Copy Number Variation in Native and Crossbred Pigs Provides Insights Into Genomic Consequences of Domestication

Sus scrofa has been domesticated under diverse environments and management systems, leading to broad variation in genetic architecture and physiological regulation. This diversity has been preserved in indigenous breeds maintained under traditional husbandry and further expanded through modern crossbreeding programs designed to combine the distinctive attributes of native and commercial lineages. To investigate how such lineage diversity is reflected at the structural genomic level, whole-genome sequencing data from 110 pigs representing 13 populations were analysed to characterize genome-wide copy number variation (CNV) patterns and identify regions showing differential CNV patterns among lineages. Comparative analysis revealed distinct CNV landscapes between indigenous and commercial groups, encompassing 282 significantly differentiated CNV regions (CNVRs). Selection signatures defined by V_ST and Wilcoxon tests highlighted genes involved in lipid metabolism (FAR2, MGLL, FASN), suggesting that CNV differences may underlie the characteristic fat-deposition traits of native breeds. Within the same analytical framework, crossbred populations exhibited inheritance patterns consistent with parental lineage influence: native-like CNVRs harboured lipid-associated genes (ADIPOR1, MLXIPL, GPIHBP1), whereas commercial-like CNVRs contained loci related to muscle development and growth (CAPN1, PDGFA, EEF1A2, SH2B1). These results collectively provide genomic insight into how CNVs reflect the effects of historical adaptation and selective breeding in domestic pigs. The differentiated CNVRs identified here encompass genes involved in fat deposition and muscle biology, suggesting potential links to trait variation across lineages. This work offers a genomic foundation for future studies integrating CNV and functional traits, and highlights the value of structural variation in informing crossbreeding and breed-improvement strategies.