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CLC number: Q319

On-line Access: 2016-12-05

Received: 2016-03-20

Revision Accepted: 2016-05-29

Crosschecked: 2016-11-07

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Citations:  Bibtex RefMan EndNote GB/T7714

 ORCID:

Jian-zhong Huang

http://orcid.org/0000-0002-0201-9130

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Journal of Zhejiang University SCIENCE B 2016 Vol.17 No.12 P.905-915

http://doi.org/10.1631/jzus.B1600125


Frequency and type of inheritable mutations induced by γ rays in rice as revealed by whole genome sequencing


Author(s):  Shan Li, Yun-chao Zheng, Hai-rui Cui, Hao-wei Fu, Qing-yao Shu, Jian-zhong Huang

Affiliation(s):  National Key Laboratory of Rice Biology, Institute of Crop Sciences, Zhejiang University, Hangzhou 310058, China; more

Corresponding email(s):   jzhuang@zju.edu.cn

Key Words:  Mutation breeding, γ, rays, Mutation spectrum, Genomic variation


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Shan Li, Yun-chao Zheng, Hai-rui Cui, Hao-wei Fu, Qing-yao Shu, Jian-zhong Huang. Frequency and type of inheritable mutations induced by γ rays in rice as revealed by whole genome sequencing[J]. Journal of Zhejiang University Science B, 2016, 17(12): 905-915.

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author="Shan Li, Yun-chao Zheng, Hai-rui Cui, Hao-wei Fu, Qing-yao Shu, Jian-zhong Huang",
journal="Journal of Zhejiang University Science B",
volume="17",
number="12",
pages="905-915",
year="2016",
publisher="Zhejiang University Press & Springer",
doi="10.1631/jzus.B1600125"
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%T Frequency and type of inheritable mutations induced by γ rays in rice as revealed by whole genome sequencing
%A Shan Li
%A Yun-chao Zheng
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T1 - Frequency and type of inheritable mutations induced by γ rays in rice as revealed by whole genome sequencing
A1 - Shan Li
A1 - Yun-chao Zheng
A1 - Hai-rui Cui
A1 - Hao-wei Fu
A1 - Qing-yao Shu
A1 - Jian-zhong Huang
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DOI - 10.1631/jzus.B1600125


Abstract: 
mutation breeding is based on the induction of genetic variations; hence knowledge of the frequency and type of induced mutations is of paramount importance for the design and implementation of a mutation breeding program. Although γ; ray irradiation has been widely used since the 1960s in the breeding of about 200 economically important plant species, molecular elucidation of its genetic effects has so far been achieved largely by analysis of target genes or genomic regions. In the present study, the whole genomes of six γ;-irradiated M2 rice plants were sequenced; a total of 144–188 million high-quality (Q>20) reads were generated for each M2 plant, resulting in genome coverage of >45 times for each plant. Single base substitution (SBS) and short insertion/deletion (Indel) mutations were detected at the average frequency of 7.5×10−6–9.8×10−6 in the six M2 rice plants (SBS being about 4 times more frequent than Indels). Structural and copy number variations, though less frequent than SBS and Indel, were also identified and validated. The mutations were scattered in all genomic regions across 12 rice chromosomes without apparent hotspots. The present study is the first genome-wide single-nucleotide resolution study on the feature and frequency of γ; irradiation-induced mutations in a seed propagated crop; the findings are of practical importance for mutation breeding of rice and other crop species.

基因组重测序分析γ射线诱发水稻可遗传变异的频率与特征

目的:研究γ射线对水稻基因组的诱变效应,明确其诱发突变的类型、分布和频率。
创新点:首次针对种子繁殖植物在全基因组范围及单核苷酸水平上揭示了γ射线诱发可遗传变异的频率与特征。
方法:利用Illumina Hiseq2000对三种γ射线剂量辐照培育的6株水稻(日本晴)M2植株进行基因组重测序,生物信息学分析确定单碱基替换(SBS)和插入缺失(Indel)突变,以及结构变异和拷贝数等变异的频率和基因组分布。利用Sanger测序、目标片段扩增或定量多聚酶链反应(qPCR)对各类突变进行验证。综合重测序和验证结果估算诱发突变频率。
结论:结果表明,γ射线既可以诱发单碱基替换,也可以诱发插入缺失突变和结构变异;水稻M2代植株中的平均突变频率达到7.5×10−6~9.8×10−6;Indel突变频率约为SBS变异的1/4,而结构变异频率更低;SBS和Indel突变随机分布在12条染色体上,无明显的突变热点。

关键词:诱变育种;γ射线;突变谱;基因组变异

Darkslateblue:Affiliate; Royal Blue:Author; Turquoise:Article

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[35]List of electronic supplementary materials

[36]Table S1 Verification of single base substitution (SBS) mutations in P2M2 and P3M3 plants

[37]Table S2 Verification of insertion and deletion (Indel) mutations in the P2M2 and P3M3 plants

[38]Table S3 Verification of structural variation (SV) mutations in P2M2 plants

[39]Table S4 Verification of copy number variation (CNV) mutations in P2M2 plants

[40]Table S5 Frequency of single base substitution (SBS) and Indel mutations in individual chromosomes of the six γ rays-mutagenized P2M2 plants (mutation numbers per million base pairs)

[41]Fig. S1 Genotyping of the selected six P2M2 plants and Nipponbare with 12 representative SSR markers

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