Selective Sweeps in Non-Breed Horses Versus Specialised Horse Breeds Using Next Generation Sequencing

The process of domestication has shaped the modern horse population and lead to an immense group of different types of breeds. In this study whole genome sequencing of ten horses of four different populations was performed, representing the high diversity of highly specialised sport horses and non-breed horse populations including Sorraia and Dulmener. Dulmener are the least non-breed horses conserved in a free-range area in Germany. The results show that the process of domestication as well as further artificial selection for specific breeding aims has shaped the development of specific biological processes in horse breeds. Whole genome sequencing was performed using an Illumina HiSeq2000. Trimmed reads were aligned to the reference horse genome EquCab2.70. On the whole, 77-81% of all mapped reads were uniquely mapping, 8-9% were multiply mapping, while 6-8% of the reads stayed unmapped. Mean coverage was about 11X-14X for samples run on one lane. Variant detection revealed >10 mio SNPs and >1 mio insertion/deletions in total. We investigated the variants for their function and distribution among non-breed and breed horses. Breed horses showed an enrichment of genes in coding regions involved in a number of important physiological processes like lipid metabolic, neurological system and muscle processes as well as a significant larger number of selective sweeps. The largest number of private polymorphisms was found in Dulmener, followed by Sorraia. In conclusion, the non-breed Dulmener and Sorraia horses are valuable resources for further insights into horse domestication.