Adaptation and possible ancient interspecies introgression in pigs identified by whole-genome sequencing

Abstract

Domestic pigs have evolved genetic adaptations to their local environmental conditions, such as cold and hot climates. We sequenced the genomes of 69 pigs from 15 geographically divergent locations in China and detected 41 million variants, of which 21 million were absent from the dbSNP database. In a genome-wide scan, we identified a set of loci that likely have a role in regional adaptations to high- and low-latitude environments within China. Intriguingly, we found an exceptionally large (14-Mb) region with a low recombination rate on the X chromosome that appears to have two distinct haplotypes in the high- and low-latitude populations, possibly underlying their adaptation to cold and hot environments, respectively. Surprisingly, the adaptive sweep in the high-latitude regions has acted on DNA that might have been introgressed from an extinct Sus species. Our findings provide new insights into the evolutionary history of pigs and the role of introgression in adaptation.

The ‘heritability’ of domestication and its functional partitioning in the pig

“…Following on McVean (2009) the percentage of admixing can be estimated by the relative position of the admixed population in the first axis, compared with those of the founder populations. This results in an Asian component estimate of~20% for Large White, which is quite similar to the figure obtained by Bianco et al (2015) using highdensity genotyping array data or by Ai et al (2015) and Bosse et al (2015) with sequence. Moreover, Figure 1a indicates that neither Spanish Iberian nor Hungarian Mangalica have been crossed with Chinese pigs, as they cluster tightly with European wild boars.…”

“…Most of the sample sequences were downloaded from the short read archive (SRA, http://www. ncbi.nlm.nih.gov/sra; Groenen et al, 2012;Rubin et al, 2012;Esteve-Codina et al, 2013;Molnár et al, 2014;Ai et al, 2015;Bianco et al, 2015), but five were specifically sequenced for this study: a wild boar from East Russia (Primorsky Krai Peninsula, WA6), a Tunisian wild boar (WE8), a Spanish wild boar from North Spain (Asturias region, WE6) and 2 Iberian pigs (IB2 and IB3). Supplementary Table 1 presents details from all samples analyzed.…”

A genome scan for selection signatures comparing farmed Atlantic salmon with two wild populations: Testing colocalization among outlier markers, candidate genes, and quantitative trait loci for production traits

“…Soft sweeps characterized by narrow divergent haplotype blocks were more common than hard sweeps characterized by wide divergent haplotype blocks in a population of maize that had undergone strong positive directional selection for ear number for 30 generations (Beissinger et al., 2014). In practice, these two scenarios represent a continuum with the long haplotype blocks of the first becoming shorter and harder to detect over millennia unless they are in a nonrecombining region of the genome (Ai et al., 2015). …”

“…Changes in the genomes of different breeds of domesticated pigs detected by comparing SNP allele frequencies with those of ancestral wild boars are attributed to nearby genes under selection (Ai et al., 2015; Li et al., 2013). Similar studies have been published in cattle (Hayes et al., 2008; The Bovine HapMap Consortium 2009) and sheep (Chessa et al., 2009).…”

Genetic diversity and population structure of six Chinese indigenous pig breeds in the Taihu Lake region revealed by sequencing data

“…2013, 2014) or whole‐genome sequencing data (Ai et al . 2015). These studies confirmed the divergent evolutions and distinct population structures of Chinese and Western pigs and revealed the adaptive evolutionary history of the pig.…”