Identification of Substitutions and Small Insertion-Deletions Induced by Carbon-Ion Beam Irradiation in Arabidopsis thaliana.
Identification of Substitutions and Small Insertion-Deletions Induced by Carbon-Ion Beam Irradiation in Arabidopsis thaliana.
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拟南芥中碳离子束照射诱导的取代和小插入缺失的鉴定。
DOI：
10.3389/fpls.2017.01851
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发表时间：
2017
影响因子：
5.6
通讯作者：
Zhou L
中科院分区：
文献类型：
--
作者：
Du Y;Luo S;Li X;Yang J;Cui T;Li W;Yu L;Feng H;Chen Y;Mu J;Chen X;Shu Q;Guo T;Luo W;Zhou L
重离子束辐照是在植物中制造突变体的主要方法之一。辐射诱变效应及其分子机制的研究是一个多学科交叉的重要课题。本研究对11个碳离子束辐照诱变后代（M3）拟南芥系进行了重测序，并对其进行了替换和小插入缺失（INDELs）分析。我们发现CIB诱导的替换（320个）多于INDELs（124个）。同时，单碱基indel比大碱基indel（≥2 bp）多见。具体来说，检测到的取代通过激活DNA序列中相邻嘧啶残基之间的共价键形成，显示出明显的C > T过渡的偏倚。在单碱基INDELs中观察到A和T偏倚，其中大多数是由均聚物或多核苷酸重复区域的复制滑移引起的。估计200-Gy CIB辐照的突变率为3.37 × 10−7 /位点。与以往的研究主要集中在表型、染色体畸变、遗传多态性或特定基因的测序分析不同，我们的研究揭示了CIB辐照诱导的全基因组分子谱和突变率。我们希望这些数据能够为解释CIB辐照植物诱变育种的潜在机制提供有价值的线索。
Heavy-ion beam irradiation is one of the principal methods used to create mutants in plants. Research on mutagenic effects and molecular mechanisms of radiation is an important subject that is multi-disciplinary. Here, we re-sequenced 11 mutagenesis progeny (M3) Arabidopsis thaliana lines derived from carbon-ion beam (CIB) irradiation, and subsequently focused on substitutions and small insertion-deletion (INDELs). We found that CIB induced more substitutions (320) than INDELs (124). Meanwhile, the single base INDELs were more prevalent than those in large size (≥2 bp). In details, the detected substitutions showed an obvious bias of C > T transitions, by activating the formation of covalent linkages between neighboring pyrimidine residues in the DNA sequence. An A and T bias was observed among the single base INDELs, in which most of these were induced by replication slippage at either the homopolymer or polynucleotide repeat regions. The mutation rate of 200-Gy CIB irradiation was estimated as 3.37 × 10−7 per site. Different from previous researches which mainly focused on the phenotype, chromosome aberration, genetic polymorphism, or sequencing analysis of specific genes only, our study revealed genome-wide molecular profile and rate of mutations induced by CIB irradiation. We hope our data could provide valuable clues for explaining the potential mechanism of plant mutation breeding by CIB irradiation.
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影响因子：
7.2
作者：
Hirano, Tomonari;Kazama, Yusuke;Abe, Tomoko
通讯作者：
Abe, Tomoko
影响因子：
4.6
作者：
Nagata K;Hashimoto C;Watanabe-Asaka T;Itoh K;Yasuda T;Ohta K;Oonishi H;Igarashi K;Suzuki M;Funayama T;Kobayashi Y;Nishimaki T;Katsumura T;Oota H;Ogawa M;Oga A;Ikemoto K;Itoh H;Kutsuna N;Oda S;Mitani H
通讯作者：
Mitani H
影响因子：
5.3
作者：
Kazama Y;Hirano T;Saito H;Liu Y;Ohbu S;Hayashi Y;Abe T
通讯作者：
Abe T
DOI：
10.1016/j.nimb.2016.06.021
发表时间：
2016-09-15
影响因子：
1.3
作者：
Luo, Shanwei;Zhou, Libin;Chen, Yuze
通讯作者：
Chen, Yuze
影响因子：
12.3
作者：
Langmead B;Trapnell C;Pop M;Salzberg SL
通讯作者：
Salzberg SL