Whole-Genome Resequencing Analysis Reveals the Local Ancestry and Selection of Kongshan Cattle

Kongshan cattle is an indigenous breed from Sichuan Province, China, characterized by their excellent meat quality, high fertility, strong disease resistance, and remarkable environmental adaptability. However, their genomic diversity has not been systematically studied. In this work, we performed whole-genome sequencing of 30 Kongshan cattle from a breeding farm and integrated these data with 113 representative commercial and indigenous cattle breeds worldwide to investigate their population structure and genetic diversity. We further analyzed the ancestral contributions to the development of the breed. The population structure revealed that Kongshan cattle possess four types of ancestral components: East Asian indicine (0.5974), East Asian taurine (0.3464), European taurine (0.0483), and Indian indicine (0.0079). The population also exhibits high nucleotide diversity, second only to pure East Asian indicine cattle. We inferred the ancestry of each variable site in the genome and, in combination with integrated haplotype score analysis, identified candidate genes related to meat quality (<i>ME1</i>, <i>ENPP2</i>, <i>GPD2</i>, <i>PDZRN4</i>, and <i>TMTC2</i>), immunity (<i>MCM6</i>, <i>MAP3K6</i>, <i>PIP4K2A</i>, <i>CDC6</i>, <i>CDC25B</i>, <i>PTAFR</i>, <i>ZC3H10</i>, and <i>NEK6</i>), and environmental adaptability (<i>KCNJ15</i>, <i>BECN1</i>, <i>AOC2</i>, <i>DUSP5</i>, and <i>ST3GAL4</i>). These findings provide valuable insights into the evolutionary history and ancestral origins of Kongshan cattle and contribute to the broader understanding, conservation, and sustainable utilization of indigenous Chinese cattle genetic resources.