Zheng Yunchao, Li Shan, Huang Jianzhong, Fan Longjiang, Shu Qingyao
Cytogenet Genome Res. 2020;160(2):100-109. doi: 10.1159/000506033. Epub 2020 Mar 7.
Chloroplasts and mitochondria are semi-autonomous organelles and have their own genomes (cytoplasmic genomes). Physical radiations (e.g., γ-rays) have been widely used in artificial mutation induction for plant germplasm enhancement and for breeding new cultivars. However, little is known at the genomic level about which kind of cytoplasmic mutations and/or characteristics could be induced in plants. The present study aimed to investigate the type, number, and distribution of inheritable cytoplasmic mutations induced by γ-rays in rice (Oryza sativa L.). Six plants were selected from the 2nd generation (M2) populations after γ-ray (137Cs) irradiation of the rice cultivar Nipponbare, 2 each for the 3 irradiation doses (150, 250, and 350 Gy), and their genomes were sequenced on an Illumina platform. Together with the whole-genome sequencing data of 3 external Nipponbare control plants, single-base substitutions (SBSs) and insertions/deletions (InDels) in chloroplast (cp) and mitochondrial (mt) genomes were identified and analyzed in-depth using bioinformatic tools. The majority of SBSs and InDels identified were background mutations in the 6 M2 plants, and the number of induced mutations varied greatly among the plants. Most induced mutations were present in a heterogeneous state, reflecting the fact that multiple cp and mt copies existed in the progenitor cells. The induced mutations were distributed in different genomic regions in the 6 M2 plants, including exonic regions, but none of them was predicted to cause nonsynonymous mutations or frameshifts. Our study thus revealed, at the genomic level, characteristics of cytoplasmic mutations induced by γ-rays in rice.
叶绿体和线粒体是半自主细胞器，拥有自己的基因组（细胞质基因组）。物理辐射（如γ射线）已被广泛用于人工诱变以增强植物种质和培育新品种。然而，在基因组水平上，对于植物中可诱导产生哪种细胞质突变和/或特征却知之甚少。本研究旨在调查γ射线诱导水稻（Oryza sativa L.）产生的可遗传细胞质突变的类型、数量和分布。从日本晴水稻品种经γ射线（137Cs）辐照后的第二代（M2）群体中选取了6株植株，3个辐照剂量（150、250和350 Gy）各选2株，并在Illumina平台上对其基因组进行测序。结合3株外部日本晴对照植株的全基因组测序数据，利用生物信息学工具对叶绿体（cp）和线粒体（mt）基因组中的单碱基替换（SBSs）和插入/缺失（InDels）进行了鉴定和深入分析。在6株M2植株中鉴定出的大多数SBSs和InDels是背景突变，且植株间诱导突变的数量差异很大。大多数诱导突变以异质状态存在，这反映了祖细胞中存在多个cp和mt拷贝这一事实。诱导突变分布在6株M2植株的不同基因组区域，包括外显子区域，但预计它们均不会导致非同义突变或移码突变。因此，我们的研究在基因组水平上揭示了γ射线诱导水稻产生的细胞质突变的特征。
