biostudies-literatureUnknown105(1)Yu JThis 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 Poultry science106180https://www.ebi.ac.uk/biostudies/studies/S-EPMC12756010biostudies-literatureUnraveling the population genetic structure and identifying candidate genes for dorsal plumage color in Liangshan Yanying chickens.PMC12756010Liu HWang QHe YChen LBai LLi RYu JXu HHuang AZhao JLi LfalseUnraveling 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 2025-01-01T00:00:00Z2025 Dec2026-05-28T03:24:39.307Z2026-05-28T03:12:15.228ZS-EPMC127560104138595810.1016/j.psj.2025.106180