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Whole-Genome Resequencing Analysis of Hanwoo and Yanbian Cattle to Identify Genome-Wide SNPs and Signatures of Selection

Over the last 30 years, Hanwoo has been selectively bred to improve economically important traits. Hanwoo is currently the representative Korean native beef cattle breed, and it is believed that it shared an ancestor with a Chinese breed, Yanbian cattle, until the last century. However, these two br...

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Autores principales: Choi, Jung-Woo, Choi, Bong-Hwan, Lee, Seung-Hwan, Lee, Seung-Soo, Kim, Hyeong-Cheol, Yu, Dayeong, Chung, Won-Hyong, Lee, Kyung-Tai, Chai, Han-Ha, Cho, Yong-Min, Lim, Dajeong
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Korean Society for Molecular and Cellular Biology 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4443289/
https://www.ncbi.nlm.nih.gov/pubmed/26018558
http://dx.doi.org/10.14348/molcells.2015.0019
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author Choi, Jung-Woo
Choi, Bong-Hwan
Lee, Seung-Hwan
Lee, Seung-Soo
Kim, Hyeong-Cheol
Yu, Dayeong
Chung, Won-Hyong
Lee, Kyung-Tai
Chai, Han-Ha
Cho, Yong-Min
Lim, Dajeong
author_facet Choi, Jung-Woo
Choi, Bong-Hwan
Lee, Seung-Hwan
Lee, Seung-Soo
Kim, Hyeong-Cheol
Yu, Dayeong
Chung, Won-Hyong
Lee, Kyung-Tai
Chai, Han-Ha
Cho, Yong-Min
Lim, Dajeong
author_sort Choi, Jung-Woo
collection PubMed
description Over the last 30 years, Hanwoo has been selectively bred to improve economically important traits. Hanwoo is currently the representative Korean native beef cattle breed, and it is believed that it shared an ancestor with a Chinese breed, Yanbian cattle, until the last century. However, these two breeds have experienced different selection pressures during recent decades. Here, we whole-genome sequenced 10 animals each of Hanwoo and Yanbian cattle (20 total) using the Illumina HiSeq 2000 sequencer. A total of approximately 3.12 and 3.07 billion sequence reads were mapped to the bovine reference sequence assembly (UMD 3.1) at an average of approximately 10.71- and 10.53-fold coverage for Hanwoo and Yanbian cattle, respectively. A total of 17,936,399 single nucleotide polymorphisms (SNPs) were yielded, of which 22.3% were found to be novel. By annotating the SNPs, we further retrieved numerous nonsynonymous SNPs that may be associated with traits of interest in cattle. Furthermore, we performed whole-genome screening to detect signatures of selection throughout the genome. We located several promising selective sweeps that are potentially responsible for economically important traits in cattle; the PPP1R12A gene is an example of a gene that potentially affects intramuscular fat content. These discoveries provide valuable genomic information regarding potential genomic markers that could predict traits of interest for breeding programs of these cattle breeds.
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spelling pubmed-44432892015-06-01 Whole-Genome Resequencing Analysis of Hanwoo and Yanbian Cattle to Identify Genome-Wide SNPs and Signatures of Selection Choi, Jung-Woo Choi, Bong-Hwan Lee, Seung-Hwan Lee, Seung-Soo Kim, Hyeong-Cheol Yu, Dayeong Chung, Won-Hyong Lee, Kyung-Tai Chai, Han-Ha Cho, Yong-Min Lim, Dajeong Mol Cells Article Over the last 30 years, Hanwoo has been selectively bred to improve economically important traits. Hanwoo is currently the representative Korean native beef cattle breed, and it is believed that it shared an ancestor with a Chinese breed, Yanbian cattle, until the last century. However, these two breeds have experienced different selection pressures during recent decades. Here, we whole-genome sequenced 10 animals each of Hanwoo and Yanbian cattle (20 total) using the Illumina HiSeq 2000 sequencer. A total of approximately 3.12 and 3.07 billion sequence reads were mapped to the bovine reference sequence assembly (UMD 3.1) at an average of approximately 10.71- and 10.53-fold coverage for Hanwoo and Yanbian cattle, respectively. A total of 17,936,399 single nucleotide polymorphisms (SNPs) were yielded, of which 22.3% were found to be novel. By annotating the SNPs, we further retrieved numerous nonsynonymous SNPs that may be associated with traits of interest in cattle. Furthermore, we performed whole-genome screening to detect signatures of selection throughout the genome. We located several promising selective sweeps that are potentially responsible for economically important traits in cattle; the PPP1R12A gene is an example of a gene that potentially affects intramuscular fat content. These discoveries provide valuable genomic information regarding potential genomic markers that could predict traits of interest for breeding programs of these cattle breeds. Korean Society for Molecular and Cellular Biology 2015-05-31 2015-05-15 /pmc/articles/PMC4443289/ /pubmed/26018558 http://dx.doi.org/10.14348/molcells.2015.0019 Text en © The Korean Society for Molecular and Cellular Biology. All rights reserved. This is an open-access article distributed under the terms of the Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-sa/3.0/
spellingShingle Article
Choi, Jung-Woo
Choi, Bong-Hwan
Lee, Seung-Hwan
Lee, Seung-Soo
Kim, Hyeong-Cheol
Yu, Dayeong
Chung, Won-Hyong
Lee, Kyung-Tai
Chai, Han-Ha
Cho, Yong-Min
Lim, Dajeong
Whole-Genome Resequencing Analysis of Hanwoo and Yanbian Cattle to Identify Genome-Wide SNPs and Signatures of Selection
title Whole-Genome Resequencing Analysis of Hanwoo and Yanbian Cattle to Identify Genome-Wide SNPs and Signatures of Selection
title_full Whole-Genome Resequencing Analysis of Hanwoo and Yanbian Cattle to Identify Genome-Wide SNPs and Signatures of Selection
title_fullStr Whole-Genome Resequencing Analysis of Hanwoo and Yanbian Cattle to Identify Genome-Wide SNPs and Signatures of Selection
title_full_unstemmed Whole-Genome Resequencing Analysis of Hanwoo and Yanbian Cattle to Identify Genome-Wide SNPs and Signatures of Selection
title_short Whole-Genome Resequencing Analysis of Hanwoo and Yanbian Cattle to Identify Genome-Wide SNPs and Signatures of Selection
title_sort whole-genome resequencing analysis of hanwoo and yanbian cattle to identify genome-wide snps and signatures of selection
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4443289/
https://www.ncbi.nlm.nih.gov/pubmed/26018558
http://dx.doi.org/10.14348/molcells.2015.0019
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