Identified Candidate Genes of Semen Trait in Three Pig Breeds Through Weighted GWAS and Multi-Tissue Transcriptome Analysis

High-quality semen is an essential factor for the success of artificial insemination, and revealing the genetic structure of pig semen traits helps improve semen quality. This study aimed to identify candidate genes associated with semen traits in three pig breeds (Duroc, Landrace, and Yorkshire) through weighted GWAS and multi-tissue transcriptome analysis. In this study, to identify candidate genes associated with semen traits in Duroc, Landrace, and Yorkshire, we performed weighted GWAS in four traits (sperm motility, sperm progressive motility, sperm abnormality rate, and total sperm count) using 936 pigs and multi-tissue transcriptome analysis using 34 tissues RNA-seq data of 5457 pigs from FarmGTEx. It was found that 16, 9, and 12 significant SNPs associated with semen traits were identified in Duroc, Landrace, and Yorkshire, with corresponding 7, 5, and 7 candidate genes in these three breeds, respectively, which may be involved in mammal spermatogenesis, testicular function, and male fertility. Moreover, we not only found the same candidate gene <i>DNAI2</i> as in previous studies but also found two new candidate genes <i>PNLDC1</i> and <i>RSPH3</i>, which were identified simultaneously in both Landrace and Yorkshire. By integrating the GWAS and multi-tissue transcriptome analysis results, we found that candidate genes associated with semen traits of three pig breeds were highly expressed in the testis tissue. The three genotypes of rs320928244 had significant effects on the expression of the <i>DYNLT1</i> gene in the testis tissue of Landrace. These results together showed that these candidate genes were mainly related to sperm motility defects. This study helps deepen the understanding of the genetic basis of semen traits and provides a theoretical foundation for improving the semen quality of Duroc, Landrace, and Yorkshire breeds.