Table_14_Multi-generation study of heavy ion beam-induced mutations and agronomic trait variations to accelerate rice breeding.xlsx

Heavy ion beam (HIB) is an effective physical mutagen that has been widely used in plant mutational breeding. Systemic knowledge of the effects caused by different HIB doses at developmental and genomic levels will facilitate efficient breeding for crops. Here we examined the effects of HIB systematically. Kitaake rice seeds were irradiated by ten doses of carbon ion beams (CIB, 25 – 300 Gy), which is the most widely used HIB. We initially examined the growth, development and photosynthetic parameters of the M1 population and found that doses exceeding 125 Gy caused significant physiological damages to rice. Subsequently, we analyzed the genomic variations in 179 M2 individuals from six treatments (25 – 150 Gy) via whole-genome sequencing (WGS). The mutation rate peaks at 100 Gy (2.66×10-7/bp). Importantly, we found that mutations shared among different panicles of the same M1 individual are at low ratios, validating the hypothesis that different panicles may be derived from different progenitor cells. Furthermore, we isolated 129 mutants with distinct phenotypic variations, including changes in agronomic traits, from 11,720 M2 plants, accounting for a 1.1% mutation rate. Among them, about 50% possess stable inheritance in M3. WGS data of 11 stable M4 mutants, including three lines with higher yields, reveal their genomic mutational profiles and candidate genes. Our results demonstrate that HIB is an effective tool that facilitates breeding, that the optimal dose range for rice is 67 – 90% median lethal dose (LD50), and that the mutants isolated here can be further used for functional genomic research, genetic analysis, and breeding.

重离子束（Heavy Ion Beam，HIB）是一类高效物理诱变剂，已被广泛应用于植物诱变育种。系统解析不同剂量重离子束在发育与基因组层面引发的生物学效应，将助力作物高效育种工作。本研究围绕重离子束的诱变效应开展系统性探究：采用当前应用最广泛的重离子束类型——碳离子束（Carbon Ion Beam，CIB），以10个梯度剂量（25~300 Gy）辐照Kitaake水稻种子。首先分析M1代群体的生长发育状态与光合参数，发现剂量超过125 Gy时会对水稻造成显著生理损伤。随后通过全基因组测序（Whole-Genome Sequencing，WGS）对6个剂量组（25~150 Gy）的179株M2代个体进行基因组变异分析，结果显示突变率在100 Gy剂量下达到峰值，为2.66×10^-7/碱基对（base pair，bp）。值得注意的是，同一M1代个体的不同穗部间共享突变的比例较低，这验证了"水稻不同穗部起源于不同祖代细胞"的假说。此外，本研究从11720株M2代植株中筛选得到129株具有显著表型变异（含农艺性状改变）的突变体，突变筛选率达1.1%，其中约50%的突变体可在M3代稳定遗传。对11株稳定遗传的M4代突变体（包含3个高产株系）进行全基因组测序，明确了其基因组突变特征与候选功能基因。本研究结果证实，重离子束是高效的诱变育种工具，水稻诱变的最优剂量范围为半数致死剂量（median lethal dose，LD50）的67%~90%；本研究筛选获得的突变体可进一步应用于功能基因组学研究、遗传分析与作物育种工作。