Development of a SNP Panel For Parentage Assignment in Sheep

The construction of accurate pedigrees is important in a variety of animal production systems and research scenarios. For example, the ability to correctly assign the paternity of offspring derived from multi-sire mating is important to producers where lambs show variation in their economic merit at slaughter. The advantages of DNA based methods for parentage assignment have long been recognized, and this study aimed to develop a robust panel of SNP for use in sheep populations. We present a core panel containing more than 90 SNP distributed across the autosomes and male specific region of the Y chromosome. This core panel was selected from a much larger set of candidate markers by re-sequencing, inheritance checking within families, testing across genotyping platforms and obtaining breed specific allele frequency data. Minor allele frequency distributions and gene diversity estimates are presented for a diverse set of major breeds, indicating the panel is likely to have broad utility. Further, concordance analysis has been performed to examine assay reproducibility between platforms (eg Sequenom versus Illumina Infinium and Fluidigm versus Infinium). The genomic location and identifier for each SNP is given to promote the panel’s implementation. Development of a single core panel of SNP for use by the international community opens the way for a high volume and low unit cost genotyping test. It may also facilitate trace-back applications and a common dataset for use in bio-security and disease outbreak diagnosis.