Population genomic analysis of Weining chicken via dd-RAD sequencing: Unraveling diversity, structure, and selective...

To characterize the genetic diversity and evolutionary patterns of four Weining chicken strains from Guizhou Province, China, we generated genome-wide single nucleotide polymorphisms (SNPs) using dd-RAD sequencing. We found that Weining chicken exhibited moderate genetic diversity, with observed heterozygosity (Ho = 0.267) lower than expected heterozygosity (He = 0.312) and a positive inbreeding coefficient (FIS ≈ 0.14), indicating some degree of inbreeding across the population. Among strains, HM showed the highest diversity while HT had the lowest. Analyses of population structure, phylogeny, principal component analysis, and admixture consistently revealed weak genetic differentiation (FST < 0.06) and frequent gene flow among strains. Kinship analysis demonstrated mostly low pairwise relatedness, with a minority of individuals exhibiting closer kinship. Selection signature scans identified multiple candidate regions; genes within these regions were significantly enriched for biological processes and pathways related to immune response (e.g., IL-17 signaling) and metabolic regulation (e.g., MAPK signaling), which were consistently highlighted in both GO and KEGG enrichment analyses. These results demonstrate that Weining chicken has moderate genetic diversity, low population differentiation, and evidence of inbreeding and gene flow, with candidate selection signals in immune and metabolic pathways (e.g., IL-17 and MAPK signaling), providing a quantitative basis for conservation and breeding programs.