Genome-wide genetic variation discovery in Chinese Taihu pig breeds using next generation sequencing.
Genome-wide genetic variation discovery in Chinese Taihu pig breeds using next generation sequencing.
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利用下一代测序发现中国太湖猪品种的全基因组遗传变异
DOI：
10.1111/age.12465
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发表时间：
2017-02
期刊：
影响因子：
2.4
通讯作者：
Pan Y
中科院分区：
文献类型：
--
作者：
Wang Z;Chen Q;Liao R;Zhang Z;Zhang X;Liu X;Zhu M;Zhang W;Xue M;Yang H;Zheng Y;Wang Q;Pan Y
中国太湖猪品种是世界猪遗传资源的宝贵组成部分，是世界上最多产的猪品种。本研究采用基因组还原测序法对太湖地区6个地方猪种的252头猪进行了基因组测序。使用Illumina Hiseq 2000以13×的平均深度（对于SNP调用）和2.3%的平均覆盖度获得总共9.5亿个良好读段。在猪的基因组中总共鉴定了122 632个indel，31 444个插入，44 056个缺失和455个CNV（拷贝数变异）。这些遗传标记中约2.3%定位在基因外显子区域，25%定位在与经济性状相关的QTL区域。KEGG途径或GO富集分析显示，被认为是大效应突变的遗传变异在22个SNP、56个indel、26个插入、28个缺失和3个CNV基因集中显著过量。在6头中国本土猪中共鉴定出343个品种特异性SNPs。本研究的结果有助于进一步从基因组水平研究这些猪的遗传多样性、群体结构、正选择信号和分子进化史，并为改进这些猪的育种和养殖提供有价值的参考。
The Chinese Taihu pig breeds are an invaluable component of the world's pig genetic resources, and they are the most prolific breeds of swine in the world. In this study, the genomes of 252 pigs of the six indigenous breeds in the Taihu Lake region were sequenced using the genotyping by genome reducing and sequencing approach. A total of 950 million good reads were obtained using an Illumina Hiseq2000 at an average depth of 13× (for SNP calling) and an average coverage of 2.3%. In total, 122 632 indels, 31 444 insertions, 44 056 deletions and 455 CNVs (copy number variants) were identified in the genomes of the pigs. Approximately 2.3% of these genetic markers were mapped to gene exon regions, and 25% were in QTL regions related to economically important traits. The KEGG pathway or GO enrichment analyses revealed that genetic variants assumed to be large‐effect mutations were significantly overrepresented in 22 SNP, 56 indel, 26 insertion, 28 deletion and three CNV gene sets. A total of 343 breed‐specific SNPs were also identified in the six Chinese indigenous pigs. The findings from this study can contribute to future investigations of the genetic diversity, population structure, positive selection signals and molecular evolutionary history of these pigs at the genome level and can serve as a valuable reference for improving the breeding and cultivation of these pigs.