SNPs for Parentage Testing and Traceability in Globally Diverse Breeds of Sheep

DNA-based parentage determination accelerates genetic improvement by increasing pedigree accuracy.  However, the utility of any “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 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. 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.