Full Text:   <2336>

Summary:  <1597>

Suppl. Mater.: 

CLC number: Q319

On-line Access: 2016-12-05

Received: 2016-03-20

Revision Accepted: 2016-05-29

Crosschecked: 2016-11-07

Cited: 0

Clicked: 4267

Citations:  Bibtex RefMan EndNote GB/T7714


Jian-zhong Huang


-   Go to

Article info.
Open peer comments

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


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

Share this article to: More |Next Article >>>

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.

@article{title="Frequency and type of inheritable mutations induced by γ rays in rice as revealed by whole genome sequencing",
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",
publisher="Zhejiang University Press & Springer",

%0 Journal Article
%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
%A Hai-rui Cui
%A Hao-wei Fu
%A Qing-yao Shu
%A Jian-zhong Huang
%J Journal of Zhejiang University SCIENCE B
%V 17
%N 12
%P 905-915
%@ 1673-1581
%D 2016
%I Zhejiang University Press & Springer
%DOI 10.1631/jzus.B1600125

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
J0 - Journal of Zhejiang University Science B
VL - 17
IS - 12
SP - 905
EP - 915
%@ 1673-1581
Y1 - 2016
PB - Zhejiang University Press & Springer
ER -
DOI - 10.1631/jzus.B1600125

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.


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。


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


[1]Abyzov, A., Urban, A.E., Snyder, M., et al., 2011. CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing. Genome Res., 21(6):974-984.

[2]Ahloowalia, B.S., Maluszynski, M., Nichterlein, K., 2004. Global impact of mutation-derived varieties. Euphytica, 135(2):187-204.

[3]Belfield, E.J., Gan, X., Mithani, A., et al., 2012. Genome-wide analysis of mutations in mutant lineages selected following fast-neutron irradiation mutagenesis of Arabidopsis thaliana. Genome Res., 22(7):1306-1315.

[4]Chen, K., Wallis, J.W., McLellan, M.D., et al., 2009. BreakDancer: an algorithm for high-resolution mapping of genomic structural variation. Nat. Methods, 6(9):677-681.

[5]Dohm, J.C., Lottaz, C., Borodina, T., et al., 2008. Substantial biases in ultra-short read data sets from high-throughput DNA sequencing. Nucl. Acids Res., 36(16):e105.

[6]Endo, M., Kumagai, M., Motoyama, R., et al., 2015. Whole-genome analysis of herbicide-tolerant mutant rice generated by Agrobacterium-mediated gene targeting. Plant Cell Physiol., 56(1):116-125.

[7]Farlow, A., Long, H., Arnoux, S., et al., 2015. The spontaneous mutation rate in the fission yeast Schizosaccharomyces pombe. Genetics, 201(2):737-744.

[8]Henry, I.M., Nagalakshmi, U., Lieberman, M.C., et al., 2014. Efficient genome-wide detection and cataloging of EMS-induced mutations using exome capture and next-generation sequencing. Plant Cell, 26(4):1382-1397.

[9]Henry, I.M., Zinkgraf, M.S., Groover, A.T., et al., 2015. A system for dosage-based functional genomics in poplar. Plant Cell, 27(9):2370-2383.

[10]Hofinger, B.J., Jing, H.C., Hammond-Kosack, K.E., et al., 2009. High-resolution melting analysis of cDNA-derived PCR amplicons for rapid and cost-effective identification of novel alleles in barley. Theor. Appl. Genet., 119(5):851-865.

[11]Jiang, C., Mithani, A., Gan, X., et al., 2011. Regenerant Arabidopsis lineages display a distinct genome-wide spectrum of mutations conferring variant phenotypes. Curr. Biol., 21(16):1385-1390.

[12]Kawakatsu, T., Kawahara, Y., Itoh, T., et al., 2013. A whole-genome analysis of a transgenic rice seed-based edible vaccine against cedar pollen allergy. DNA Res., 20(6):623-631.

[13]Lagoda, P.J.L., 2012. Effects of radiation on living cells and plants. In: Shu, Q.Y., Forster, B.P., Nakagawa, H. (Eds.), Plant Mutation Breeding and Biotechnology. CABI Publishing, Wallingford, p.123-134.

[14]Lee, M.H., Moon, Y.R., Chung, B.Y., et al., 2009. Practical use of chemical probes for reactive oxygen species produced in biological systems by γ-irradiation. Radiat. Phys. Chem., 78(5):323-327. https://dx.doi.org/10.1016/j.radphyschem.2009.03.001

[15]Li, H., Handsaker, B., Wysoker, A., et al., 2009. The Sequence Alignment/Map format and SAMtools. Bioinformatics, 25(16):2078-2079.

[16]Lu, H.P., Edwards, M., Wang, Q.Z., et al., 2015. Expression of cytochrome P450 CYP81A6 in rice: tissue specificity, protein subcellular localization, and response to herbicide application. J. Zhejiang Univ.-Sci. B (Biomed. & Biotechnol.), 16(2):113-122.

[17]Miyao, A., Nakagome, M., Ohnuma, T., et al., 2012. Molecular spectrum of somaclonal variation in regenerated rice revealed by whole-genome sequencing. Plant Cell Physiol., 53(1):256-264.

[18]Mohd-Yusoff, N.F., Ruperao, P., Tomoyoshi, N.E., et al., 2015. Scanning the effects of ethyl methanesulfonate on the whole genome of Lotus japonicus using second-generation sequencing analysis. G3, 5(4):559-567.

[19]Morita, R., Kusaba, M., Iida, S., et al., 2009. Molecular characterization of mutations induced by gamma irradiation in rice. Genes Genet. Syst., 84(5):361-370.

[20]Naito, K., Kusaba, M., Shikazono, N., et al., 2005. Transmissible and nontransmissible mutations induced by irradiating Arabidopsis thaliana pollen with γ-rays and carbon ions. Genetics, 169(2):881-889.

[21]Nakamura, K., Oshima, T., Morimoto, T., et al., 2011. Sequence-specific error profile of Illumina sequencers. Nucl. Acids Res., 39(13):e90.

[22]Nawaz, Z., Shu, Q.Y., 2014. Molecular nature of chemically and physically induced mutants in plants: a review. Plant Genetic Res., 12(S1):S74-S78.

[23]Ness, R.W., Morgan, A.D., Colegrave, N., et al., 2012. Estimate of the spontaneous mutation rate in Chlamydomonas reinhardtii. Genetics, 192(4):1447-1454.

[24]Ness, R.W., Morgan, A.D., Vasanthakrishnan, R.B., et al., 2015. Extensive de novo mutation rate variation between individuals and across the genome of Chlamydomonas reinhardtii. Genome Res., 25(11):1739-1749.

[25]Ossowski, S., Schneeberger, K., Lucas-Lledó, J.I., et al., 2010. The rate and molecular spectrum of spontaneous mutations in Arabidopsis thaliana. Science, 327(5961):92-94.

[26]Park, M.H., Rhee, H., Park, J.H., et al., 2014. Comprehensive analysis to improve the validation rate for single nucleotide variants detected by next-generation sequencing. PLoS ONE, 9(1):e86664.

[27]Peng, S.T., Zhuang, J.Y., Yan, Q.C., et al., 2003. SSR markers selection and purity detection of major hybrid rice combinations and their parents in China. Chin. J. Rice Sci., 17(1):1-5 (in Chinese).

[28]Pettersson, C., Hettinger, G., 1967. Dosimetry of high-energy electron radiation based on the ferrous sulphate dosimeter. Acta Radiol. Ther. Phys. Biol., 6(2):160-176.

[29]Prina, A.R., Landau, A.M., Pacheco, M.G., 2012. Chimeras and mutant gene transmission. In: Shu, Q.Y., Forster, B.P., Nakagawa, H. (Eds.), Plant Mutation Breeding and Biotechnology. CABI Publishing, Wallingford, p.181-189.

[30]Tan, Y.Y., Fu, H.W., Zhao, H.J., et al., 2013. Functional molecular markers and high-resolution melting curve analysis of low phytic acid mutations for marker-assisted selection in rice. Mol. Breeding, 31(3):517-528.

[31]Wang, K., Li, M.Y., Hakonarson, H., 2010. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucl. Acids Res., 38(16):e164.

[32]Yoshihara, R., Nozawa, S., Hase, Y., et al., 2013. Mutational effects of γ-rays and carbon ion beams on Arabidopsis seedlings. J. Radiat. Res., 54(6):1050-1056.

[33]Zheng, X.G., Chen, L., Lou, Q.J., et al., 2014. Changes in DNA methylation pattern at two seedling stages in water saving and drought-resistant rice variety after drought stress domestication. Rice Sci., 21(5):262-270.

[34]Zhu, Y.O., Siegal, M.L., Hall, D.W., et al., 2014. Precise estimates of mutation rate and spectrum in yeast. PNAS, 111(22):e2310-e2318.

[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

Open peer comments: Debate/Discuss/Question/Opinion


Please provide your name, email address and a comment

Journal of Zhejiang University-SCIENCE, 38 Zheda Road, Hangzhou 310027, China
Tel: +86-571-87952783; E-mail: cjzhang@zju.edu.cn
Copyright © 2000 - 2023 Journal of Zhejiang University-SCIENCE