Whole Genome Re-Sequencing of Individual Horses and Analyses of Genetic and Structural Variation

Whole genome re-sequencing was performed for twelve horses to mean depths of 15-35x. A broad spectrum of diverse breeds was included like highly selected horse breeds and non-breed horses. Quality of sequence data was determined via estimating the false-negative and false-positive rates based on equine SNP50 genotypings. Sequence reads, together with publicly available equine HiSeq-Illumina WGS data, were used to call SNPs and small insertion/deletions as well as structural variants. Structural variants were called using the genome modeling tool Pindel. Detection of ROHs (runs of homozygosity) was done in a sliding window approach for 50 and 500 consectutive homozygous SNPs. For all ROHs, genetic and structural variants detected their functional significance was tested using gene models of EquCab2.0. In addition, these variants were searched for evolutionary conserved elements and ENCODE tracks. In total, an average number of 3492 ROHs were detected in windows of a minimum of 50 consecutive homozygous SNPs and an average number of 292 ROHs in windows of 500 consecutive homozygous SNPs. In non-breed horses, 166 variants with predicted high or moderate effects within 50-SNP-ROHs and 5 variants within 500-SNP-ROHs could be filtered out. Breed horses harbored no variants with high or moderate effects in their private ROHs. Comparative analysis of homozygous stretches common in all horses displayed three ROHs which were all located in the region of KITLG, the ligand of KIT known to be involved in melanogenesis, haematopoiesis and gametogenesis.