Genomic analyses identify distinct patterns of selection in domesticated pigs and Tibetan wild boars

Abstract

We report the sequencing at 131× coverage, de novo assembly and analyses of the genome of a female Tibetan wild boar. We also resequenced the whole genomes of 30 Tibetan wild boars from six major distributed locations and 18 geographically related pigs in China. We characterized genetic diversity, population structure and patterns of evolution. We searched for genomic regions under selection, which includes genes that are involved in hypoxia, olfaction, energy metabolism and drug response. Comparing the genome of Tibetan wild boar with those of neighboring Chinese domestic pigs further showed the impact of thousands of years of artificial selection and different signatures of selection in wild boar and domestic pig. We also report genetic adaptations in Tibetan wild boar that are associated with high altitudes and characterize the genetic basis of increased salivation in domestic pig.

Sympatric speciation revealed by genome-wide divergence in the blind mole ratSpalax

“…Olfaction, developed in Spalax (17), is under stronger selection in basalt than in the chalk population, possibly due to higher food diversity and chemical resources in basalt. Likewise, soil moisture is higher in basalt than in chalk (14), increasing odor saturability in the soil and enhancing olfactory reception (18,19). Finally, sensory perception of chemical stimuli may increase during the colonization of the chalk ancestors into the novel basalt niche (20) due to the higher level of selective pressure for mate choice.…”

Mining the pig genome to investigate the domestication process

“…The complex demographic history of the pig led researchers to use the empirically observed distributions of a number of statistics as a method for identifying candidate regions affected by selective sweeps (for example, Rubin et al, 2012;Li et al, 2013;Wilkinson et al, 2013). Nevertheless, this method does not rely on an underlying evolutionary model (see review in Ross-Ibarra et al, 2007), and candidate regions must therefore be validated in some way using an independent approach.…”

“…The authors argued that the phenotypic evolution of domestic pigs may be governed by a number of variants with large phenotypic effects. Li et al (2013) aimed to avoid the ascertainment bias associated with the Duroc pig reference sequence using a Tibetan wild boar genome sequenced de novo. Genetic comparison of Tibetan wild boars Although the process of domestication in pigs and other species is complex, we can hypothesize several scenarios for the evolution of the pig genome.…”

“…At the genome level, wild boars and domestic pigs from the same geographic location (Europe, Asia) exhibit low population differentiation but high differentiation among locations. Reduced variability in domestic pigs compared with wild boars has been observed in Asia (Groenen et al, 2012;Li et al, 2013), suggesting a genome-wide effect of the demographic population reduction produced by domestication. Nevertheless, this general reduction of variability is not observed in domesticated European populations.…”

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

“…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).…”