Genome-wide association study reveals the genetic basis of meat quality traits in Sichuan Shelduck

Sichuan Shelduck, a unique Chinese indigenous duck breed, exhibits superior meat quality traits, but its genetic basis has not been systematically evaluated. This study assessed meat quality traits, including pH, color, shear force, moisture, and intramuscular fat (IMF) in 240 Sichuan Shelducks (123 males and 117 females). At 90 days, males exhibited higher IMF (2.83% ± 0.58 vs. 2.79% ± 0.63, P < 0.01) and moisture content (76.35% ± 1.04 vs. 75.68% ± 2.3, P < 0.01), but lower shear force (31.00 ± 9.11 N), compared with females (33.32 ± 10.03 N). Phenotypic correlation analysis revealed that moisture content was positively correlated with flesh color and tenderness. SNP-based heritability estimates were moderate to high for moisture (0.42), meat lightness (L*, 0.39), and IMF (0.34). Genome-wide association studies (GWAS) identified 29 significant SNPs for IMF on chromosome 21, with the peak SNP (chr21:2210804 T > C) near STK4 explaining 19.68% of the phenotypic variance. GO functional analysis results speculated that STK4 may be involved in adipocyte differentiation through the FoxO/MAPK pathway. Transcriptomic analysis of pectoral muscle with high versus low IMF highlighted enrichment of DGAT2 in Glycerolipid metabolism and PPAR signaling pathways. Regression analysis prioritized RALY for its role in cholesterol homeostasis. These candidate genes (STK4, DGAT2, RALY) and associated molecular markers provide a genetic basis for improving Sichuan Shelduck meat quality in breeding programs.