Analyses of pig genomes provide insight into porcine demography and evolution

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.

Figure 1. Phylogeny of the six mammals used in the dN/dS analysis.

KEGG pathways with genes that show accelerated evolution for each of the six mammals used in the dN/dS analysis. The bar charts show the individual dN/dS and dS values for each of the six mammals. The dN/dS and dS values refer to the time period of each of the six individual lineages. The number of proteins that show significantly accelerated dN/dS ratios in each lineage varies from 84 in the mouse to 311 in the pig lineage. Pathways significantly (P < 0.05) enriched within this group of genes are also shown with the number of genes shown in brackets. HPI, Helicobacter pylori infection. PowerPoint slide

Figure 2. Distribution of heterozygosity for individual pig genomes.

Shown is the distribution of the heterozygosity as the log₂(SNPs) per 10k bin. a, Wild Sus scrofa: blue, south China; green, north China; orange, Italian; red, Dutch. b, Breeds: blue, Chinese breeds (Jiangquhai, Meishan, Xiang); red–yellow, European breeds (Hampshire, large white, landrace). Note that the Hampshire breed is a North American breed of European origin. PowerPoint slide

Figure 3. Demographic history of wild boars.

Demographic history was inferred using a hidden Markov model (HMM) approach as implemented in pairwise sequentially Markovian coalescence (PSMC). In the absence of known mutation rates for pig, we used the default mutation rate for human (μ) of 2.5 × 10⁻⁸. For the generation time (g) we used an estimate of 5 years. The Last Glacial Maximum (LGM) is highlighted in grey. WB_nl, wild boar Netherlands; WB_it, wild boar Italy; WB_Nch, wild boar north China; WB_Sch, wild boar south China. PowerPoint slide

Figure 4. Putative selective sweep region around the ERI2 gene on SSC3.

The y axis shows the log-transformed value of the ratio for the observed/expected derived allele frequency using a sliding window at a bin size of 50,000 bp. The x axis shows the position on SSC3 in base pairs. PowerPoint slide