Whole-Genome Resequencing Reveals Genetic Diversity and Selection Signatures in Honghe Cattle

Honghe cattle were formally recognized as the eighth indigenous cattle breed in Yunnan Province, a region in southwestern China characterized by complex geography and variable climates that have shaped distinctive local cattle germplasm. In this study, we generated whole-genome resequencing data from 62 Honghe cattle and compared them with additional reference samples from other breeds. The results revealed that Honghe cattle are predominantly of indicine origin (54.7% East Asian indicine, 26.5% South Asian indicine and 18.8% taurine), with relatively high genetic diversity. Runs of homozygosity analysis revealed low inbreeding (FROH = 0.032) and identified 52 ROH islands, the strongest of which (chr7) harbored a protein homeostasis gene cluster (HSPA9, SIL1, DNAJC18). For selection signatures, we applied multiple methods, including composite likelihood ratio test (CLR), integrated haplotype score (iHS), fixation index (FST) and cross-population extended haplotype homozygosity (XP-EHH) to identify selective sweeps in the Honghe cattle genome. We detected several candidate genes associated with important traits, such as HMGA2 (body size) and MCM6 (milk production). Functional enrichment analyses revealed pathways related to immune response, protein absorption, energy metabolism, and lipid metabolism. In addition, Y-chromosomal haplotype analysis revealed that Honghe cattle predominantly belong to the Y3 lineage (Y1 4.5%, Y2 9.1%, Y3 86.4%). These findings inform strategies for improving production efficiency and guiding breeding programs in Honghe cattle.