A genome-wide scan for signatures of directional selection in domesticated pigs
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A genome-wide scan for signatures of directional selection in domesticated pigs. / Moon, Sunjin; Kim, Tae Hun; Lee, Kyung Tai; Kwak, Woori; Lee, Taeheon; Lee, Si Woo; Kim, Myung Jick; Cho, Kyuho; Kim, Namshin; Chung, Won Hyong; Sung, Samsun; Park, Taesung; Cho, Seoae; Groenen, Martien A.M.; Nielsen, Rasmus; Kim, Yuseob; Kim, Heebal.
In: BMC Genomics, Vol. 16, No. 1, 130, 25.02.2015.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - A genome-wide scan for signatures of directional selection in domesticated pigs
AU - Moon, Sunjin
AU - Kim, Tae Hun
AU - Lee, Kyung Tai
AU - Kwak, Woori
AU - Lee, Taeheon
AU - Lee, Si Woo
AU - Kim, Myung Jick
AU - Cho, Kyuho
AU - Kim, Namshin
AU - Chung, Won Hyong
AU - Sung, Samsun
AU - Park, Taesung
AU - Cho, Seoae
AU - Groenen, Martien A.M.
AU - Nielsen, Rasmus
AU - Kim, Yuseob
AU - Kim, Heebal
PY - 2015/2/25
Y1 - 2015/2/25
N2 - 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 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. 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.
AB - 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 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. 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.
KW - Directional selection
KW - Domestication
KW - Pig
KW - Quantitative traits
KW - Selective sweep
UR - http://www.scopus.com/inward/record.url?scp=84924136440&partnerID=8YFLogxK
U2 - 10.1186/s12864-015-1330-x
DO - 10.1186/s12864-015-1330-x
M3 - Journal article
C2 - 25765548
AN - SCOPUS:84924136440
VL - 16
JO - BMC Genomics
JF - BMC Genomics
SN - 1471-2164
IS - 1
M1 - 130
ER -
ID: 222642246