Genetic and regulatory architecture of meat yield traits in commercial pig populations

Abstract Background Lean meat percentage (LMP), longissimus muscle area (LMA), and longissimus muscle depth (LMD) are critical carcass traits that directly impact meat yield and the economic efficiency of swine production. Although genome-wide association studies (GWAS) have identified numerous loci associated with these traits, the functional characterization of candidate quantitative trait loci (QTLs) and their regulatory mechanisms is still limited and poses significant challenges. Here, we conducted GWAS in 4593 pigs from three commercial populations (Yorkshire, Landrace and Duroc) to identify loci associated with LMP, LMA and LMD. We further integrated integrative chromatin accessibility, histone modifications, chromatin interaction information, and dual-luciferase reporter assays to identify candidate QTLs with potential regulatory functions. Candidate genes were subsequently prioritized using single-nucleus RNA sequencing, Phenome-wide association analysis, and Mendelian randomization. Results This multi-layered approach prioritized candidate regulatory QTLs associated with LMP, LMA and LMD, and identified high-confidence candidate genes potentially involved in the regulation of meat yield traits. For LMP, WWOX and ABL1 showed the strongest evidence in Yorkshire and Landrace population, respectively. For LMA, PHB1 and BAZ2A showed the strongest evidence in the Yorkshire and combined-population, respectively. SLC16A7 was specifically associated with both LMP and LMA in Landrace. For LMD, ENSSSCG00000045482 and RSPO4 showed the strongest evidence in Yorkshire pigs, while XPO4 was identified in the combined-population analysis. These genes may influence muscle metabolic homeostasis, muscle proliferation, hypertrophy, and atrophy through interactions with myogenic transcription factors and key signaling pathways such as PPAR-RXR and Wnt/β-catenin. Conclusions These findings provide new insights into the genetic and regulatory basis of meat yield traits in pigs and highlight candidate regulatory QTLs and genes for future functional validation and precision breeding applications aimed at improving pork yield.