Abstract

Radiation has been widely used for rice germplasm innovation. The molecular mechanisms by which radiation induces mutations at the genome level require further investigation. To determine the pattern of DNA polymorphisms induced by radiation in the M1 population, we performed whole-genome sequencing of the rice cultivar Gaogengnuo, which was subjected to two ⁶⁰Co γ-radiation doses, generating the 300 Gy group and the 400 Gy group (11.2 Gy min^–1). A total of 356,314 and 588.414 single nucleotide polymorphisms (SNPs), 73,495 and 95,807 insertion/deletion polymorphisms (InDels), 9075 and 8852 structural variations and 5100 and 4252 copy number variations were identified in the 300 Gy group and 400 Gy group, respectively, based on the Nipponbare genome. Through an integrative analysis of resequencing data, we identified 609,209 SNPs and 67,885 InDels that differed between the 300 Gy and Gaogengnuo groups and 632,745 SNPs and 69,899 InDels that differed between the 400 Gy and Gaogengnuo groups. We also detected 2682 homozygous SNPs and 2988 homozygous InDels that were present in the Gaogengnuo, 300 Gy and 400 Gy groups. Gene Ontology clustering showed that the mutated genes in the 300 Gy and 400 Gy groups were classified into two main categories, molecular function and biological process, suggesting that genes associated with molecular functions and biological processes were susceptible to γ-radiation.

中文翻译：

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全基因组重测序技术表征粳稻新品种Gaogengnuo M1群体中γ射线诱导的DNA多态性

摘要

辐射已被广泛用于水稻种质创新。辐射诱导基因组水平突变的分子机制需要进一步研究。为了确定在M1群体中由辐射诱导的DNA多态性模式，我们对水稻品种Gaogengnuo进行了全基因组测序，对这两个品种进行了两次⁶⁰ Coγ辐射剂量处理，产生了300 Gy组和400 Gy组（ 11.2 Gy分钟^–1）。300 Gy组和400 Gy组分别鉴定出总共356,314和588.414个单核苷酸多态性（SNP），73,495和95,807个插入/缺失多态性（InDels），9075和8852个结构变异以及5100和4252个拷贝数变异，基于日本晴的基因组。通过对重测序数据的综合分析，我们确定了300 Gy和Gaogengnuo组之间差异的609,209个SNP和67,885个InDel，以及400 Gy和Gaogengnuo组之间差异的632,745个SNP和69,899 InDel。我们还检测了高根牛，300 Gy和400 Gy组中存在的2682个纯合SNP和2988个纯合InDel。基因本体聚类表明，300 Gy和400 Gy组中的突变基因分为分子功能和生物学过程两大类，