Identifying pleiotropic genes for backfat thickness and semen traits in pigs using GWAS summary data

Backfat thickness is a key carcass trait reflecting fat deposition in pigs, while semen quality represents a critical measure of boar reproductive performance in artificial insemination systems. Despite their economic importance, the genetic relationship between these traits remains largely unexplored. In this study, we applied the PLACO method under the composite null hypothesis to identify genes affecting adjusted backfat thickness at 100 kg (BFT_100), semen volume (SEMVOL), and sperm motility (SPMOT). The consistency and heterogeneity of pleiotropic gene effects were evaluated using Pearson correlation and Cochran's Q test, and protein-protein interaction (PPI) networks were constructed based on the STRING database. Generalized summary-data-based Mendelian Randomization (GSMR) was employed to investigate potential genetic associations between BFT_100 and semen traits. We identified 99 significant pleiotropic genes (FDR < 0.05), including seven genes (PACSIN1, TTC26, PSMD13, PKHD1, VARS2, MDFI, MRPS10) associated with all three traits. Approximately 57.5% of genes exhibited positive correlations between traits, while 42.5% showed negative correlations. PPI analysis revealed that these genes formed interconnected networks enriched in energy metabolism and immune-related pathways. GSMR indicated a significant positive genetic effect of BFT_100 on SEMVOL (β = 19.09, P = 1.545 × 10-7) but a negative effect on SPMOT (β = -0.0051, P = 0.0138). These results reveal the complex genetic links between fat deposition and semen traits, highlight key pleiotropic genes, and suggest mechanisms by which adiposity may influence reproductive performance, providing valuable insights for molecular breeding and genetic improvement in pigs.