Evaluation of the Saline–Alkaline Tolerance of Rice (Oryza sativa L.) Mutants Induced by Heavy-Ion Beam Mutagenesis

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

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.

Physiological and Transcriptomic Analyses Reveal the Effects of Carbon-Ion Beam on Taraxacum kok-saghyz Rodin Adventitious Buds

Taraxacum kok-saghyz Rodin (TKS) has great potential as an alternative natural-rubber (NR)-producing crop. The germplasm innovation of TKS still faces great challenges due to its self-incompatibility. Carbon-ion beam (CIB) irradiation is a powerful and non-species-specific physical method for mutation creation. Thus far, the CIB has not been utilized in TKS. To better inform future mutation breeding for TKS by the CIB and provide a basis for dose-selection, adventitious buds, which not only can avoid high levels of heterozygosity, but also further improve breeding efficiency, were irradiated here, and the dynamic changes of the growth and physiologic parameters, as well as gene expression pattern were profiled, comprehensively. The results showed that the CIB (5-40 Gy) caused significant biological effects on TKS, exhibiting inhibitory effects on the fresh weight and the number of regenerated buds and roots. Then,15 Gy was chosen for further study after comprehensive consideration. CIB-15 Gy resulted in significant oxidative damages (hydroxyl radical (OH^•) generation activity, 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical-scavenging activity and malondialdehyde (MDA) content) and activated the antioxidant system (superoxide dismutase (SOD), catalase (CAT), peroxidase (POD), and ascorbate peroxidase (APX)) of TKS. Based on RNA-seq analysis, the number of differentially expressed genes (DEGs) peaked at 2 h after CIB irradiation. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that DNA-replication-/repair- (mainly up-regulated), cell-death- (mainly up-regulated), plant-hormone- (auxin and cytokinin, which are related to plant morphogenesis, were mainly down-regulated), and photosynthesis- (mainly down-regulated) related pathways were involved in the response to the CIB. Furthermore, CIB irradiation can also up-regulate the genes involved in NR metabolism, which provides an alternative strategy to elevate the NR production in TKS in the future. These findings are helpful to understand the radiation response mechanism and further guide the future mutation breeding for TKS by the CIB.

Integrated metabolomic and transcriptomic strategies to reveal alkali-resistance mechanisms in wild soybean during post-germination growth stage

The keys to alkali-stress resistance of barren-tolerant wild soybean lay in enhanced reutilization of reserves in cotyledons as well as improved antioxidant protection and organic acid accumulation in young roots. Soil alkalization of farmlands is increasingly serious, adversely restricting crop growth and endangering food security. Here, based on integrated analysis of transcriptomics and metabolomics, we systematically investigated changes in cotyledon weight and young root growth in response to alkali stress in two ecotypes of wild soybean after germination to reveal alkali-resistance mechanisms in barren-tolerant wild soybean. Compared with barren-tolerant wild soybean, the dry weight of common wild soybean cotyledons under alkali stress decreased slowly and the length of young roots shortened. In barren-tolerant wild soybean, nitrogen-transport amino acids asparagine and glutamate decreased in cotyledons but increased in young roots, and nitrogen-compound transporter genes and genes involved in asparagine metabolism were significantly up-regulated in both cotyledons and young roots. Moreover, isocitric, succinic, and L-malic acids involved in the glyoxylate cycle significantly accumulated and the malate synthetase gene was up-regulated in barren-tolerant wild soybean cotyledons. In barren-tolerant wild soybean young roots, glutamate and glycine related to glutathione metabolism increased significantly and the glutathione reductase gene was up-regulated. Pyruvic acid and citric acid involved in pyruvate-citrate metabolism increased distinctly and genes encoding pyruvate decarboxylase and citrate synthetase were up-regulated. Integrated analysis showed that the keys to alkali-stress resistance of barren-tolerant wild soybean lay in enhanced protein decomposition, amino acid transport, and lipolysis in cotyledons as well as improved antioxidant protection and organic acid accumulation in young roots. This study provides new ideas for the exploitation and utilization of wild soybean resources.

Editorial to the Special Issue "Eco-Physiological and Molecular Basis of Stress Tolerance in Plants"

Farmers are currently facing the challenge of producing sufficient crop yield [...].

Targeted Identification of Rice Grain-Associated Gene Allelic Variation Through Mutation Induction, Targeted Sequencing, and Whole Genome Sequencing Combined with a Mixed-Samples Strategy

BACKGROUND

The mining of new allelic variation and the induction of new genetic variability are the basis for improving breeding efficiency.

RESULTS

In this study, in total, 3872 heavy ion-irradiated M₂ generation rice seeds and individual leaves were collected. The grain length was between 8 and 10.22 mm. The grain width was between 1.54 and 2.87 mm. The results showed that there was extensive variation in granulotype. The allelic variation in GS3 and GW5 was detected in 484 mixed samples (8:1) using targeted sequencing technology, and 12 mixed samples containing potential mutations and 15 SNPs were obtained; combined with Sanger sequencing and phenotype data, 13 key mutants and their corresponding SNPs were obtained; protein structural and functional analysis of key mutants screened out 6 allelic variants leading to altered grain shape, as well as the corresponding mutants, including long-grain mutants GS3-2 and GS3-7, short-grain mutants GS3-3 and GS3-5, wide-grain mutant GW5-1 and narrow-grain mutant GW5-4; whole genome sequencing identified new grain length gene allelic variants GS3-G1, GS3-G2 and GS3-G3.

CONCLUSION

Based on the above studies, we found 6 granulotype mutants and 9 granulotype-related allelic variants, which provided new functional gene loci and a material basis for molecular breeding and genotype mutation and phenotype analysis. We propose a method for targeted identification of allelic variation in rice grain type genes by combining targeted sequencing of mixed samples and whole genome sequencing. The method has the characteristics of low detection cost, short detection period, and flexible detection of traits and genes.