Population structure and signatures of selection in Horpa sheep

Abstract Horpa sheep, an indigenous sheep breed native to the high-altitude regions of the Xizang Autonomous Region in China, are characterized by distinctive adaptive and economic traits. Whole-genome resequencing and comparative analyses of different sheep populations have been performed to investigate population structures and selection signals. However, the ancestry and genetic basis underlying the adaptation of Horpa sheep remain unknown. In this study, 20 Horpa sheep samples were collected from the Xizang Autonomous Region, and publicly available whole-genome sequencing data from 44 individuals representing other sheep populations were combined. The genetic homogeneity and close phylogenetic relationship between Horpa sheep and Gansu Xizang sheep may reflect shared ancestry, historical migration, and geographic isolation. Some candidate genes potentially associated with high-altitude adaptation were consistently detected across the five selection methods [composite likelihood ratio (CLR), integrated haplotype score (iHS), population differentiation index ( F ST ), nucleotide diversity ratio ( θ π ratio) and cross-population extended haplotype homozygosity (XP-EHH)], such as MITF , a key regulator of pigmentation and protection against ultraviolet radiation, and ACSL6, which participates in lipid metabolism and energy homeostasis. Furthermore, candidate genomic regions enriched for quantitative trait loci (QTLs) that are associated with production traits, particularly body weight, were identified. These findings provide candidate genomic evidence for understanding the genetic basis of putative high-altitude adaptation and local population divergence and offer a useful framework for the strategic conservation and breeding of Horpa sheep.