Genome-wide association study reveals novel loci associated with body size and carcass yields in Shaoxing ducks

Shaoxing ducks are a dual-purpose breed renowned for their delectable meat quality high egg-laying performance, and robust adaptability, leading to a growing market presence. Despite their economic significance, the genetic mechanisms influencing carcass growth in Shaoxing ducks remain largely unexplored. This study utilized genome-wide association studies (GWAS) and haplotype-sharing analysis to identify genomic regions and candidate genes associated with body size and carcass yield traits in this breed. Our investigation identified 50 genes associated with 18 body size and carcass yield traits. Notably, the RSPO3 and SPATA13 genes exhibited significant correlations with breast muscle weight (BMW) and leg muscle weight (LMW) traits. Additionally, COL6A3 was significantly associated with eviscerated weight% (EWP) and half-eviscerated weight% (HEWP) traits. Genes such as FGF9, LATS2, and PFKP, known for their roles in muscle development and energy metabolism, may also influence LMW traits. Through linkage disequilibrium and haplotype-sharing analyses, we identified a haplotype on chromosome 3 significantly linked to LMW. These genes and the identified haplotype hold promise as candidate markers for molecular breeding programs aimed at improving carcass traits in Shaoxing ducks. Furthermore, we utilized a bootstrap test to validate the reliability of GWAS results derived from small experimental samples, enhancing the robustness of our findings. The methodology and code for this bootstrap test are accessible at https://github.com/xuwenwu248/bootstrap.sh/commit/07db59d129c24c384ba2c43f9bb3f8d62fce845b .