SNPs for parentage testing and traceability in globally diverse breeds of sheep

Authors: Heaton, Michael - Mike; Leymaster, Kreg; KALBFLEISCH, THEODORE - University Of Louisville; KIJAS, JAMES - Commonwealth Scientific And Industrial Research Organisation (CSIRO); CLARKE, SHANNON - Agresearch; MCEWAN, JOHN - Agresearch; MADDOX, JILLIAN - Meat And Livestock Australia; BASNAYAKE, VERONICA - Geneseek Inc, A Neogen Company; PETRIK, DUSTIN - Geneseek Inc, A Neogen Company; SIMPSON, BARRY - Geneseek Inc, A Neogen Company; Smith, Timothy - Tim; Chitko-Mckown, Carol

Submitted to: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/19/2014
Publication Date: 4/16/2014
Citation: Heaton, M.P., Leymaster, K.A., Kalbfleisch, T.S., Kijas, J.W., Clarke, S.M., McEwan, J., Maddox, J.F., Basnayake, V., Petrik, D.T., Simpson, B., Smith, T.P., Chitko-McKown, C.G. 2014. SNPs for parentage testing and traceability in globally diverse breeds of sheep. PLoS One. 9(4):e94851. DOI: 10.1371/JOURNAL.PONE.0094851.

Interpretive Summary: In large sheep flocks, multiple rams are often used together as a team to increase mating efficiency. However, this hinders paternity assignment and represents a barrier for using genetic evaluation systems. Moreover, female traits cannot be directly measured in males, and thus, the accuracy of ram breeding values is diminished by errors in assigning his female offspring. Although parentage can be accurately determined with single nucleotide polymorphisms (SNPs), the utility of a particular “parentage SNP” varies greatly among breeds. Our aims were to identify parentage SNPs with exceptional qualities for use in globally diverse breeds and then to develop a subset for use in North American sheep. One hundred and sixty-three parentage SNPs derived from the International Sheep Genomics Consortium were identified for widespread use in 74 breeds from 32 countries and/or islands. One subset of 109 parentage SNPs was developed for use in North American sheep and successfully tested in a US Department of Agriculture research flock. The same markers also provide unique molecular identifiers for tracing sheep products to their points of origin. Because these parentage SNPs were selected from a globally diverse collection of many breeds, they will likely be useful in breeds around the world. The 163 parentage SNPs reported here facilitate the commercial development of high-throughput technologies for implementing economical parentage testing and improving pedigree estimates. With more accurate pedigrees, producers can make faster genetic progress and raise more, healthy sheep on less land with less labor.

Technical Abstract: DNA-based parentage determination accelerates genetic improvement in sheep by increasing pedigree accuracy. Single nucleotide polymorphism (SNP) markers can be used for determining parentage and to provide unique molecular identifiers for tracing sheep products to their source. However, the utility of a particular “parentage SNP” varies by breed depending on its minor allele frequency (MAF) and its sequence context. Our aims were to identify parentage SNPs with exceptional qualities for use in globally diverse breeds and to develop a subset for use in North American sheep. Starting with genotypes from 2,915 sheep and 74 breed groups provided by the International Sheep Genomics Consortium (ISGC), we analyzed 47,693 autosomal SNPs by multiple criteria and selected 163 with desirable properties for parentage testing. On average, each of the 163 SNPs was highly informative (MAF = 0.3) in 48 ± 5 breed groups. Nearby polymorphisms that could otherwise confound genetic testing were identified by whole genome and Sanger sequencing of sheep from 54 breed groups. A genetic test with 109 of the 163 parentage SNPs was developed for matrix-assisted laser desorption/ionization—time-of-flight mass spectrometry. The scoring rates and accuracies for these 109 SNPs were greater than 99% in a panel of North American sheep. In a blinded set of 96 families (sire, dam, and non-identical twin lambs), each parent of every lamb was identified without using the other parent’s genotype. In ISGC breed groups, the median estimates for probability of a coincidental match between two animals (PI), and the fraction of potential adults excluded from parentage (PE) were 1.1 x 10( 39) and 0.999987, respectively, for the 109 SNPs combined. The availability of a well-characterized set of 163 parentage SNPs facilitates the development of high-throughput genetic technologies for implementing accurate and economical parentage testing and traceability in many of the world’s sheep breeds.