Unraveling the population genetic structure and identifying candidate genes for dorsal plumage color in Liangshan Yanying chickens

This study aimed to investigate the genetic diversity and population structure of Liangshan Yanying chickens and to explore the genetic basis of dorsal plumage color changes from day-old to 12 weeks of age, thereby supporting conservation and breeding strategies. A total of 11,859,518 SNPs were obtained after quality control. The average observed heterozygosity (Ho = 0.280) was lower than the expected heterozygosity (He = 0.312). The minor allele frequency (MAF) ranged predominantly between 0.10 and 0.20 (27.3 %). The LD decay analysis showed a maximum R² of 0.27. Identity-by-state (IBS) distances suggested low kinship among individuals. A total of 1,726 ROH segments were identified, resulting in a low average inbreeding coefficient (FROH) of 0.0125, indicating moderate genetic diversity accompanied by a mild deficit of heterozygosity and suggesting the presence of mild inbreeding or past selection. GWAS revealed that candidate genes on chromosome 11 (DEF8, TCF25, TUBB3, DBNDD1, and MC1R) were associated with light/dark mottled plumage, while genes on chromosome 1 (GRM5, TYR, LOC121107450, and CTSC) were linked to the presence/absence of coloration. Overall, the Liangshan Yanying chicken population shows evidence of effective conservation. The variation in feather color is primarily associated with the MC1R, TYR, and other related regulatory genes, offering valuable genetic insights for the maintenance of color patterns and for the development of molecular-assisted breeding strategies.