Genomic Polymorphism in Six Diverse Horse Breeds

To better understand the biological impact of genetic variation we need to quantify the diversity of polymorphism, both in sequence and structure. Currently, the archive of genetic variation in the horse is primarily based on the single Thoroughbred mare used to generate the reference sequence (EquCab2.0) and doesn’t describe many structural variants. Therefore, to enrich that archive, we used Illumina paired-end technology to re-sequence six horse genomes from diverse breeds (Arabian, Percheron, American Miniature, Brazilian Mangalargo Marchadore, a native Mongolian and a Tennessee walking horse). Sequence reads were aligned with BWA and the Genome Analysis Tool Kit (GATK) HaplotypeCaller module was used to call Single Nucleotide Polymorphisms (SNPs) and insertion/deletion (INDELs) polymorphisms. We used ControlFreec to obtain copy number variations and SVDetect to detect large structural variants on each genome. The functional impact of these variants was predicted using ENSEMBL gene models and the SNPeff program. The average depth of coverage of the aligned reads ranged from 10.03 for the Miniature horse to 16.78 for the Tennessee Walking horse. In total, we discovered 8,128,658 SNPs and 834,748 INDELs in the six genomes. Relative to the chromosome size, the highest proportion of SNPs was in chromosome 12 (0.5 %) followed by chromosome 20 (0.4%), two chromosomes bearing highly complex regions important for immunity.  We detected a considerable genetic variation within the six horses, some of which affected entire genes or exons. Understanding this variation facilitates a better understanding of the genetic architecture and its impact on the adaptation.