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

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• 作者：Sunjin Moon (1) (12) (2)
  Tae-Hun Kim (3)
  Kyung-Tai Lee (3)
  Woori Kwak (4) (5)
  Taeheon Lee (1)
  Si-Woo Lee (3)
  Myung-Jick Kim (6)
  Kyuho Cho (7)
  Namshin Kim (8)
  Won-Hyong Chung (8)
  Samsun Sung (5)
  Taesung Park (9)
  Seoae Cho (5)
  Martien AM Groenen (10)
  Rasmus Nielsen (11)
  Yuseob Kim (2)
  Heebal Kim (1) (4) (5)
  
  1. Department of Agricultural biotechnology ; Seoul National University ; Seoul ; 151-921 ; Republic of Korea
  12. Current address ; Department of Genome Sciences ; University of Washington ; Seattle ; WA ; USA
  2. Department of Life Science and Division of EcoScience ; Ewha Womans University ; Seoul ; 120-750 ; Republic of Korea
  3. Animal Genomics and Bioinformatics Division ; National Institute of Animal Science ; Rural Development Administration ; Suwon ; 441-706 ; Republic of Korea
  4. Interdisciplinary Program in Bioinformatics ; Seoul National University ; Seoul ; 151-747 ; Republic of Korea
  5. C&K Genomics ; Seoul National University Research Park ; Seoul ; 151-919 ; Republic of Korea
  6. Animal Genetic Resources Station ; National Institute of Animal Science ; Rural Development Administration ; Suwon ; 441-706 ; Republic of Korea
  7. Swine Science Division ; National Institute of Animal Science ; Rural Development Administration ; Suwon ; 441-706 ; Republic of Korea
  8. Korean Bioinformation Center ; Korea Research Institute of Bioscience and Biotechnology ; Daejeon ; 305-806 ; Republic of Korea
  9. Department of Statistics ; Seoul National University ; Seoul ; Republic of Korea
  10. Animal Breeding and Genomics Centre ; Wageningen University ; De Elst 1 ; 6708 WD ; Wageningen ; The Netherlands
  11. Department of Integrative Biology and Department of Statistics ; University of California Berkeley ; Berkeley ; CA ; 94820 ; USA
  
• 关键词：Pig ; Domestication ; Selective sweep ; Directional selection ; Quantitative traits
• 刊名：BMC Genomics
• 出版年：2015
• 出版时间：December 2015
• 年：2015
• 卷：16
• 期：1
• 全文大小：3,246 KB
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• 刊物主题：Life Sciences, general; Microarrays; Proteomics; Animal Genetics and Genomics; Microbial Genetics and Genomics; Plant Genetics & Genomics;
• 出版者：BioMed Central
• ISSN：1471-2164

文摘

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.