Dataset Information

A high throughput single nucleotide polymorphism multiplex assay for parentage assignment in New Zealand sheep.

ABSTRACT: Accurate pedigree information is critical to animal breeding systems to ensure the highest rate of genetic gain and management of inbreeding. The abundance of available genomic data, together with development of high throughput genotyping platforms, means that single nucleotide polymorphisms (SNPs) are now the DNA marker of choice for genomic selection studies. Furthermore the superior qualities of SNPs compared to microsatellite markers allows for standardization between laboratories; a property that is crucial for developing an international set of markers for traceability studies. The objective of this study was to develop a high throughput SNP assay for use in the New Zealand sheep industry that gives accurate pedigree assignment and will allow a reduction in breeder input over lambing. This required two phases of development--firstly, a method of extracting quality DNA from ear-punch tissue performed in a high throughput cost efficient manner and secondly a SNP assay that has the ability to assign paternity to progeny resulting from mob mating. A likelihood based approach to infer paternity was used where sires with the highest LOD score (log of the ratio of the likelihood given parentage to likelihood given non-parentage) are assigned. An 84 "parentage SNP panel" was developed that assigned, on average, 99% of progeny to a sire in a problem where there were 3,000 progeny from 120 mob mated sires that included numerous half sib sires. In only 6% of those cases was there another sire with at least a 0.02 probability of paternity. Furthermore dam information (either recorded, or by genotyping possible dams) was absent, highlighting the SNP test's suitability for paternity testing. Utilization of this parentage SNP assay will allow implementation of progeny testing into large commercial farms where the improved accuracy of sire assignment and genetic evaluations will increase genetic gain in the sheep industry.

SUBMITTER: Clarke SM

PROVIDER: S-EPMC3989167 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

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A high throughput single nucleotide polymorphism multiplex assay for parentage assignment in New Zealand sheep.

Clarke Shannon M SM Henry Hannah M HM Dodds Ken G KG Jowett Timothy W D TW Manley Tim R TR Anderson Rayna M RM McEwan John C JC

PloS one 20140416 4

Accurate pedigree information is critical to animal breeding systems to ensure the highest rate of genetic gain and management of inbreeding. The abundance of available genomic data, together with development of high throughput genotyping platforms, means that single nucleotide polymorphisms (SNPs) are now the DNA marker of choice for genomic selection studies. Furthermore the superior qualities of SNPs compared to microsatellite markers allows for standardization between laboratories; a propert ...[more]

PMID: 24740141

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Project description:BACKGROUND:Parentage assignment is usually based on a limited number of unlinked, independent genomic markers (microsatellites, low-density single nucleotide polymorphisms (SNPs), etc.). Classical methods for parentage assignment are exclusion-based (i.e. based on loci that violate Mendelian inheritance) or likelihood-based, assuming independent inheritance of loci. For true parent-offspring relations, genotyping errors cause apparent violations of Mendelian inheritance. Thus, the maximum proportion of such violations must be determined, which is complicated by variable call- and genotype error rates among loci and individuals. Recently, genotyping using high-density SNP chips has become available at lower cost and is increasingly used in genetics research and breeding programs. However, dense SNPs are not independently inherited, violating the assumptions of the likelihood-based methods. Hence, parentage assignment usually assumes a maximum proportion of exclusions, or applies likelihood-based methods on a smaller subset of independent markers. Our aim was to develop a fast and accurate trio parentage assignment method for dense SNP data without prior genotyping error- or call rate knowledge among loci and individuals. This genomic relationship likelihood (GRL) method infers parentage by using genomic relationships, which are typically used in genomic prediction models. RESULTS:Using 50 simulated datasets with 53,427 to 55,517 SNPs, genotyping error rates of 1-3% and call rates of?~?80 to 98%, GRL was found to be fast and highly (~?99%) accurate for parentage assignment. An iterative approach was developed for training using the evaluation data, giving similar accuracy. For comparison, we used the Colony2 software that assigns parentage and sibship simultaneously to increase the power of the likelihood-based method and found that it has considerably lower accuracy than GRL. We also compared GRL with an exclusion-based method in which one of the parameters was estimated using GRL assignments.This method was slightly more accurate than GRL. CONCLUSIONS:We show that GRL is a fast and accurate method of parentage assignment that can use dense, non-independent SNPs, with variable call rates and unknown genotyping error rates. By offering an alternative way of assigning parents, GRL is also suitable for estimating the expected proportion of inconsistent parent-offspring genotypes for exclusion-based models.

Dataset Information

A high throughput single nucleotide polymorphism multiplex assay for parentage assignment in New Zealand sheep.

Publications

A high throughput single nucleotide polymorphism multiplex assay for parentage assignment in New Zealand sheep.

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