Integrative Advances in Pig Genomics: From Reference Assemblies and Evolutionary History to the Mechanistic Dissection of Key Traits.

Pigs are a major source of animal protein and an important model for studying domestication, adaptation, and the genetics of complex traits. Over the past decade, pig genomics has progressed from generating reference assemblies and variant catalogues toward reconstructing population history and interpreting phenotypic divergence with greater resolution. Improvements in reference continuity, breed-matched assemblies, and pangenome/graph representations reduce reference bias in repeat-rich and structural-variant-prone regions, strengthening cross-population comparisons and fine-mapping across cohorts. Time-stratified ancient genomes provide an explicit temporal framework for evaluating lineage turnover and gene flow and support a multi-stage, network-based view of domestication. In parallel, genetic analyses of growth, carcass composition, meat quality, and disease resilience increasingly integrate association signals with regulatory annotation, gene expression, and tissue- or stage-specific context. Across these lines of work, maintaining comparability across reference frameworks remains central, including stable coordinate systems, robust imputation resources, and reproducible approaches for structural-variant genotyping. Together, these developments support more consistent inference and interpretation while providing a clearer basis for translation in breeding and biomedical research with attention to genetic diversity.