Genome-Wide Association Study of Abdominal and Intramuscular Fat Deposition Traits in Huainan Yellow-Feathered Chickens.

The Huainan yellow-feathered chicken is a prized local breed known for its high-quality meat. However, excessive abdominal fat deposition adversely affects feed efficiency and carcass quality. This study aimed to identify genetic markers and candidate genes associated with fat traits to facilitate marker-assisted selection (MAS) using genome-wide association studies (GWAS). A total of 220 chickens were phenotyped for abdominal fat weight (AFW), abdominal fat percentage (AFP), intramuscular fat of pectoral muscle (IFPM), and intramuscular fat of leg muscle (IFLM). GWAS based on whole-genome resequencing revealed significant SNPs for AFW and AFP on chromosomes 1, 2, 7, 10, 13, and 35, annotating genes including GRIA1, CYP1A1, CYP1A2, and SCAMP2. For IFPM and IFLM, significant loci were identified on chromosomes 1, 2, 4, 5, 6, 9, 12, 23, 25, 26, and 28, highlighting genes such as LRP4, FABP3, and ADAMTS9. Functional enrichment analysis showed involvement of steroid hormone biosynthesis, retinol metabolism, and cytochrome P450 pathways in abdominal fat deposition, while Wnt and MAPK signaling pathways regulated intramuscular fat. These findings provide molecular targets for genetic selection to improve fat traits in Huainan chickens.