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.

Paddy mesocosms comprising of rice (Oryza sativa), snail (Pomacea canaliculata), and worm (Tubifex tubifex) were used to assess the damage caused by two acids (HNO3 and H2SO4) at predicted no-effect concentration (PNEC) and hazardous concentration for 50% of species (HC50) levels. In the fourth week, the fresh weight and shoot height of O. sativa at H2SO4-HC50 were reduced by 83.2% and 30.3%, respectively. Wilted leaves (%) at HC50 were approximately twice that at PNEC. No P. canaliculata and T. tubifex were recovered at HC50. At H2SO4-PNEC, the length and weight of P. canaliculata were reduced by 7.4% and 25.9%, respectively, whereas fewer adult (46.5%) and juvenile (84%) T. tubifex were recovered. In the 20th week, rice growth and productivity were correlated with initial pH (pHi) and nitrogen levels. Poor correlation with chlorophyll at the active tillering stage suggests the disturbance of nutrient uptake by roots. Partial least squares path modeling (PLS-PM) results further supported that the pHi directly affects grain yield and quality, as well as plant growth. The indirect effect via intervening fourth-week-variables was also substantial. Therefore, it is important to measure initial pH upon acid spill to estimate the risk to the paddy ecosystem. Information on the change in soil properties associated with acidity will also aid in predicting the yield and quality of grain to be harvested.

Brassinosteroids (BRs) are essential regulators of plant architecture. Understanding how BRs control plant height and leaf angle would facilitate development of new plant type varieties by biotechnology. A number of mutants involved in BR biosynthesis have been isolated but many of them lack detailed genetic analysis. Here, we report the isolation and characterization of a severe dwarf mutant, chromosome segment deleted dwarf 1 (csdd1), which was deficient in BR biosynthesis in rice. We isolated the mutant by screening a tissue culture-derived population, cloned the gene by mapping, and confirmed its function by complementary and RNAi experiments, combined with physiological and chemical analysis. We showed that the severe dwarf phenotype was caused by a complete deletion of a cytochrome P450 gene, CYP90D2/D2, which was further confirmed in two independent T-DNA insertion lines in different genetic backgrounds and by RNA interference. Our chemical analysis suggested that CYP90D2/D2 might catalyze C-3 dehydrogenation step in BR biosynthesis. We have demonstrated that the CYP90D2/D2 gene plays a more important role than previously reported. Allelic mutations of CYP90D2/D2 confer varying degrees of dwarfism and leaf angle, thus providing useful information for molecular breeding in grain crop plants.