Genome-wide association study implicates possible causal genes for growth, fatness, and reproductive traits in pig

Growth, fatness, and reproductive traits are key economic traits that significantly influence the efficiency and long-term sustainability of commercial pig production. While genome-wide association study (GWAS) has proven to be an effective approach for identifying genetic variants associated with key traits, the significant loci identified by GWAS do not necessarily correspond to the true causal genes. To address this, we performed GWAS on 4 560 pigs from three populations to investigate six traits: right teat number (RTN), left teat number (LTN), body length (BL), body height (BH), BW and backfat thickness (BFT). We incorporated three post-GWAS analyses: expression quantitative trait loci mapping, Bayesian colocalisation analysis, and Mendelian randomisation to prioritise candidate causal genes. Genes supported by at least two independent lines of evidence were prioritised as high-confidence causal candidates. GWAS identified one novel lead single nucleotide polymorphism (SNP) on Sus scrofa chromosome 7 (SSC7) for teat number and two new lead SNPs for BFT on SSC1 and SSC18. A total of 16 and 23 potential causal genes were identified for LTN and RTN, respectively. Among these, four genes (ABCD4, ALDH6A1, ENTPD5, and ISCA2) were supported by all four lines of evidence for both traits. For BL, four out of ten candidate genes (ABCD4, PTGR2, ENTPD5 and FAM161B) received full support. For BFT, two of 23 genes (EXOSC2 and USP20) were fully supported. Regarding BW, among six genes, ASS1 ranked the highest and was supported by three lines of evidence. For BH, 12 genes, including PTK6 and STMN3, were supported by two lines of evidence. In summary, the integration of GWAS with multiple post-GWAS analyses provides a powerful and systematic strategy to refine association signals and prioritise putative causal genes. The novel loci and candidate genes identified expand genetic resources for marker-assisted selection and provide insights into the genetic basis of growth performance and reproductive traits in the pig industry.