中国科学院机构知识库网格
Chinese Academy of Sciences Institutional Repositories Grid
首页 机构 成果 学者
  
  1. CAS IR Grid
  2. 近代物理研究所
  3. 中国科学院近代物理研究所
  4. 生物物理研究室
Strategies for identification of mutations induced by carbon-ion beam irradiation in Arabidopsis thaliana by whole genome re-sequencing

文献类型：期刊论文

作者Wang, Jufang1; Du, Yan3; Luo, Shanwei2,3; Yu, Lixia3; Cui, Tao2,3; Chen, Xia2,3; Yang, Jiangyan3; Li, Xin3; Li, Wenjian3; Zhou, Libin3
刊名MUTATION RESEARCH-FUNDAMENTAL AND MOLECULAR MECHANISMS OF MUTAGENESIS
出版日期2018
卷号807页码:21-30
关键词Carbon-ion beam irradiation Whole genome re-sequencing Mutation Data sieving strategy Association analysis
ISSN号0027-5107
DOI10.1016/j.mrfmmm.2017.12.001
英文摘要Heavy-ion beam irradiation is a powerful physical mutagen that has been used to create numerous mutant materials in plants. These materials are an essential resource for functional genomics research in the post-genome era. The advent of Next-Generation Sequencing (NGS) technology has promoted the study of functional genomics and molecular breeding. A wealth of information can be gathered from whole genome re-sequencing; however, understanding the molecular mutation profile at genome wide, as well as identifying causal genes for a given phenotype are big challenging issues for researchers. The huge outputs created by NGS make it difficult to capture key information. It is worthy to explore an effective and efficient data-sieving strategy for mutation scanning at whole genome scale. Re-sequencing data from one laboratory wild type (Columbia) and eleven M-3 Arabidopsis thaliana lines derived from carbon-ion beam irradiation were used in present study. Both the number and different combinations of samples used for analysis affected the sieving results. The result indicated that using six samples was sufficient to filter out the shared mutation (background interference) sites as well as to identify the true mutation sites in the whole genome. The final number of candidate mutation sites could be further narrowed down by combining traditional rough map-based cloning. Our results demonstrated the feasibility of a parallel sequencing analysis as an efficient tool for the identification of mutations induced by carbon-ion beam irradiation. For the first time, we presented different analysis strategies for handling massive parallel sequencing data sets to detect the mutations induced by carbon-ion beam irradiation in Arabidopsis thaliana with low false-positive rate, as well as to identify the causative nucleotide changes responsible for a mutant phenotype.
WOS关键词QUANTITATIVE TRAIT LOCI ; LOTUS-JAPONICUS ; DNA ; MUTANT ; RICE ; POPULATIONS ; INDUCTION ; DISCOVERY ; GENETICS ; CLONING
资助项目National Key Research and Development Program[2016YFD0102106] ; Strategic Priority Research Program of the Chinese Academy of Sciences (CAS)[XDA08040111] ; National Natural Science Foundation of China[11405234] ; National Natural Science Foundation of China[U1432126] ; National Natural Science Foundation of China[11705249] ; Light of West China Program[Y506020] ; Light of West China Program[Y606020] ; Youth Innovation Promotion Association of the CAS[2015337] ; Science and Technology Research Project of Gansu Province[17JR5RA307]
WOS研究方向Biotechnology & Applied Microbiology ; Genetics & Heredity ; Toxicology
语种英语
WOS记录号WOS:000425137200003
出版者ELSEVIER SCIENCE BV
资助机构National Key Research and Development Program ; Strategic Priority Research Program of the Chinese Academy of Sciences (CAS) ; National Natural Science Foundation of China ; Light of West China Program ; Youth Innovation Promotion Association of the CAS ; Science and Technology Research Project of Gansu Province
源URL[http://119.78.100.186/handle/113462/46311]  
专题近代物理研究所_生物物理研究室
通讯作者Zhou, Libin
作者单位1.Chinese Acad Sci, Inst Modern Phys, Key Lab Space Radiobiol Gansu Prov, Lanzhou 730000, Gansu, Peoples R China
2.Univ Chinese Acad Sci, Coll Life Sci, Beijing 100049, Peoples R China
3.Chinese Acad Sci, Inst Modern Phys, Biophys Grp, Lanzhou 730000, Gansu, Peoples R China
推荐引用方式
GB/T 7714		 Wang, Jufang,Du, Yan,Luo, Shanwei,et al. Strategies for identification of mutations induced by carbon-ion beam irradiation in Arabidopsis thaliana by whole genome re-sequencing[J]. MUTATION RESEARCH-FUNDAMENTAL AND MOLECULAR MECHANISMS OF MUTAGENESIS,2018,807:21-30.
APA Wang, Jufang.,Du, Yan.,Luo, Shanwei.,Yu, Lixia.,Cui, Tao.,...&Zhou, Libin.(2018).Strategies for identification of mutations induced by carbon-ion beam irradiation in Arabidopsis thaliana by whole genome re-sequencing.MUTATION RESEARCH-FUNDAMENTAL AND MOLECULAR MECHANISMS OF MUTAGENESIS,807,21-30.
MLA Wang, Jufang,et al."Strategies for identification of mutations induced by carbon-ion beam irradiation in Arabidopsis thaliana by whole genome re-sequencing".MUTATION RESEARCH-FUNDAMENTAL AND MOLECULAR MECHANISMS OF MUTAGENESIS 807(2018):21-30.

入库方式： OAI收割

来源：近代物理研究所

浏览0
下载0
收藏0
其他版本

除非特别说明，本系统中所有内容都受版权保护，并保留所有权利。