Whole-genome resequencing revealed genetic diversity and the haplotype containing MC1R associated with black coat color in Liangshan sheep

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Coat color was an economic trait in sheep, and identifying the causal variations affecting its diverse phenotypes had long been of interest. We performed whole-genome sequencing (WGS) to investigate the genetic composition and conducted a genome-wide association study (GWAS) for coat color using our lab data for 115 sheep (80 newly sequenced) from four Liangshan populations. Additionally, we retrieved public data for 104 sheep (from six other breeds) and 44 wild sheep. Our study revealed that the Liangshan sheep population exhibited moderate genetic diversity and a closer genetic relationship with Yunnan sheep. Using WGS data, we performed a GWAS to identify genetic loci and causal variants influencing the black coat pigmentation in 115 Liangshan sheep (i.e., 85 white coat LSS vs. 30 black coat LSB). GWAS identified a 1.526 Mb region (including the MC1R gene) on CHI14, spanning from 12,982,495 bp to 14,508,891 bp, as significantly associated with black coat (− log 10 P > 8.67). MC1R was highly expressed in the LSB group (mean = 15.394), significantly higher than in the LSS group (mean = 2.371; P = 0.032). A contingency table analysis revealed a highly significant difference in genotype frequencies at the MC1R mutation site c.361G > A between the LSB and LSS populations (Fisher’s exact test, P = 8.268 × 10 –25 ). Molecular docking results further demonstrated that the c.361G > A mutation in MC1R of the LSB population disrupted a hydrogen bond between MC1R residue Asn121 and ASIP residue Phe119, reducing their molecular interaction. Haplotype analysis showed that 96.67% of LSB individuals carried the H2 haplotype, with strong linkage disequilibrium ( r 2 = 1) maintained across the region. This study clarified the population structure of Liangshan sheep and confirmed the MC1R c.361G > A mutation as a key locus influencing the black coat of LSB, potentially acting via the H2 haplotype.

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