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

Abstract

Pig genomics now serves two main uses: improving pig breeding and supporting biomedical research. Many key variants lie in repeat-rich regions or involve structural changes, where older references and linear pipelines can lose sequence, place reads incorrectly, or miss real haplotypes. New assemblies that are breed-specific, near gap-free, and increasingly telomere to telomere reduce these problems and improve routine variant detection. Pangenomes and graph approaches also help by capturing sequences absent from a single reference, which makes comparisons across breeds and cohorts more reliable. Ancient DNA and time-resolved data further show that domestication involved repeated movements and gene flow, which affects how we interpret selection signals. For economic traits, the focus is shifting from locating signals to explaining what they change by linking associations to regulatory annotation and tissue or stage-specific expression. Consistent coordinates and variant definitions are essential for results that can be reproduced and applied in breeding. Keywords: pig, genomics, pangenome, structural variation, economic traits, breeding applications