Whole-Genome Resequencing Reveals Genetic Diversity and Selective Sweep Signatures in Wuling Cattle

Background: Wuling cattle are a native breed in southern China and primarily inhabit mountainous regions. They are distributed across three geographically distinct mountainous regions and were historically classified into three local populations: Enshi cattle (western Hubei), Sinan cattle (eastern Guizhou) and Xiangxi cattle (western Hunan). Here, we aim to elucidate the genetic relationships and describe the genetic characteristics of Wuling cattle across these regions. Methods: We performed whole-genome resequencing of 20 Sinan cattle, together with public data of 10 Enshi cattle, 20 Xiangxi cattle and 65 cattle from four reference continental groups. Reads were aligned to the ARS-UCD1.2 reference genome. Genetic differences between different cattle breeds were assessed through analyses of population structure and genetic diversity. Selective signals in Wuling cattle were identified using single-population selective analysis and local ancestry inference, whilst potential differences between different Wuling cattle subpopulations were pinpointed using cross-population selective analysis. Results: On the basis of whole-genome resequencing data, Enshi, Sinan and Xiangxi cattle share highly similar genetic backgrounds (with similar ancestral lineages comprising East Asian taurine and East Asian indicine) and negligible genetic differentiation (the pairwise F_ST among Enshi cattle, Sinan cattle and Xiangxi cattle was approximately 0.01), supporting their classification as a single breed-Wuling cattle. Selective sweep analysis in Wuling cattle revealed multiple genomic regions under selection associated with key biological processes, including reproduction, fat deposition, feed efficiency, skeletal and muscle development, and immune response. Part of these regions is derived from East Asian indicine, related with SYTL1, TMEM222, WDTC1 and SLC9A1. Furthermore, Wuling cattle are found in various regions, where geographical conditions vary. Distinct selective signals were also observed among regional groups of Wuling cattle, likely reflecting adaptation to their diverse local environments. Conclusions: This study provides a comprehensive genomic characterization of Wuling cattle, outlines the selection signals for Wuling cattle, whilst demonstrating that different geographical environments have generated unique selection pressures within the Wuling cattle population. Providing a genetic guidelines for the conservation and sustainable utilization of their genetic resources.