Whole-genome resequencing shows numerous genes with nonsynonymous SNPs in the Japanese native cattle Kuchinoshima-Ushi.
Whole-genome resequencing shows numerous genes with nonsynonymous SNPs in the Japanese native cattle Kuchinoshima-Ushi.
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DOI：
10.1186/1471-2164-12-103
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发表时间：
2011-02-10
期刊：
影响因子：
4.4
通讯作者：
Kono T
中科院分区：
文献类型：
--
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
由于日本本土牛Kuchinoshima-Ushi被隔离在一个小岛上，并且它们的血统受到了严格的保护，因此迄今为止，人们认为在这个牛品种中保存了许多有价值的基因组变异。在这项研究中，我们评估了这个品种的遗传特征，包括单核苷酸多态性（SNP）的信息，全基因组测序使用基因组分析仪II。总共产生64.2Gb的序列，其中86%的获得的读段用BWA成功地映射到参考序列（Btau 4.0）。平均而言，93%的基因组被读段覆盖，并且映射读段的数量对应于覆盖区域的15.8倍覆盖。从这些数据中，我们确定了630万个SNP，其中超过550万个（87%）是新的。在牛序列组装中注释的SNP中，在蛋白质编码区中发现了20，432个，其中包含4，643个基因中的11，713个非同义SNP。此外，系统发育分析使用的序列数据从10个基因（超过10 kbp）表明，Kuchinoshima-Ushi是明显不同于欧洲国内品种的牛。这些结果为进一步研究Kuchinoshima-Ushi群体的遗传学和含SNP基因的功能提供了框架，这将有助于理解牛重要经济性状表型变异的分子基础，并有助于改善国内牛品种的内在缺陷。
Because the Japanese native cattle Kuchinoshima-Ushi have been isolated in a small island and their lineage has been intensely protected, it has been assumed to date that numerous and valuable genomic variations are conserved in this cattle breed. In this study, we evaluated genetic features of this breed, including single nucleotide polymorphism (SNP) information, by whole-genome sequencing using a Genome Analyzer II. A total of 64.2 Gb of sequence was generated, of which 86% of the obtained reads were successfully mapped to the reference sequence (Btau 4.0) with BWA. On an average, 93% of the genome was covered by the reads and the number of mapped reads corresponded to 15.8-fold coverage across the covered region. From these data, we identified 6.3 million SNPs, of which more than 5.5 million (87%) were found to be new. Out of the SNPs annotated in the bovine sequence assembly, 20,432 were found in protein-coding regions containing 11,713 nonsynonymous SNPs in 4,643 genes. Furthermore, phylogenetic analysis using sequence data from 10 genes (more than 10 kbp) showed that Kuchinoshima-Ushi is clearly distinct from European domestic breeds of cattle. These results provide a framework for further genetic studies in the Kuchinoshima-Ushi population and research on functions of SNP-containing genes, which would aid in understanding the molecular basis underlying phenotypic variation of economically important traits in cattle and in improving intrinsic defects in domestic cattle breeds.
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影响因子：
2.9
作者：
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