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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

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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