Whole-genome Analysis of a Quarter Horse Mare

In this study we identified genetic variants, including single nucleotide polymorphisms (SNPs), insertion/deletion polymorphisms (INDELs), and copy number variants (CNVs) in the genome of an individual Quarter Horse mare using next-generation sequencing.  Massively parallel paired-end sequencing was used to generate an average of 24.7X coverage of the horse’s genome. Reads were mapped to approximately 97% of the reference Thoroughbred genome and then examined for SNPs, INDELS, and CNVs.  Identified genetic variants were annotated to determine their impact on gene structure and function.  Additionally, the Quarter Horse was genotyped for mutations of known diseases and for variants associated with particular traits.  Functional clustering analysis of genetic variants revealed that most of the genetic variation in the horse’s genome was enriched in sensory perception, signal transduction, and immunity and defense pathways. Collectively, this is the first sequencing of a horse genome by next-generation sequencing and the first genomic sequence of an individual Quarter Horse mare. Our data show extensive genetic variation between the Quarter Horse and reference Thoroughbred genomes and uncover genetic variants potentially underlying traits distinguishing the two breeds.