title: Frequency and type of inheritable mutations induced by γ rays in rice as revealed by whole genome sequencing.
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 M2rice plants were sequenced; a total of 144-188 million high-quality (Q>20) reads were generated for each M2plant, 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 7.5×10-6-9.8×10-6in the six M2rice 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.
authors.affiliation: National Key Laboratory of Rice Biology, Institute of Crop Sciences, Zhejiang University, Hangzhou 310058, China.|Institute of Nuclear Agricultural Sciences, Zhejiang University, Hangzhou 310029, China.
authors.forename: Shan
authors.initials: S
authors.lastname: Li
authors.affiliation: National Key Laboratory of Rice Biology, Institute of Crop Sciences, Zhejiang University, Hangzhou 310058, China.|Hubei Collaborative Innovation Center for Grain Industry, Jingzhou 434025, China.
authors.forename: Yun-Chao
authors.initials: YC
authors.lastname: Zheng
authors.affiliation: Institute of Nuclear Agricultural Sciences, Zhejiang University, Hangzhou 310029, China.
authors.forename: Hai-Rui
authors.initials: HR
authors.lastname: Cui
authors.affiliation: Jiaxing Academy of Agricultural Sciences, Jiaxing 314016, China.
authors.forename: Hao-Wei
authors.initials: HW
authors.lastname: Fu
authors.affiliation: National Key Laboratory of Rice Biology, Institute of Crop Sciences, Zhejiang University, Hangzhou 310058, China.|Hubei Collaborative Innovation Center for Grain Industry, Jingzhou 434025, China.
authors.forename: Qing-Yao
authors.initials: QY
authors.lastname: Shu
authors.affiliation: National Key Laboratory of Rice Biology, Institute of Crop Sciences, Zhejiang University, Hangzhou 310058, China.|Institute of Nuclear Agricultural Sciences, Zhejiang University, Hangzhou 310029, China.
authors.forename: Jian-Zhong
authors.initials: JZ
authors.lastname: Huang
mesh_terms: D001947:Breeding; D018556:Crops, Agricultural / Q000235:genetics; D056915:DNA Copy Number Variations; D005720:Gamma Rays; D018745:Genome, Plant; D059014:High-Throughput Nucleotide Sequencing; D009154:Mutation; D012275:Oryza / Q000235:genetics*
keywords: Genomic variation; Mutation breeding; Mutation spectrum; γ rays