Analyses of pig genomes provide insight into porcine demography and evolution

TLDR

Pigs have coevolved with humans for 10 000 years, with domestication and breeding shaping their genomes, and wild pigs originated in Southeast Asia before spreading across Eurasia, resulting in a large repertoire of olfactory receptor genes. The study assembles and analyzes a female Duroc pig genome and compares it with wild and domestic pig genomes from Europe and Asia. We assembled the genome of a female Duroc pig and compared it to wild and domestic pig genomes from Europe and Asia. We found a deep phylogenetic split between European and Asian wild boars about 1 Myr ago, selective sweeps in RNA‑processing genes, rapid evolution of immune‑response and olfactory genes, and identified many putative disease‑causing variants that make the pig a valuable biomedical model.

Abstract

For 10,000 years pigs and humans have shared a close and complex relationship. From domestication to modern breeding practices, humans have shaped the genomes of domestic pigs. Here we present the assembly and analysis of the genome sequence of a female domestic Duroc pig (Sus scrofa) and a comparison with the genomes of wild and domestic pigs from Europe and Asia. Wild pigs emerged in South East Asia and subsequently spread across Eurasia. Our results reveal a deep phylogenetic split between European and Asian wild boars ∼1 million years ago, and a selective sweep analysis indicates selection on genes involved in RNA processing and regulation. Genes associated with immune response and olfaction exhibit fast evolution. Pigs have the largest repertoire of functional olfactory receptor genes, reflecting the importance of smell in this scavenging animal. The pig genome sequence provides an important resource for further improvements of this important livestock species, and our identification of many putative disease-causing variants extends the potential of the pig as a biomedical model.