Weighted single-step GWAS identified candidate genes associated with semen traits in Rhode Island Red chickens

Semen quality traits in chickens are critical indicators reflecting reproductive efficiency, breeding progress, and economic profitability in the poultry industry. Understanding the genetic architecture and enabling targeted genetic improvement of these traits are essential for enhancing poultry production efficiency. In this study, we estimated genetic parameters and performed weighted single-step GWAS for five semen traits in RIR chickens to reveal their genetic architecture and identify key candidate genes and QTLs associated with semen quality. The results showed that heritability estimates for SEVOL, SECON, SPMOT, SPABR, and SPCOUNT ranged from 0.097 to 0.322, indicating low to moderate heritability. 29 significant QTL regions and 12 candidate genes (NFKB1, UBE2D3, PPP3CA, EIF4E, H2AFZ, DOCK2, MTNR1A, TACC3, ADCYAP1, GFRA1, ABLIM1, and CASP7) associated with semen traits were identified by WssGWAS. These QTL regions were located on chromosomes 4 and 13 for SEVOL, chromosome 4 for SPMOT, and chromosomes 2 and 6 for SPABR. Interestingly, four prominent consecutive QTL regions were shared between SEVOL and SPMOT. These QTL were located at 59.83-61.43 Mb, explaining 11.55% and 16.33% of the genetic variance for SEVOL and SPMOT, respectively. The largest-effect SNPs within these four QTL intervals exhibited significant effects on both semen volume and sperm motility, and these markers could be used for marker-assisted selection of semen traits. This study provides further insights into the genetic architecture of chicken semen traits, improves our understanding of their molecular regulation, and identifies valuable QTL and candidate genes. These findings offer a scientific basis for genetic improvement and marker-assisted selection of semen quality.