Hanjing Sha

Lodging is one of the major problems in rice production. However, few genes that can explain the culm strength within the temperate japonica subspecies have been identified. In this study, we identified OsRLCK191, which encodes receptor-like cytoplasmic kinase and plays critical roles in culm strength. OsRLCK191 mutants were produced by the CRISPR-Cas9 DNA-editing system. Compared with wild types (WTs), the bending moment of the whole plant (WP), the bending moment at breaking (BM), and the section modulus (SM) were decreased in rlck191 significantly. Although there is no significant decrease in the culm length of rlck191 compared with the WT; in the mutant, except the length of the fourth internode being significantly increased, the lengths of other internodes are significantly shortened. In addition, the yield traits of panicle length, thousand-seed weight, and seed setting rate decreased significantly in rlck191. Moreover, RNA-seq experiments were performed at an early stage of rice panicle differentiation in shoot apex. The differentially expressed genes (DEGs) are mainly involved in cell wall biogenesis, cell wall polysaccharide metabolic processes, cellar component biogenesis, and DNA-binding transcription factors. Transcriptome analysis of the cell wall biological process pathways showed that major genes that participated in the cytokinin oxidase/dehydrogenase family, cellulose synthase catalytic subunit genes, and ethylene response factor family transcription factor were related to culm strength. Our research provides an important theoretical basis for analyzing the lodging resistance mechanism and lodging resistance breeding of temperate japonica.

Aphelenchoides besseyi is considered one of the most damaging plant parasitic nematodes to rice and can cause white tip disease. It was first discovered in Kyushu, Japan in 1915 and introduced into...

Key message A novel Hd3a allele strongly promoting rice heading date was identified, and it functions through florigen activation complex (FAC) and was selected during the spread of rice cultivation to high-latitude areas. Abstract Heading date is a critical agronomic trait for rice that determines the utilization of light and temperature conditions and thereby affects grain yield. Rice is a short day (SD) plant, and its photoperiodic information is processed by complex pathways and integrated by florigens to control flowering. In this study, we identified a novel allele for the florigen gene Heading date 3a (Hd3a), characterized by a C435G substitution in its coding region, by a genome-wide association study (GWAS) approach in a panel of 199 high-latitude japonica rice varieties. The C435G substitution induces plants to flower 10 days earlier in high-latitude area (long day condition). Then, we mutated C435 to G in Hd3a by prime editing and found the point mutation plants flowered 12 days earlier. Further molecular experiments showed the novel Hd3a protein can interact with GF14b protein and increase the expression of OsMADS14, the output gene of florigen activation complex (FAC). Molecular signatures of selection indicated that the novel Hd3a allele was selected during the process of rice cultivation expansion into high-latitude areas. Collectively, these results provide new insights into heading date regulation in high-latitude areas and advance improvements to rice adaptability to enhance crop yield.

Rice has 48 ubiquitin-conjugating enzymes, and the functions of most of these enzymes have not been elucidated. In the present study, a T-DNA insertional mutant named R164, which exhibited a significant decrease in the length of primary and lateral roots, was used as the experimental material to explore the potential function of OsUBC11. Analysis using the SEFA-PCR method showed that the T-DNA insertion was present in the promoter region of OsUBC11 gene, which encodes ubiquitin-conjugating enzyme (E2), and activates its expression. Biochemical experiments showed that OsUBC11 is a lysine-48-linked ubiquitin chain-forming conjugase. OsUBC11 overexpression lines showed the same root phenotypes. These results demonstrated that OsUBC11 was involved in root development. Further analyses showed that the IAA content of R164 mutant and OE3 line were significantly lower compared with wild-type Zhonghua11. Application of exogenous NAA restored the length of lateral and primary roots in R164 and OsUBC11 overexpression lines. Expression of the auxin synthesis regulating gene OsYUCCA4/6/7/9, the auxin transport gene OsAUX1, auxin/indole-3-acetic acid (Aux/IAA) family gene OsIAA31, auxin response factor OsARF16 and root regulator key genes, including OsWOX11, OsCRL1, OsCRL5 was significantly down-regulated in OsUBC11 overexpressing plants. Collectively, these results indicate that OsUBC11 modulates auxin signaling, ultimately affecting root development at the rice seedling stage.

Low-temperature germination (LTG) is an important agronomic trait for rice (Oryza sativa). Japonica rice generally has greater capacity for germination at low temperatures than the indica subpopulation. However, the genetic basis and molecular mechanisms underlying this complex trait are poorly understood. Here, we report that OsUBC12, encoding an E2 ubiquitin-conjugating enzyme, increases low-temperature germinability in japonica, owing to a transposon insertion in its promoter enhances its expression. Natural variation analysis revealed transposon insertion in the OsUBC12 promoter mainly in the japonica lineage. Notably, the genomic region carrying the japonica OsUBC12 locus (with the transposon insertion) has been introgressed into the modern elite indica two-line male sterile lines Y58S and J4155S. Further molecular analysis showed that OsUBC12 may negatively regulate ABA signaling. OsUBC12-regulated seed germination and ABA signaling mainly depend on a conserved active site required for ubiquitin-conjugating enzyme activity. Furthermore, OsUBC12 directly associates with rice SUCROSE NON-FERMENTING 1-RELATED PROTEIN KINASE 1.1 (OsSnRK1.1), promoting its degradation. In contrast to OsUBC12, OsSnRK1.1 inhibits LTG by enhancing ABA signaling. These findings shed light on the possible genomic contributions of introgressions of the japonica OsUBC12 locus to trait improvements of indica rice cultivars and provide genetic reference points for improving LTG in indica rice.

The objective of this study was to investigate the effects of drought stress on the activity of antioxidant enzymes and osmotic adjustment substance content in the tillering period of drought-sensitive and drought-tolerant rice cultivars. The results showed that the superoxide dismutase (SOD), peroxidase (POD), catalase activity (CAT), hydrogen peroxide content, soluble protein content and soluble sugar content increased with the accumulation of time and intensity of drought stress. Compared with the drought-sensitive cultivar, drought-resistant cultivar had a smaller photosynthetic affected area, longer CAT enzyme activity duration, and lower H₂O₂ accumulation. Unlike POD and CAT enzymes, which maintain the ability to scavenge hydrogen peroxide under long drought conditions, ascorbate peroxidase (APX) enzymes seem to be a rapid response mechanism to scavenge hydrogen peroxide under drought stress. Under a −10 kPa water potential, using soluble sugars on the osmotic adjustment ability of the drought-resistant cultivars was more efficient; under −40 kPa water potential, drought-resistant cultivars can maintain relative high levels of ascorbate (ASA) content in the short term. After the restoration of irrigation, the indices gradually returned to control levels. The ASA content showed faster accumulation ability in drought-resistant cultivars and faster recovery. The soluble protein content recovered more slowly in drought-sensitive cultivars under the −40 kPa treatment. Drought-resistant cultivars showed stronger resistance to drought in the −10 kPa treatment and obtained similar yield to the control, while the drought-sensitive cultivars were more obviously affected by the drought stress.