title: A genome-wide scan for signatures of directional selection in domesticated pigs.
abstract: BACKGROUND
  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.
  
  
  RESULTS
  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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Department of Agricultural biotechnology, Seoul National University, Seoul, 151-921, Republic of Korea. sunjin@snu.ac.kr.|Department of Life Science and Division of EcoScience, Ewha Womans University, Seoul, 120-750, Republic of Korea. sunjin@snu.ac.kr.|Current address: Department of Genome Sciences, University of Washington, Seattle, WA, USA. sunjin@snu.ac.kr.
authors.forename: Sunjin
authors.initials: S
authors.lastname: Moon
authors.affiliation: Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Suwon, 441-706, Republic of Korea. thkim63@korea.kr.
authors.forename: Tae-Hun
authors.initials: TH
authors.lastname: Kim
authors.affiliation: Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Suwon, 441-706, Republic of Korea. leekt@korea.kr.
authors.forename: Kyung-Tai
authors.initials: KT
authors.lastname: Lee
authors.affiliation: Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 151-747, Republic of Korea. asleofn@naver.com.|C&K Genomics, Seoul National University Research Park, Seoul, 151-919, Republic of Korea. asleofn@naver.com.
authors.forename: Woori
authors.initials: W
authors.lastname: Kwak
authors.affiliation: Department of Agricultural biotechnology, Seoul National University, Seoul, 151-921, Republic of Korea. taeheon@snu.ac.kr.
authors.forename: Taeheon
authors.initials: T
authors.lastname: Lee
authors.affiliation: Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Suwon, 441-706, Republic of Korea. eunkyo1@empal.com.
authors.forename: Si-Woo
authors.initials: SW
authors.lastname: Lee
authors.affiliation: Animal Genetic Resources Station, National Institute of Animal Science, Rural Development Administration, Suwon, 441-706, Republic of Korea. kimmjk@korea.kr.
authors.forename: Myung-Jick
authors.initials: MJ
authors.lastname: Kim
authors.affiliation: Swine Science Division, National Institute of Animal Science, Rural Development Administration, Suwon, 441-706, Republic of Korea. kyuhocho@korea.kr.
authors.forename: Kyuho
authors.initials: K
authors.lastname: Cho
authors.affiliation: Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-806, Republic of Korea. deepreds@kribb.re.kr.
authors.forename: Namshin
authors.initials: N
authors.lastname: Kim
authors.affiliation: Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-806, Republic of Korea. whchung@kribb.re.kr.
authors.forename: Won-Hyong
authors.initials: WH
authors.lastname: Chung
authors.affiliation: C&K Genomics, Seoul National University Research Park, Seoul, 151-919, Republic of Korea. samsun.sung@gmail.com.
authors.forename: Samsun
authors.initials: S
authors.lastname: Sung
authors.affiliation: Department of Statistics, Seoul National University, Seoul, Republic of Korea. tspark@stats.snu.ac.kr.
authors.forename: Taesung
authors.initials: T
authors.lastname: Park
authors.affiliation: C&K Genomics, Seoul National University Research Park, Seoul, 151-919, Republic of Korea. seoae@cnkgenomics.com.
authors.forename: Seoae
authors.initials: S
authors.lastname: Cho
authors.affiliation: Animal Breeding and Genomics Centre, Wageningen University, De Elst 1, 6708 WD, Wageningen, The Netherlands. Martien.Groenen@wur.nl.
authors.forename: Martien Am
authors.initials: MA
authors.lastname: Groenen
authors.affiliation: Department of Integrative Biology and Department of Statistics, University of California Berkeley, Berkeley, CA, 94820, USA. rasmus_nielsen@berkeley.edu.
authors.forename: Rasmus
authors.initials: R
authors.lastname: Nielsen
authors.affiliation: Department of Life Science and Division of EcoScience, Ewha Womans University, Seoul, 120-750, Republic of Korea. yuseob@ewha.ac.kr.
authors.forename: Yuseob
authors.initials: Y
authors.lastname: Kim
authors.affiliation: Department of Agricultural biotechnology, Seoul National University, Seoul, 151-921, Republic of Korea. heebal@snu.ac.kr.|Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 151-747, Republic of Korea. heebal@snu.ac.kr.|C&K Genomics, Seoul National University Research Park, Seoul, 151-919, Republic of Korea. heebal@snu.ac.kr.
authors.forename: Heebal
authors.initials: H
authors.lastname: Kim
mesh_terms: D000818:Animals; D000829:Animals, Domestic / Q000235:genetics; D001947:Breeding; D002874:Chromosome Mapping; D016678:Genome; D006239:Haplotypes / Q000235:genetics; D055432:Metabolomics; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D018094:Receptors, Metabotropic Glutamate / Q000235:genetics; D012098:Reproduction; D012641:Selection, Genetic; D017422:Sequence Analysis, DNA; D034421:Sus scrofa / Q000235:genetics; D013552:Swine
chemical_list: D018094:Receptors, Metabotropic Glutamate