Discovery of rare mutations in extensively pooled DNA samples using multiple target enrichment
文献类型：期刊论文
| 作者 | Chi, Xu1; Zhang, Yingchun; Xue, Zheyong; Feng, Laibao; Liu, Huaqing2; Wang, Feng2; Qi, Xiaoquan
|
| 刊名 | PLANT BIOTECHNOLOGY JOURNAL
 |
| 出版日期 | 2014 |
| 卷号 | 12期号:6页码:709-717 |
| 关键词 | NGS induced mutation detection large samples pooling multiplexed target enrichment |
| ISSN号 | 1467-7644 |
| DOI | 10.1111/pbi.12174 |
| 文献子类 | Article |
| 英文摘要 | Chemical mutagenesis is routinely used to create large numbers of rare mutations in plant and animal populations, which can be subsequently subjected to selection for beneficial traits and phenotypes that enable the characterization of gene functions. Several next-generation sequencing (NGS)-based target enrichment methods have been developed for the detection of mutations in target DNA regions. However, most of these methods aim to sequence a large number of target regions from a small number of individuals. Here, we demonstrate an effective and affordable strategy for the discovery of rare mutations in a large sodium azide-induced mutant rice population (F-2). The integration of multiplex, semi-nested PCR combined with NGS library construction allowed for the amplification of multiple target DNA fragments for sequencing. The 8 x 8 x 8 tridimensional DNA sample pooling strategy enabled us to obtain DNA sequences of 512 individuals while only sequencing 24 samples. A stepwise filtering procedure was then elaborated to eliminate most of the false positives expected to arise through sequencing error, and the application of a simple Student's t-test against position-prone error allowed for the discovery of 16 mutations from 36 enriched targeted DNA fragments of 1024 mutagenized rice plants, all without any false calls. |
| 学科主题 | Biotechnology & Applied Microbiology ; Plant Sciences |
| 出版地 | HOBOKEN |
| 电子版国际标准刊号 | 1467-7652 |
| WOS关键词 | POPULATIONS ; PCR ; POLYMORPHISMS ; AMPLIFICATION ; GENERATION ; GENES ; AZIDE |
| WOS研究方向 | Biotechnology & Applied Microbiology ; Plant Sciences |
| 语种 | 英语 |
| WOS记录号 | WOS:000339488200007 |
| 出版者 | WILEY |
| 资助机构 | National Transgenic Megaproject of China [2013ZX08009001] ; Chinese National Programs for Fundamental Research and Development [2013CB127000] |
| 源URL | [http://ir.ibcas.ac.cn/handle/2S10CLM1/27271]  |
| 专题 | 中科院植物分子生理学重点实验室 |
| 作者单位 | 1.Chinese Acad Sci, Inst Bot, Key Lab Plant Mol Physiol, Beijing, Peoples R China 2.Chinese Acad Sci, Grad Univ, Beijing, Peoples R China 3.Fujian Acad Agr Sci, Fujian Prov Key Lab Genet Engn Agr, Fuzhou, Peoples R China |
| 推荐引用方式 GB/T 7714 | Chi, Xu,Zhang, Yingchun,Xue, Zheyong,et al. Discovery of rare mutations in extensively pooled DNA samples using multiple target enrichment[J]. PLANT BIOTECHNOLOGY JOURNAL,2014,12(6):709-717. |
| APA | Chi, Xu.,Zhang, Yingchun.,Xue, Zheyong.,Feng, Laibao.,Liu, Huaqing.,...&Qi, Xiaoquan.(2014).Discovery of rare mutations in extensively pooled DNA samples using multiple target enrichment.PLANT BIOTECHNOLOGY JOURNAL,12(6),709-717. |
| MLA | Chi, Xu,et al."Discovery of rare mutations in extensively pooled DNA samples using multiple target enrichment".PLANT BIOTECHNOLOGY JOURNAL 12.6(2014):709-717. |
入库方式： OAI收割
来源：植物研究所
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