Resequencing-Based GWAS Highlights SNP and Indel Loci and lncRNA Candidates for Carcass Yield and Meat Quality in Yellow-Feathered Broilers.

Carcass and meat quality traits are economically important in poultry breeding. To investigate their genetic architecture and identify potential candidate regulators, we performed whole-genome resequencing (WGS) and an integrative genome-wide association study (GWAS) on 315 breast muscle samples from yellow-feathered broilers, jointly analyzing SNP and Indels across 14 carcass and meat quality traits. We identified about 13.5 million SNPs and 1.24 million Indels. Across 14 carcass and meat quality traits, 364 significant SNPs (p < 1.0 × 106) and 52 significant Indels (p < 1.0 × 10-6) were detected, clustering into nine genomic regions. Key candidate genes included CNTN5 for leg muscle percentage, SORCS1 for crude fat (CF), CNN3 for shear force, and APOB and SQLE for total cholesterol. We further used tissue-specific transcriptome-derived lncRNA annotations to identify candidate lncRNAs located within ±100 kb of significant GWAS loci. These lncRNAs were prioritized as genomic-proximity-based candidates for future functional validation. Functional enrichment analysis indicated involvement of PI3K-Akt and Wnt signaling pathways, lipid metabolism, and cytoskeletal regulation. These findings provide new insights into the genetic basis of carcass yield and meat quality traits in yellow-feathered chickens and offer molecular markers and regulatory candidates for future molecular breeding strategies.