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

## TL;DR

Advances in pig genomics improve breeding and biomedical research by enhancing reference assemblies, understanding domestication history, and linking genetic variants to traits like growth and disease resilience.

## Contribution

The paper highlights integrative genomic approaches, including breed-specific assemblies, pangenomes, and regulatory annotations, to better interpret pig traits and evolution.

## Key findings

- Breed-specific, near gap-free assemblies improve variant detection in repeat-rich and structural variant-prone regions.
- Ancient DNA and time-resolved data reveal domestication involved repeated movements and gene flow.
- Integration of association signals with regulatory annotation and expression data enhances understanding of economic 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.

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.