Time Course Analysis of Genome-Wide Identification of Mutations Induced by and Genes Expressed in Response to Carbon Ion Beam Irradiation in Rice (Oryza sativa L.)

doi:10.3390/genes12091391

	Time Course Analysis of Genome-Wide Identification of Mutations Induced by and Genes Expressed in Response to Carbon Ion Beam Irradiation in Rice (Oryza sativa L.)
	Zhang, Jian 2; Peng, Ziai 2; Liu, Qiling 2; Yang, Guili 2; Zhou, Libin 1; Li, Wenjian 1; Wang, Hui 2; Chen, Zhiqiang 2; Guo, Tao 2
刊名	GENES
	2021-09-01
卷号	12 期号:9 页码:15
关键词	carbon ion beam (CIB) whole-genome sequencing (WGS) RNA-seq mutation characteristics initial DNA damage DNA repair-related genes
DOI	10.3390/genes12091391
通讯作者	Guo, Tao(guoguot@scau.edu.cn)
英文摘要	Heavy-ion irradiation is a powerful mutagen and is widely used for mutation breeding. In this study, using whole-genome sequencing (WGS) and RNA sequencing (RNA-seq) techniques, we comprehensively characterized these dynamic changes caused by mutations at three time points (48, 96, and 144 h after irradiation) and the expression profiles of rice seeds irradiated with C ions at two doses. Subsequent WGS analysis revealed that more mutations were detected in response to 40 Gy carbon ion beam (CIB) irradiation than 80 Gy of CIB irradiation at the initial stage (48 h post-irradiation). In the mutants generated from both irradiation doses, single-base substitutions (SBSs) were the most frequent type of mutation induced by CIB irradiation. Among the mutations, the predominant ones were C:T and A:G transitions. CIB irradiation also induced many short InDel mutations. RNA-seq analysis at the three time points showed that the number of differentially expressed genes (DEGs) was highest at 48 h post-irradiation. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of the DEGs showed that the "replication and repair" pathway was enriched specifically 48 h post-irradiation. These results indicate that the DNA damage response (DDR) and the mechanism of DNA repair tend to quickly start within the initial stage (48 h) after irradiation.
资助项目	Key Research and Development Project of Guangdong Province[2018B020206002] ; Molecular Characteristics of Rice Genomic Variation Induced by Carbon Ion Beam Radiation ; National Key Technology Research and Development Program of China[2016YFD0102102] ; earmarked fund for the Modern Agro-Industry Technology Research System[CARS-01-12]
WOS关键词	CLUSTERED DNA-DAMAGE ; ARABIDOPSIS ; REPAIR ; MAINTAINS ; SPECTRUM ; RECA
WOS研究方向	Genetics & Heredity
语种	英语
出版者	MDPI
WOS记录号	WOS:000699683500001
资助机构	Key Research and Development Project of Guangdong Province ; Molecular Characteristics of Rice Genomic Variation Induced by Carbon Ion Beam Radiation ; National Key Technology Research and Development Program of China ; earmarked fund for the Modern Agro-Industry Technology Research System
内容类型	期刊论文
源URL	[http://119.78.100.186/handle/113462/136273]
专题	中国科学院近代物理研究所
通讯作者	Guo, Tao
作者单位	1.Chinese Acad Sci, Inst Modern Phys, Lanzhou 730000, Peoples R China 2.South China Agr Univ, Natl Engn Res Ctr Plant Space Breeding, Guangzhou 510642, Peoples R China
推荐引用方式 GB/T 7714	Zhang, Jian,Peng, Ziai,Liu, Qiling,et al. Time Course Analysis of Genome-Wide Identification of Mutations Induced by and Genes Expressed in Response to Carbon Ion Beam Irradiation in Rice (Oryza sativa L.)[J]. GENES,2021,12(9):15.
APA	Zhang, Jian.,Peng, Ziai.,Liu, Qiling.,Yang, Guili.,Zhou, Libin.,...&Guo, Tao.(2021).Time Course Analysis of Genome-Wide Identification of Mutations Induced by and Genes Expressed in Response to Carbon Ion Beam Irradiation in Rice (Oryza sativa L.).GENES,12(9),15.
MLA	Zhang, Jian,et al."Time Course Analysis of Genome-Wide Identification of Mutations Induced by and Genes Expressed in Response to Carbon Ion Beam Irradiation in Rice (Oryza sativa L.)".GENES 12.9(2021):15.