A genome-wide scan for signatures of directional selection in domesticated pigs

• DOI: 10.1186/s12864-015-1330-x
• Publication Date: 2015-02-24T01:07:01Z
• Authors: Sunjin Moon; Tae-Hun Kim; Kyung-Tai Lee; Woori Kwak; Taeheon Lee; Si-Woo Lee; Myung-Jick Kim; Kyuho Cho; Namshin Kim; Won-Hyong Chung; Samsun Sung; Taesung Park; Seoae Cho; Martien AM Groenen; Rasmus Nielsen; Yuseob Kim; Heebal Kim
• Keywords: Bioinformatics; Swine; Sus scrofa; 612; Directional selection; Breeding; Receptors, Metabotropic Glutamate; Medical and Health Sciences; Polymorphism, Single Nucleotide; Domestication; 03 medical and health sciences; Genetic; Information and Computing Sciences; Receptors; Metabotropic Glutamate; Genetics; Animals; Metabolomics; Polymorphism; Selection, Genetic; Domestic; Selection; Selective sweep; 2. Zero hunger; Pig; 0303 health sciences; Genome; Reproduction; Human Genome; Pig; Domestication; Selective sweep; Directional selection; Quantitativetraits; Quantitative traits; Chromosome Mapping; Single Nucleotide; DNA; Sequence Analysis, DNA; Biological Sciences; Haplotypes; Animals, Domestic; Sequence Analysis; Biotechnology; Research Article

Animal 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.Whole-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 F ST-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.We 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.