Genome-Wide Resequencing Reveals Genetic Diversity and Selection Signatures in Two Indigenous Goat Populations From Xizang.

Abstract

Zhangmu goats and Chentang black goats are valuable local goat genetic resources in Shigatse, Xizang. Due to long-term geographic isolation and small population size, their genetic diversity and adaptive genetic basis remain poorly understood. In this study, whole-genome resequencing was performed on 30 Zhangmu goats and 30 Chentang black goats. By calculating indicators such as observed heterozygosity (HO), expected heterozygosity (HE), nucleotide diversity (π), and inbreeding coefficient (FIS), the genetic diversity of the two populations was comprehensively assessed, and their selection signatures were analyzed using both Fst and XP-CLR. The results showed that both Zhangmu goats and Chentang black goats exhibited relatively low but detectable levels of genetic diversity, with clear genetic differentiation from wild goats. Population structure analysis indicated that the two indigenous populations possessed relatively independent genetic backgrounds. Combined Fst and XP-CLR analyses identified multiple candidate genes associated with hypoxia adaptation (ARNT), immune response (CD274, PTPN7), growth and development (FGF5, MYOM3), and reproductive regulation (GDF5, MEIOB). Functional enrichment analysis revealed that these candidate genes were mainly enriched in GO terms such as nucleoplasm, and in pathways such as the calcium signaling pathway and propanoate metabolism. These results provide genomic insights into the genetic characteristics of Zhangmu goats and Chentang black goats, and offer a theoretical basis for the conservation and sustainable utilization of indigenous goat genetic resources in Xizang.