Population structure and selective signature analysis of local sheep breeds in Xinjiang, China based on high-density SNP chip

Abstract The frigid and droughty climate of Xinjiang in China has given rise to unique indigenous sheep breeds with strong adaptability and resistance. In order to investigate the genetic mechanism of adaptability of Xinjiang sheep to local extreme environment, We conducted population genetic structure analysis for three native Xinjiang sheep breeds, Altay sheep (ALT), Bashbay Sheep (BSBC) and Duolang sheep (DLC), and two foreign sheep breeds, Suffolk and Dorset, using the Ovine Infinium HD SNP BeadChip(680K). The results indicate that Xinjiang sheep and foreign sheep have completely different genetic and evolutionary histories. Principal component analysis (PCA) and phylogenetic tree can distinguish the five sheep breeds based on their different geospatial positions, and the domestication level of Xinjiang sheep is lower than that of foreign sheep breeds. In addition, we obtained 459 genes in total by using two selection signal scanning methods, the fixation index (Fst) analysis and the cross-population extended haplotype homozygosity test (XP-EHH). Through enrichment analysis, candidate genes related to fat and energy metabolism (PID1, VEGFA, and PCBP2, et al.), reproduction (HDAC1, BMP5, and GDF9, et al.), as well as additional candidate genes pertaining to sheep's other environmental adaptability (ATF6, NFIB, and VIL1) have been discovered. This study provides a basis for the protection and utilization of local sheep germplasm resources in Xinjiang, and offers molecular data references for exploring the genetic mechanisms of sheep adaptation to extremely cold and arid environments.