Genome-wide adaptive selection and functional annotation of regulatory variation in the Yangxin pig

BACKGROUND: Local adaptation drives complex traits in domestic animals, but the roles of positive and balancing selection in Chinese indigenous pig breeds remain unclear. We performed whole-genome resequencing of 79 Yangxin pigs and applied positive and balance selection, integrated findings with PigQTLdb and FarmGTEx. RESULTS: In this study, we detected ~ 98 Mb of the genome under adaptive selection, mainly involving non-coding variants. Positive selection signals were concentrated in regulatory regions affected to muscle traits, whereas balancing selection was enriched at loci associated with reproduction. The strongest overlap with regulatory elements was observed in muscle tissue. Additionally, significant enrichment of the Hippo signaling pathway was detected in testis. DNA-level annotation revealed reproductive QTL to be most overrepresented in balancing-selection regions. Notable candidate genes and pathways include VGLL3 and Hippo signaling, and oxytocin, circadian entrainment, vascular smooth muscle contraction, and adrenergic signaling. CONCLUSION: These results underscore a regulatory basis for muscle phenotype variation, and the role of balancing selection in preserving fertility-related diversity. Our findings provide genomic markers for breeding and conservation strategies aimed at enhancing productivity in the Yangxin pig.