Strategies for identification of mutations induced by carbon-ion beam irradiation in Arabidopsis thaliana by whole genome re-sequencing

doi:10.1016/j.mrfmmm.2017.12.001

	Strategies for identification of mutations induced by carbon-ion beam irradiation in Arabidopsis thaliana by whole genome re-sequencing
	Wang, Jufang1 ; Du, Yan3 ; Luo, Shanwei 2,3; Yu, Lixia3 ; Cui, Tao 2,3; Chen, Xia 2,3; Yang, Jiangyan3 ; Li, Xin3 ; Li, Wenjian3 ; Zhou, Libin 3
刊名	MUTATION RESEARCH-FUNDAMENTAL AND MOLECULAR MECHANISMS OF MUTAGENESIS
	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
DOI	10.1016/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.
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关键词	QUANTITATIVE TRAIT LOCI ; LOTUS-JAPONICUS ; DNA ; MUTANT ; RICE ; POPULATIONS ; INDUCTION ; DISCOVERY ; GENETICS ; CLONING
WOS研究方向	Biotechnology & Applied Microbiology ; Genetics & Heredity ; Toxicology
语种	英语
出版者	ELSEVIER SCIENCE BV
WOS记录号	WOS:000425137200003
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
内容类型	期刊论文
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.