Whole-Genome Resequencing Analysis of Hanwoo and Yanbian Cattle to Identify Genome-Wide SNPs and Signatures of Selection.
Whole-Genome Resequencing Analysis of Hanwoo and Yanbian Cattle to Identify Genome-Wide SNPs and Signatures of Selection.
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DOI：
10.14348/molcells.2015.0019
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发表时间：
2015-05
影响因子：
3.8
通讯作者：
Lim D
中科院分区：
文献类型：
--
作者：
Choi JW;Choi BH;Lee SH;Lee SS;Kim HC;Yu D;Chung WH;Lee KT;Chai HH;Cho YM;Lim D
在过去的30年里，为了提高重要的经济性状，人们选择性地培育了韩宇。韩牛是目前具有代表性的韩国本土肉牛品种，据信，直到上个世纪，它与中国的延边牛有共同的祖先。然而，近几十年来，这两个品种经历了不同的选择压力。在这里，我们使用Illumina HiSeq 2000测序仪对汉宇牛和延边牛各10头（共20头）进行了全基因组测序。共有31.2和30.7亿个序列被映射到牛参考序列汇编（UMD 3.1）上，汉宇牛和延边牛的平均覆盖率分别约为10.71和10.53倍。共获得17936,399个单核苷酸多态性（snp），其中22.3%为新多态性。通过注释SNPs，我们进一步检索了许多可能与牛感兴趣的性状相关的非同义SNPs。此外，我们进行了全基因组筛选，以检测整个基因组的选择特征。我们找到了几种有希望的选择性清除，它们可能对牛的重要经济性状负责；PPP1R12A基因是一个可能影响肌内脂肪含量的基因的例子。这些发现为潜在的基因组标记提供了有价值的基因组信息，这些基因组标记可以预测这些牛品种的育种计划感兴趣的性状。
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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影响因子：
4.4
作者：
Kawahara-Miki R;Tsuda K;Shiwa Y;Arai-Kichise Y;Matsumoto T;Kanesaki Y;Oda S;Ebihara S;Yajima S;Yoshikawa H;Kono T
通讯作者：
Kono T
影响因子：
1.2
作者：
Cingolani, Pablo;Platts, Adrian;Ruden, Douglas M.
通讯作者：
Ruden, Douglas M.
影响因子：
30.8
作者：
Daetwyler, Hans D.;Capitan, Aurelien;Hayes, Ben J.
通讯作者：
Hayes, Ben J.
影响因子：
2.1
作者：
Dadi, Hailu;Lee, Seung-Hwan;Kim, Kwan-Suk
通讯作者：
Kim, Kwan-Suk
DOI：
10.1093/bioinformatics/btp698
发表时间：
2010-03-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Li H;Durbin R
通讯作者：
Durbin R