Integrative pigGTEx resource with GWAS reveals genetic mechanism underlying semen quality in boars

Abstract

Semen quality is one of the most important indicators of boar reproductive performance. In the past, boar breeding has mostly emphasized characteristics such as lean meat percentage, feed conversion efficiency, and growth rate, while overlooking the genetic improvement of reproductive traits. This study employs advanced multi-omics approaches, such as transcriptome-wide association studies (TWAS) and colocalization between genome-wide association studies (GWAS) and expression quantitative trait loci (eQTLs), to provide a comprehensive understanding of the genetic mechanisms governing semen quality traits in boars. Here, we collected 190,000 ejaculate records across 11 semen quality traits from 3,604 Duroc boars. The heritability of semen quality traits ranged from 0.095 to 0.343. Genetic correlations between semen quality traits varied from −0.802 to 0.661, and phenotypic correlations ranged from −0.833 to 0.776. Single-trait GWAS identified 19 independent variants, corresponding to 13 quantitative trait loci (QTLs). By integrating PigGTEx and FAANG resources, we combined TWAS and colocalization analyses to reveal genetic regulation of semen quality traits. Notably, both GWAS and colocalization analyses pinpointed the DCAF12 as a crucial gene associated with multiple semen quality traits. Additionally, the ZSCAN9 gene and the variant rs322211455 were found to significantly affect sperm motility (SPMOT), possibly through hypothalamic-pituitary-gonadal axis. PheWAS further highlighted an association between rs322211455 and sperm abnormality rate, demonstrating the crucial role of ZSCAN9 in male fertility. This study reveals the genetic basis and regulatory mechanisms underlying semen quality traits in Duroc boars, identifying key candidate genes such as DCAF12 and ZSCAN9. These findings provide important insight into the genetic regulation of semen quality in boars.