A 6-bp deletion in exon 8 of the TYRP1 gene underlies brown coat colour development in Zhaotong pigs.

Coat colour is among the most distinctive phenotypic traits for pig breed identification. Zhaotong pigs (ZTs), indigenous pigs in China, present two coat colour types: black and brown. However, the key genes and regulatory mechanisms responsible for coat colour variation remain unknown. In this study, we analysed the whole-genome resequencing data of 1110 individuals, including 43 pig breeds, Eurasian wild boars, and an outgroup. Population genetic structure analysis, including principal component analysis (PCA), phylogenetic tree construction, and admixture analysis, revealed that ZTs present unique genetic characteristics. Using selective sweep analysis of the black population vs brown population of ZTs and a genome-wide association study (GWAS) targeting coat colour, we identified tyrosinase-related protein 1 (TYRP1) and nuclear factor I B (NFIB) as two important functional genes that influence coat colour in ZTs. A mutation at the g.209726926_209726931del locus in exon 8 of the TYRP1 gene results in decreased eumelanin synthesis, leading to the brown coat colour of ZTs. Our study is the first to systematically elucidate the molecular genetic mechanisms underlying coat colour formation in ZTs, providing essential theoretical foundations for the conservation of indigenous pig genetic resources and the development of new specialized breeds.