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Whole-genome resequencing analyses of five pig breeds, including Korean wild and native, and three European origin breeds

Pigs have been one of the most important sources of meat for humans, and their productivity has been substantially improved by recent strong selection. Here, we present whole-genome resequencing analyses of 55 pigs of five breeds representing Korean native pigs, wild boar and three European origin b...

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Autores principales: Choi, Jung-Woo, Chung, Won-Hyong, Lee, Kyung-Tai, Cho, Eun-Seok, Lee, Si-Woo, Choi, Bong-Hwan, Lee, Sang-Heon, Lim, Wonjun, Lim, Dajeong, Lee, Yun-Gyeong, Hong, Joon-Ki, Kim, Doo-Wan, Jeon, Hyeon-Jeong, Kim, Jiwoong, Kim, Namshin, Kim, Tae-Hun
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4535618/
https://www.ncbi.nlm.nih.gov/pubmed/26117497
http://dx.doi.org/10.1093/dnares/dsv011
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author Choi, Jung-Woo
Chung, Won-Hyong
Lee, Kyung-Tai
Cho, Eun-Seok
Lee, Si-Woo
Choi, Bong-Hwan
Lee, Sang-Heon
Lim, Wonjun
Lim, Dajeong
Lee, Yun-Gyeong
Hong, Joon-Ki
Kim, Doo-Wan
Jeon, Hyeon-Jeong
Kim, Jiwoong
Kim, Namshin
Kim, Tae-Hun
author_facet Choi, Jung-Woo
Chung, Won-Hyong
Lee, Kyung-Tai
Cho, Eun-Seok
Lee, Si-Woo
Choi, Bong-Hwan
Lee, Sang-Heon
Lim, Wonjun
Lim, Dajeong
Lee, Yun-Gyeong
Hong, Joon-Ki
Kim, Doo-Wan
Jeon, Hyeon-Jeong
Kim, Jiwoong
Kim, Namshin
Kim, Tae-Hun
author_sort Choi, Jung-Woo
collection PubMed
description Pigs have been one of the most important sources of meat for humans, and their productivity has been substantially improved by recent strong selection. Here, we present whole-genome resequencing analyses of 55 pigs of five breeds representing Korean native pigs, wild boar and three European origin breeds. 1,673.1 Gb of sequence reads were mapped to the Swine reference assembly, covering ∼99.2% of the reference genome, at an average of ∼11.7-fold coverage. We detected 20,123,573 single-nucleotide polymorphisms (SNPs), of which 25.5% were novel. We extracted 35,458 of non-synonymous SNPs in 9,904 genes, which may contribute to traits of interest. The whole SNP sets were further used to access the population structures of the breeds, using multiple methodologies, including phylogenetic, similarity matrix, and population structure analysis. They showed clear population clusters with respect to each breed. Furthermore, we scanned the whole genomes to identify signatures of selection throughout the genome. The result revealed several promising loci that might underlie economically important traits in pigs, such as the CLDN1 and TWIST1 genes. These discoveries provide useful genomic information for further study of the discrete genetic mechanisms associated with economically important traits in pigs.
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spelling pubmed-45356182015-08-17 Whole-genome resequencing analyses of five pig breeds, including Korean wild and native, and three European origin breeds Choi, Jung-Woo Chung, Won-Hyong Lee, Kyung-Tai Cho, Eun-Seok Lee, Si-Woo Choi, Bong-Hwan Lee, Sang-Heon Lim, Wonjun Lim, Dajeong Lee, Yun-Gyeong Hong, Joon-Ki Kim, Doo-Wan Jeon, Hyeon-Jeong Kim, Jiwoong Kim, Namshin Kim, Tae-Hun DNA Res Full Papers Pigs have been one of the most important sources of meat for humans, and their productivity has been substantially improved by recent strong selection. Here, we present whole-genome resequencing analyses of 55 pigs of five breeds representing Korean native pigs, wild boar and three European origin breeds. 1,673.1 Gb of sequence reads were mapped to the Swine reference assembly, covering ∼99.2% of the reference genome, at an average of ∼11.7-fold coverage. We detected 20,123,573 single-nucleotide polymorphisms (SNPs), of which 25.5% were novel. We extracted 35,458 of non-synonymous SNPs in 9,904 genes, which may contribute to traits of interest. The whole SNP sets were further used to access the population structures of the breeds, using multiple methodologies, including phylogenetic, similarity matrix, and population structure analysis. They showed clear population clusters with respect to each breed. Furthermore, we scanned the whole genomes to identify signatures of selection throughout the genome. The result revealed several promising loci that might underlie economically important traits in pigs, such as the CLDN1 and TWIST1 genes. These discoveries provide useful genomic information for further study of the discrete genetic mechanisms associated with economically important traits in pigs. Oxford University Press 2015-08 2015-06-27 /pmc/articles/PMC4535618/ /pubmed/26117497 http://dx.doi.org/10.1093/dnares/dsv011 Text en © The Author 2015. Published by Oxford University Press on behalf of Kazusa DNA Research Institute. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Full Papers
Choi, Jung-Woo
Chung, Won-Hyong
Lee, Kyung-Tai
Cho, Eun-Seok
Lee, Si-Woo
Choi, Bong-Hwan
Lee, Sang-Heon
Lim, Wonjun
Lim, Dajeong
Lee, Yun-Gyeong
Hong, Joon-Ki
Kim, Doo-Wan
Jeon, Hyeon-Jeong
Kim, Jiwoong
Kim, Namshin
Kim, Tae-Hun
Whole-genome resequencing analyses of five pig breeds, including Korean wild and native, and three European origin breeds
title Whole-genome resequencing analyses of five pig breeds, including Korean wild and native, and three European origin breeds
title_full Whole-genome resequencing analyses of five pig breeds, including Korean wild and native, and three European origin breeds
title_fullStr Whole-genome resequencing analyses of five pig breeds, including Korean wild and native, and three European origin breeds
title_full_unstemmed Whole-genome resequencing analyses of five pig breeds, including Korean wild and native, and three European origin breeds
title_short Whole-genome resequencing analyses of five pig breeds, including Korean wild and native, and three European origin breeds
title_sort whole-genome resequencing analyses of five pig breeds, including korean wild and native, and three european origin breeds
topic Full Papers
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4535618/
https://www.ncbi.nlm.nih.gov/pubmed/26117497
http://dx.doi.org/10.1093/dnares/dsv011
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