Whole-genome analyses of Korean native and Holstein cattle breeds by massively parallel sequencing.
A main goal of cattle genomics is to identify DNA differences that account for variations in economically important traits. In this study, we performed whole-genome analyses of three important cattle breeds in Korea--Hanwoo, Jeju Heugu, and Korean Holstein--using the Illumina HiSeq 2000 sequencing p...
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doaj-e4bf66798b31451b953b14949f754a002020-11-25T02:05:17ZengPublic Library of Science (PLoS)PLoS ONE1932-62032014-01-0197e10112710.1371/journal.pone.0101127Whole-genome analyses of Korean native and Holstein cattle breeds by massively parallel sequencing.Jung-Woo ChoiXiaoping LiaoPaul StothardWon-Hyong ChungHeoyn-Jeong JeonStephen P MillerSo-Young ChoiJeong-Koo LeeBokyoung YangKyung-Tai LeeKwang-Jin HanHyeong-Cheol KimDongkee JeongJae-Don OhNamshin KimTae-Hun KimHak-Kyo LeeSung-Jin LeeA main goal of cattle genomics is to identify DNA differences that account for variations in economically important traits. In this study, we performed whole-genome analyses of three important cattle breeds in Korea--Hanwoo, Jeju Heugu, and Korean Holstein--using the Illumina HiSeq 2000 sequencing platform. We achieved 25.5-, 29.6-, and 29.5-fold coverage of the Hanwoo, Jeju Heugu, and Korean Holstein genomes, respectively, and identified a total of 10.4 million single nucleotide polymorphisms (SNPs), of which 54.12% were found to be novel. We also detected 1,063,267 insertions-deletions (InDels) across the genomes (78.92% novel). Annotations of the datasets identified a total of 31,503 nonsynonymous SNPs and 859 frameshift InDels that could affect phenotypic variations in traits of interest. Furthermore, genome-wide copy number variation regions (CNVRs) were detected by comparing the Hanwoo, Jeju Heugu, and previously published Chikso genomes against that of Korean Holstein. A total of 992, 284, and 1881 CNVRs, respectively, were detected throughout the genome. Moreover, 53, 65, 45, and 82 putative regions of homozygosity (ROH) were identified in Hanwoo, Jeju Heugu, Chikso, and Korean Holstein respectively. The results of this study provide a valuable foundation for further investigations to dissect the molecular mechanisms underlying variation in economically important traits in cattle and to develop genetic markers for use in cattle breeding.http://europepmc.org/articles/PMC4081042?pdf=render |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Jung-Woo Choi Xiaoping Liao Paul Stothard Won-Hyong Chung Heoyn-Jeong Jeon Stephen P Miller So-Young Choi Jeong-Koo Lee Bokyoung Yang Kyung-Tai Lee Kwang-Jin Han Hyeong-Cheol Kim Dongkee Jeong Jae-Don Oh Namshin Kim Tae-Hun Kim Hak-Kyo Lee Sung-Jin Lee |
spellingShingle |
Jung-Woo Choi Xiaoping Liao Paul Stothard Won-Hyong Chung Heoyn-Jeong Jeon Stephen P Miller So-Young Choi Jeong-Koo Lee Bokyoung Yang Kyung-Tai Lee Kwang-Jin Han Hyeong-Cheol Kim Dongkee Jeong Jae-Don Oh Namshin Kim Tae-Hun Kim Hak-Kyo Lee Sung-Jin Lee Whole-genome analyses of Korean native and Holstein cattle breeds by massively parallel sequencing. PLoS ONE |
author_facet |
Jung-Woo Choi Xiaoping Liao Paul Stothard Won-Hyong Chung Heoyn-Jeong Jeon Stephen P Miller So-Young Choi Jeong-Koo Lee Bokyoung Yang Kyung-Tai Lee Kwang-Jin Han Hyeong-Cheol Kim Dongkee Jeong Jae-Don Oh Namshin Kim Tae-Hun Kim Hak-Kyo Lee Sung-Jin Lee |
author_sort |
Jung-Woo Choi |
title |
Whole-genome analyses of Korean native and Holstein cattle breeds by massively parallel sequencing. |
title_short |
Whole-genome analyses of Korean native and Holstein cattle breeds by massively parallel sequencing. |
title_full |
Whole-genome analyses of Korean native and Holstein cattle breeds by massively parallel sequencing. |
title_fullStr |
Whole-genome analyses of Korean native and Holstein cattle breeds by massively parallel sequencing. |
title_full_unstemmed |
Whole-genome analyses of Korean native and Holstein cattle breeds by massively parallel sequencing. |
title_sort |
whole-genome analyses of korean native and holstein cattle breeds by massively parallel sequencing. |
publisher |
Public Library of Science (PLoS) |
series |
PLoS ONE |
issn |
1932-6203 |
publishDate |
2014-01-01 |
description |
A main goal of cattle genomics is to identify DNA differences that account for variations in economically important traits. In this study, we performed whole-genome analyses of three important cattle breeds in Korea--Hanwoo, Jeju Heugu, and Korean Holstein--using the Illumina HiSeq 2000 sequencing platform. We achieved 25.5-, 29.6-, and 29.5-fold coverage of the Hanwoo, Jeju Heugu, and Korean Holstein genomes, respectively, and identified a total of 10.4 million single nucleotide polymorphisms (SNPs), of which 54.12% were found to be novel. We also detected 1,063,267 insertions-deletions (InDels) across the genomes (78.92% novel). Annotations of the datasets identified a total of 31,503 nonsynonymous SNPs and 859 frameshift InDels that could affect phenotypic variations in traits of interest. Furthermore, genome-wide copy number variation regions (CNVRs) were detected by comparing the Hanwoo, Jeju Heugu, and previously published Chikso genomes against that of Korean Holstein. A total of 992, 284, and 1881 CNVRs, respectively, were detected throughout the genome. Moreover, 53, 65, 45, and 82 putative regions of homozygosity (ROH) were identified in Hanwoo, Jeju Heugu, Chikso, and Korean Holstein respectively. The results of this study provide a valuable foundation for further investigations to dissect the molecular mechanisms underlying variation in economically important traits in cattle and to develop genetic markers for use in cattle breeding. |
url |
http://europepmc.org/articles/PMC4081042?pdf=render |
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