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

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 166 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 74 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 1.1×10(−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.

Penalized classification for optimal statistical selection of markers from high-throughput genotyping: application in sheep breeds

“…For example, Allen et al (2010) in a study on Irish cattle, reported a set of 43 SNPs for breed identification on the basis of allele frequency. Heaton et al (2014) identified 163 SNPs for use in parentage testing and traceability in sheep, using the minor allele frequency (>0.3). In Mastrangelo et al (2014), a subset of 119 SNPs was tested to evaluate their ability to assign individuals to the same groups that have been used in the present study.…”

Selection of discriminant SNP markers for breed and geographic assignment of Italian sheep

“…However, the development of high throughput SNP platforms for livestock genomes has opened new perspectives for breed traceability. The BovineSNP50 and the OvineSNP50 BeadChip (Illumina, Inc., San Diego, CA), for example, have been widely used for investigating population genetic structures (Gautier et al, 2009), testing parentage (Heaton et al, 2014), studying selection signatures (Pintus et al, 2014;Kijas et al, 2012), and for calculating genomic breeding values . As a result, several thousands of animals of different breeds have been genotyped in many countries.…”

The power of 28 microsatellite markers for parentage testing in sheep

“…However, it has been reported that DNA fingerprinting using MST markers could be cost effective for Australian Merino breeders if full pedigrees had been used in estimating EBVs by the BLUP procedure [3]. In addition, a review on recently common use of MST marker and SNP marker panels show affordability by researchers and farmers with future breeding perspectives [24,25,27,28,29]. However, SNPs, in terms of genetic information, are biallelic markers considered as a step backwards.…”

“…A typical microsatellite parentage test can be affordable for USD 25-35 per sheep. SNP of 100 markers tests, on the other hand, can be purchased for USD 15-20. Recently, for many reasons, SNPs have become the focus of efforts to improve sheep parentage testing [29]. However, SNP genotyping technologies are not available and affordable in each country and for each farmer.…”