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Non-Random Distribution of EMS-Induced Mutations Reveals Preference for Open Chromatin and Expressed Genes in Rice

文献类型： 外文期刊

作者： Yao, Xue-Feng 1 ; Liu, Yanhong 2 ; Li, Zhiyong 2 ; Jiang, Guo-Qiang 1 ; Wang, Wensheng 2 ; Lu, Hong 3 ; Li, Huihui 2 ; Lu, Zefu 2 ; Liu, Chun-Ming 1 ;

作者机构： 1.Chinese Acad Sci, Inst Bot, Key Lab Plant Mol Physiol, State Key Lab Forage Breeding by Design & Utilizat, Beijing 100093, Peoples R China

2.Chinese Acad Agr Sci, Inst Crop Sci, State Key Lab Crop Gene Resources & Breeding, Beijing 100081, Peoples R China

3.China Golden Marker Co LTD, Beijing 102206, Peoples R China

4.Peking Univ, Sch Adv Agr Sci, Beijing 100091, Peoples R China; Beijing Acad Agr & Forestry Sci, Maize Res Inst, Beijing 100097, Peoples R China; Chinese Acad Sci, Inst Genet & Dev Biol, Beijing 100101, Peoples R China; Chinese Acad Agr Sci, Agr Genom Inst Shenzhen, Shenzhen 518000, Peoples R China

关键词： chromatin accessibility; EMS mutagenesis; natural variations

期刊名称：ADVANCED SCIENCE （ 影响因子：14.1； 五年影响因子：15.6 ）

ISSN：

年卷期： 2025 年

页码：

收录情况： SCI

摘要： Mutagenesis is an effective strategy to generate genetic resources for functional genomics and crop improvement. It is widely accepted that chemical-induced mutations are randomly distributed across the genome. However, the randomness of such mutations remains a matter of scientific debate due to a lack of systematic investigation. Although the basic features of mutations induced by different mutagens are known, it remains unresolved whether these mutations correlate with the chromatin state and gene expression. In this study, genomes of the wild-type and 4,619 mutagenized M3 lines derived from treatment with two concentrations of ethyl methane sulfonate (EMS) are sequenced, identifying over 7 million single-nucleotide mutations (SNPms) that covered over 97% of genes in the rice genome. Comprehensive analyses integrated with genomic, epigenomic, and expression data revealed that SNPms are more frequently located in open chromatin regions and actively expressed genes. Within expressed genes, heterozygous SNPms are enriched both upstream and downstream of transcription start sites (TSSs), whereas homozygous SNPms are enriched significantly in the upstream regions. These findings demonstrate that EMS-induced mutations are non-randomly distributed across the rice genome, with a preference for functionally important genomic regions.

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