Equine Parentage Testing with SNPs and beyond: developing a platform independent panel

Abstract

Centuries of selective equine breeding have led to a remarkable diversity of horse breeds each with unique traits. To maintain these breeds, studbooks require parentage testing to guarantee lineage. To determine parentage, the industry assays length polymorphisms in short tandem repeats (STRs) established by the International Society of Animal Genetics (ISAG). However, STRs have significant limitations including challenges with accurately determining genotype, relatively low number of STRs assayed, and low throughput. For these reasons, most other animal breeds including cattle, dog, goats, and sheep use single nucleotide polymorphisms (SNPs) for parentage identification. To this end, the ISAG has introduced a panel of SNPs. Here, we further demonstrate the utility of equine SNP genotyping. Importantly, we show that a number of the ISAG SNPs are not compatible with widely-used, short-read, next generation sequencing (NGS) technologies. Fortunately, SNPs are abundant, and we propose an alternative panel that is platform independent and are all ISAG proposed SNPs. We demonstrate that SNP parentage genotyping is extremely robust and enables additional assays including breed identification and can be readily expanded to also assay equine genetic diseases.