scheme employed has not been successful in improving the results per breeding value analysis. While this does not preclude the existence of a method that uses prior family size information for improving the process, further results for the UQPS method are not shown here.
- the FP method performed slightly poorer than the BP method (even though it obtained a greater proportion of correct parentage assignments; not shown). Therefore further results are shown for BP in preference to FP, as an example of a 'single pedigree' method. Further results are shown only for the situation where birth and rearing rank is estimated.
- DNA markers Many factors may affect the amount of genetic progress achieved using DNA markers. These include; the number of DNA markers used, missing animals and genotypes from the dataset, and the heritability of the trait under test. In order to assess the impact of these factors on genetic progress, a number of simulation runs were performed. Results are presented as the degree of genetic progress achieved in progeny using DNA pedigrees compared to the true pedigree.
- the best pedigree method described here has made no use of measures of confidence (e.g. ratio of probability of the best to the second best pair of parents) in the parentage chosen. It could be possible to improve this simple method by excluding cases where there is another possible parentage with a similar probability.
- the example shows a method were prior information on family size distribution is used. This method did not appear to improve the procedure. There may be alternative weighting schemes, or alternative use of the weights (e.g. a weighted mean of breeding values), which would improve the procedure. In some situations there may be prior information on sire family sizes, or on conception date ranges for particular sires. The method could be extended to utilize such information.
- the inventors have developed a number of methods for estimating breeding values wherein the first three steps of the parentage procedure are identical, but differ in the manner in which the breeding values are calculated.
- sampling approaches detailed in methods 3 and 4 above arose due to computing limitations whereby flocks larger than 3000 could not currently be handled by the inverse matrix approach outlined in method 2.
- standard genetic evaluation software can be used, which can handle data sets of the size that are currently handled by such software.
- computing time may be is increased over method 2 by the need to evaluate many sets of sampled pedigrees, this computing requirement can be dispersed across many computers. Therefore, larger evaluations can be calculated in the same amount of time as the previous procedure.
- sampling methods 3 and 4 Another advantage of the sampling methods 3 and 4 is the ability to continue to use the system for the following year's cycle for the animals and for the next generation, without a need to increase to a larger computing capacity which is required by the method 2.
- the advantage being in the use of the standard software and the number of iterations to get the accuracy required commercially.
- Method 2 has the advantage that it is more useful and versatile for smaller herds of animals. With advances in computing it is anticipated that the inverse matrix approach could be used for flocks larger than 3000 and it is anticipated that alternative systems would likely make use of an inverse matrix approach.
- This example is as for example 1 , except that one of the parentage markers is, or is linked to a quantitative trait locus (QTL) and the association between marker and QTL alleles in the parent generation is known.
- QTL quantitative trait locus
- Two situations are investigated by extensions to the simulations described in example 1. The first is genotype assisted selection (GAS) where the marker confers knowledge of the QTL genotype, and the number of favourable QTL alleles is used as a covariate in the genetic analysis. Final genetic value is found by adding the estimated value of the covariate times the number of favourable QTL alleles to the estimated polygenic (non-QTL) breeding value.
- GAS genotype assisted selection
- MAS marker assisted selection
- the sire's QTL genotype and association with the linked marker genotype is assumed to be known.
- Parameters of the simulation were as described above (for example 1), with the addition of a QTL with an additive effect of one residual standard deviation (8.4), at a recombination fraction of 0.01 from the linked marker (relevant for MAS only).
- the relative (to knowing the true pedigree) genetic progress when selecting progeny was 99% for GAS, and 85% for MAS.
- GAS does not rely on parentage for determining the QTL genotype, and therefore progress in this component of the genetic value is the same regardless of pedigree assignment.
- MAS does rely on parentage (only the sire for this simulation) to provide information on the progeny QTL genotype, and therefore is more affected by the ability to assign parentage.
- the procedure may be applied to any species provided polymorphic genetic markers are available, and the set of possible parents can be determined and
- DNA-sampled DNA-sampled.
- the following table gives references, for a variety of animal species, for sets of markers that could possibly be used in this setting. In most cases the reference is to sets of markers that have been used to create linkage maps for that species.
- the breeding population parameters were chosen to be within the range suggested by Bentsen and Olesen (2002, Aquaculture 204:349-359), being 50 parent families with 50 progeny per family. Each grandparent cohort consisted of 30 families, having 20 progeny each. Each family had distinct parents, and for parentage assignment, it was assumed that the mating pairs were known. A panel of six markers were used, with frequencies taken from those estimated for the Stuart population of Chinook salmon from the study of Beacham et al. (2003, Fishery Bulletin 101 :243-259). The first six loci scored in this study were used. The trait was simulated to be unaffected by any fixed effects, although sex was fitted as a fixed effect in the genetic evaluation. The sampling system outlined in example 2 was used for genetic evaluation. For this example, 50 samples were used for averaging to obtain breeding values, and the process was replicated 10 times.
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Priority Applications (2)
Application Number | Priority Date | Filing Date | Title |
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AU2004212103A AU2004212103B2 (en) | 2003-02-14 | 2004-02-16 | Animal testing procedure |
GB0515484A GB2412435B (en) | 2003-02-14 | 2004-02-16 | Animal testing procedure |
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NZ524237 | 2003-02-14 | ||
NZ524237A NZ524237A (en) | 2003-02-14 | 2003-02-14 | Use of DNA markers to establish breeding values of individual animals and computer software therefor |
Publications (2)
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WO2004072227A2 true WO2004072227A2 (en) | 2004-08-26 |
WO2004072227A3 WO2004072227A3 (en) | 2004-09-16 |
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PCT/NZ2004/000028 WO2004072227A2 (en) | 2003-02-14 | 2004-02-16 | Animal testing procedure |
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AU (1) | AU2004212103B2 (en) |
GB (1) | GB2412435B (en) |
NZ (1) | NZ524237A (en) |
WO (1) | WO2004072227A2 (en) |
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US20050260603A1 (en) | 2002-12-31 | 2005-11-24 | Mmi Genomics, Inc. | Compositions for inferring bovine traits |
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NZ524237A (en) | 2005-10-28 |
AU2004212103B2 (en) | 2008-01-24 |
WO2004072227A3 (en) | 2004-09-16 |
GB2412435B (en) | 2007-02-14 |
GB0515484D0 (en) | 2005-08-31 |
AU2004212103A1 (en) | 2004-08-26 |
GB2412435A (en) | 2005-09-28 |
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