High energy ion beams are effective physical mutagens for mutation induction in plants. Due to their high linear energy transfer (LET) property, they are known to generate single nucleotide variations (SNVs) and insertion/deletions (InDels, <50 bp) as well as structural variations (SVs). However, due to the technical difficulties to identify SVs, studies on ion beam induced SVs by genome sequencing have so far been limited in numbers and inadequate in nature, and knowledge of SVs is scarce with regards to their characteristics. In the present study, we identified and validated SVs in six M₄ plants (designated as Ar_50, Ar_100, C_150, C_200, Ne_50 and Ne_100 according to ion beam types and irradiation doses), two each induced by argon (⁴⁰Ar¹⁸⁺), carbon (¹²C⁶⁺) and neon (²⁰Ne¹⁰⁺) ion beams and performed in depth analyses of their characteristics. In total, 22 SVs were identified and validated, consisting of 11 deletions, 1 duplication, and 4 intra-chromosomal and 6 inter-chromosomal translocations. There were several SVs larger than 1 kbp. The SVs were distributed across the whole genome with an aggregation with SNVs and InDels only in the Ne_50 mutants. An enrichment of a 11-bp wide G-rich DNA motif 'GAAGGWGGRGG' was identified around the SV breakpoints. Three mechanisms might be involved in the SV formation, i.e., the expansion of tandem repeats, transposable element insertion, and non-allelic homologous recombination. Put together, the present study provides a preliminary view of SVs induced by Ar, C and Ne ion beam radiations, and as a pilot study, it contributes to our understanding of how SVs might form after ion beam irradiation in rice.

高能离子束是植物突变诱导的有效物理诱变剂。由于它们的高线性能量转移 (LET) 特性，已知它们会产生单核苷酸变异 (SNV) 和插入/缺失 (InDels, <50 bp) 以及结构变异 (SV)。然而，由于识别SVs的技术难度，迄今为止通过基因组测序对离子束诱导的SVs的研究数量有限且性质不足，并且关于SVs的特征的知识很少。在本研究中，我们在 6 个 M ₄植物（根据离子束类型和辐照剂量分别命名为 Ar_50、Ar_100、C_150、C_200、Ne_50 和 Ne_100）中鉴定并验证了 SV，其中两个由氩（⁴⁰ Ar ¹⁸⁺）诱导， 碳 （¹² C ⁶⁺ ) 和氖 ( ²⁰ Ne ¹⁰⁺) 离子束并对其特性进行了深入分析。总共鉴定和验证了 22 个 SV，包括 11 个缺失、1 个重复、4 个染色体内易位和 6 个染色体间易位。有几个大于 1 kbp 的 SV。SV 分布在整个基因组中，仅在 Ne_50 突变体中具有 SNV 和 InDels 的聚集。在 SV 断点周围鉴定出一个 11 bp 宽的富含 G 的 DNA 基序“GAAGGWGGGRGG”的富集。SV的形成可能涉及三种机制，即串联重复序列的扩增、转座子插入和非等位基因同源重组。综上所述，本研究提供了由 Ar、C 和 Ne 离子束辐射引起的 SV 的初步视图，作为一项试点研究，