Evolutionary dynamics of copy number variation in pig genomes in the context of adaptation and domestication

Abstract

Background: Copy number variable regions (CNVRs) can result in drastic phenotypic differences and may therefore be subject to selection during domestication. Studying copy number variation in relation to domestication is highly relevant in pigs because of their very rich natural and domestication history that resulted in many different phenotypes. To investigate the evolutionary dynamic of CNVRs, we applied read depth method on next generation sequence data from 16 individuals, comprising wild boars and domestic pigs from Europe and Asia. Results: We identified 3,118 CNVRs with an average size of 13 kilobases comprising a total of 39.2 megabases of the pig genome and 545 overlapping genes. Functional analyses revealed that CNVRs are enriched with genes related to sensory perception, neurological process and response to stimulus, suggesting their contribution to adaptation in the wild and behavioral changes during domestication. Variations of copy number (CN) of antimicrobial related genes suggest an ongoing process of evolution of these genes to combat food-borne pathogens. Likewise, some genes related to the omnivorous lifestyle of pigs, like genes involved in detoxification, were observed to be CN variable. A small portion of CNVRs was unique to domestic pigs and may have been selected during domestication. The majority of CNVRs, however, is shared between wild and domesticated individuals, indicating that domestication had minor effect on the overall diversity of CNVRs. Also, the excess of CNVRs in non-genic regions implies that a major part of these variations is likely to be (nearly) neutral. Comparison between different populations showed that larger populations have more CNVRs, highlighting that CNVRs are, like other genetic variation such as SNPs and microsatellites, reflecting demographic history rather than phenotypic diversity.

Global copy number analyses by next generation sequencing provide insight into pig genome variation

“…We also compared CNVRs in this study with previous pig CNV studies [24, 25, 35, 36, 39, 41, 42]. After merging the results of recent reports, a total of 849 out of 3,131 CNVRs (27.75%) with the length of 33.02 Mb in our study overlapped with those previously reported (see Table 4).…”

Mining the pig genome to investigate the domestication process

“…By mean of whole-genome resequencing, Rubin et al (2012) observed a reduced number of candidate regions with fixed or highfrequency nonsense mutations, leading to the conclusion that gene inactivation did not had an important role in the pig domestication and breeding processes. A similar pattern was found in regions containing copy number variants (Rubin et al, 2012; see also Paudel et al, 2013). Nevertheless, Rubin et al (2012) identified an excess of nonsynonymous-derived substitutions in domesticated pigs, a result that is expected if selective events predominate during and after domestication.…”

Artificial selection on introduced Asian haplotypes shaped the genetic architecture in European commercial pigs

“…The KIT gene is a very well-known gene that is involved in coat colour [23]. European pigs contain a copy number variable dominant white allele, mostly in homozygous form [21,48]. We clearly see European haplotypes surrounding this gene rather than Asian, suggesting selection against introgression at this locus.…”