Ion beams are physical mutagens used for plant and microbe breeding that cause mutations via a mechanism distinct from those of chemical mutagens or gamma rays. We utilized whole-exome sequencing of rice DNA in order to understand the properties of ion beam-induced mutations in a genome-wide manner. DNA libraries were constructed from selected carbon-ion-beam-induced rice mutants by capturing with a custom probes covering 66.3 M bases of nearly all exons and miRNAs predicted in the genome. A total of 56 mutations, including 24 single nucleotide variations, 23 deletions, and 5 insertions, were detected in five mutant rice lines (two dwarf and three early-heading-date mutants). The mutations were distributed among all 12 chromosomes, and the average mutation frequency in the M1 generation was estimated to be 2.7 × 10-7 per base. Many single base insertions and deletions were associated with homopolymeric repeats, whereas larger deletions up to seven base pairs were observed at polynucleotide repeats in the DNA sequences of the mutation sites. Of the 56 mutations, six were classified as high-impact mutations that caused a frame shift or loss of exons. A gene that was functionally related to the phenotype of the mutant was disrupted by a high-impact mutation in four of the five lines tested, suggesting that whole-exome sequencing of ion-beam-irradiated mutants could facilitate the detection of candidate genes responsible for the mutant phenotypes.

中文翻译：

---

离子束诱导的突变体的基因组测序有助于检测负责水稻中突变体表型的候选基因。

离子束是用于植物和微生物育种的物理诱变剂，其通过不同于化学诱变剂或伽马射线的机理引起突变。我们利用水稻DNA的全外显子测序，以了解全基因组范围内离子束诱导的突变的特性。DNA库是通过使用定制的探针捕获的，从选定的碳离子束诱导的水稻突变体中构建的，该探针涵盖了基因组中预测的几乎所有外显子和miRNA的66.3 M碱基。在五个突变稻系中检测到总共56个突变，包括24个单核苷酸变异，23个缺失和5个插入（两个矮化和三个早期抽穗日期突变体）。突变分布在所有12条染色体中，M1代的平均突变频率估计为每碱基2.7×10-7。许多单碱基的插入和缺失与均聚物重复相关，而在突变位点的DNA序列中的多核苷酸重复处观察到较大的缺失，多达七个碱基对。在这56个突变中，有6个被归类为高影响力突变，这些突变导致移码或外显子丢失。在五个测试品系中的四个品系中，与突变体表型功能相关的基因被高影响突变所破坏，这表明离子束辐照突变体的全外显子测序可以促进对引起突变的候选基因的检测。突变表型。六个被归类为引起框移或外显子丢失的高影响突变。在五个测试的品系中，有四个与突变表型功能相关的基因被高强度突变所破坏，这表明对离子束辐照的突变体进行全外显子测序可以促进对引起突变的候选基因的检测。突变表型。六个被归类为引起框移或外显子丢失的高影响突变。在五个测试品系中的四个品系中，与突变体表型功能相关的基因被高影响突变所破坏，这表明离子束辐照突变体的全外显子测序可以促进对引起突变的候选基因的检测。突变表型。