Abstract
<title>Abstract</title> <p> Lufeng cattle ( <italic>Bos indicus</italic> ) are a representative indigenous indicine breed from southern China with extensive variation in background pigmentation and white-pattern distribution. However, the evolutionary history and genetic architecture underlying these traits remain largely uncharacterized. We integrated whole-genome resequencing data from 291 Lufeng cattle with 213 publicly available bovine genomes and employed genome-wide association studies, haplotype characterization, introgression inference, and epigenomic profiling. Population genomic analyses demonstrated a predominantly East Asian indicine genetic background with detectable Gaur and Banteng ancestry. D-statistics, local ancestry inference, and haplotype analyses supported historical introgression and retention of wild bovine-related haplotypes. GWAS identified two regions associated with distinct coat-color components: a chromosome 10 locus related to white-pattern distribution and a chromosome 18 locus influencing background pigmentation. The chromosome 10 region exhibited extended linkage disequilibrium, differentiated haplotypes, wild bovine-related ancestry, and active regulatory epigenomic features, suggesting that introgression and regulatory variation contributed to white-pattern distribution. In contrast, the chromosome 18 locus showed a dosage-dependent effect on pigmentation and harbored candidate genes, including <italic>SPIRE2</italic> , <italic>FANCA</italic> , and <italic>MC1R</italic> . These findings support a dual-component model in which background pigmentation and white-pattern distribution are influenced by partially independent genetic mechanisms. More broadly, historical introgression, haplotype variation, regulatory mechanisms, and multilocus architecture may collectively shape complex phenotypic diversity in indigenous cattle. This study advances our understanding of coat-color evolution and the evolutionary history of southern Chinese cattle and provides a genomic framework for conserving and sustainably utilizing indigenous cattle genetic resources. </p>