Genetic basis and origin of coat color in Leiqiong cattle.

Coat color polymorphism in domestic animals provides a robust framework for elucidating mechanisms of species adaptation, domestication, and genomic diversity. Leiqiong cattle, a representative indicine breed from southern China, are predominantly yellow-coated, although a subset exhibits a solid black phenotype. To determine the genetic basis of this variation, a genome-wide association study (GWAS) was performed in 212 Leiqiong bulls. A pronounced association signal was detected on chromosome 6 within the fifth intron of the gene, providing the first evidence of the potential influence of on bovine coat color variation. Integration of these results with publicly available genomic datasets and haplotype analyses indicated that the yellow coat phenotype is derived from Indian indicine ancestry, whereas the black coat phenotype emerged through introgression from wild bovine lineages and artificial hybridization with Wagyu cattle. Comparative analysis of Indian indicine cattle with divergent coat colors revealed distinct haplotypes within a shared background, suggesting an ancient and complex domestication history underlying coat color variation. These findings provide direct evidence that introgression has shaped phenotypic variation in East Asian cattle and offer novel insights into the genetic architecture of pigmentation, with implications for future breeding strategies.