Abstract
BackgroundAnimal domestication involved drastic phenotypic changes driven by strong artificial selection and also resulted in new populations of breeds, established by humans. This study aims to identify genes that show evidence of recent artificial selection during pig domestication.ResultsWhole-genome resequencing of 30 individual pigs from domesticated breeds, Landrace and Yorkshire, and 10 Asian wild boars at ~16-fold coverage was performed resulting in over 4.3 million SNPs for 19,990 genes. We constructed a comprehensive genome map of directional selection by detecting selective sweeps using an FST-based approach that detects directional selection in lineages leading to the domesticated breeds and using a haplotype-based test that detects ongoing selective sweeps within the breeds. We show that candidate genes under selection are significantly enriched for loci implicated in quantitative traits important to pig reproduction and production. The candidate gene with the strongest signals of directional selection belongs to group III of the metabolomics glutamate receptors, known to affect brain functions associated with eating behavior, suggesting that loci under strong selection include loci involved in behaviorial traits in domesticated pigs including tameness.ConclusionsWe show that a significant proportion of selection signatures coincide with loci that were previously inferred to affect phenotypic variation in pigs. We further identify functional enrichment related to behavior, such as signal transduction and neuronal activities, for those targets of selection during domestication in pigs.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1330-x) contains supplementary material, which is available to authorized users.
Highlights
Animal domestication involved drastic phenotypic changes driven by strong artificial selection and resulted in new populations of breeds, established by humans
We tested if simple demographic structure can explain such patterns of haplotypes, by constructing a simple demographic model for the three populations resulting from two population splits, the Population structure We resequenced the whole genomes of Yorkshire (n = 16), Landrace (n = 14), and Asian wild boar (n = 10) at an average depth (± s.e) of 16.1 ± 0.8, 14.6 ± 0.5, and 15.4 ± 0.4, respectively
We find that the extremely low haplotype diversity observed in Yorkshire and Landrace is not generated by the simulation even when a recombination rate of zero is used (Figure 2)
Summary
Animal domestication involved drastic phenotypic changes driven by strong artificial selection and resulted in new populations of breeds, established by humans. This study aims to identify genes that show evidence of recent artificial selection during pig domestication. Mutations conferring new favorable phenotypes will be subject to a ‘selective sweep’, a rapid increase in allele frequency by artificial selection. Breeds affected by such sweeps will harbor large genetic. Recent genome-wide scans in diverse breeds aimed to uncover the genetic basis for phenotypic variation in pigs [3,4] showed that selection mapping approaches can detect comprehensive signatures of intense artificial selection that have led to the formation of well-defined breeds, suggesting that domestic animals can serve as models for deciphering complex phenotype-genotype association through selection mapping [3].
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