Rice, being a major staple food crop and sensitive to salinity conditions, bears heavy yield losses due to saline soil. Although some salt responsive genes have been identified in rice, their applications in developing salt tolerant cultivars have resulted in limited achievements. Herein, we used bioinformatic approaches to perform a meta-analysis of three transcriptome datasets from salinity and control conditions in order to reveal novel genes and the molecular pathways underlying rice response to salt. From a total of 28,432 expressed genes, we identify 457 core differentially expressed genes (DEGs) constitutively responding to salt, regardless of the stress duration, genotype, or the tissue. Gene co-expression analysis divided the core DEGs into three different modules, each of them contributing to salt response in a unique metabolic pathway. Gene ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses highlighted key biological processes and metabolic pathways involved in the salt response. We identified important novel hub genes encoding proteins of different families including CAM, DUF630/632, DUF581, CHL27, PP2-13, LEA4-5, and transcription factors, which could be functionally characterized using reverse genetic experiments. This novel repertoire of candidate genes related to salt response in rice will be useful for engineering salt tolerant varieties.

Drought is a serious problem, which causes heavy yield losses for rice. Heat-shock factors (HSFs) had been implicated in tolerance to drought and high temperature. However, there has not been much functional characterization and mechanism clarification in rice. Previously, we found an HSF gene, OsHSFA3, was highly related with drought tolerance after screening from 10,000 different samples. Herein, we cloned the OsHSFA3 from rice and overexpressed it in Arabidopsis thaliana to study its regulatory mechanism of drought tolerance. Phenotypic and physiological assays of the transgenic Arabidopsis lines showed that overexpression of OsHSFA3 confers drought tolerance by reducing water loss and reactive oxygen species (ROS) levels, whereas it increases abscisic acid (ABA) levels. However, enzymatic antioxidants such as activity levels of superoxide dismutase, peroxidase and catalase were not significantly different between wild type and transgenic lines. Instead, we observed a significant increase in polyamine content, which was correlated with increased AtADC1, AtADC2, SPDS1 and SPMS expression levels. In silico and in vivo analyses confirmed that OsHSFA3 is a nuclear-localized gene. In addition, OsHSFA3 can bind to the promoter of AtADC1 and OsADC via a yeast one-hybrid assay. Overall, this study reveals that OsHSFA3 improves drought tolerance in Arabidopsis not only by increasing ABA levels, but also by modulating polyamine levels to maintain ROS homeostasis, therefore it could be a strong candidate to develop drought-tolerant rice cultivars.

Background: Soil salinization is a threat to food security. China is rich in saline land resources for potential and current utilization. The cultivation and promotion of salt-tolerant rice varieties can greatly improve the utilization of this saline land. The super hybrid rice Chaoyouqianhao (CY1000) is one of the most salt-tolerant rice varieties and is widely used, but the molecular mechanism underlying its salt tolerance is not clear.Results: In this study, the characteristics of CY1000 and its parents were evaluated in the field and laboratory. The results showed that aboveground parts of CY1000 were barely influenced by salt stress, while the roots were less affected than those of its parents. A comparative transcriptomic strategy was used to analyze the differences in the response to salt stress among the male and female parents of CY1000 at the seedling stage and the model indica rice 93–11. We found that the salt tolerance of CY1000 was mainly inherited from its male parent R900, and its female parent GX24S showed hardly any salt tolerance. To adapt to salt stress, CY1000 and R900 upregulated the expression of genes associated with soluble component synthesis and cell wall synthesis and other related genes and downregulated the expression of most genes related to growth material acquisition and consumption. In CY1000 and R900, the expression of genes encoding some novel key proteins in the ubiquitination pathway was significantly upregulated. After treatment with MG-132, the salt tolerance of CY1000 and R900 was significantly decreased and was almost the same as that of the wild type after salt stress treatment, indicating that ubiquitination played an important role in the salt tolerance mechanism of CY1000. At the same time, we found that some transcription factors were also involved in the salt stress response, with some transcription factors responding only in hybrid CY1000, suggesting that salt tolerance heterosis might be regulated by transcription factors in rice.Conclusion: Our results revealed that the ubiquitination pathway is important for salt tolerance in rice, and several novel candidate genes were identified to reveal a novel salt tolerance regulation network. Additionally, our work will help clarify the mechanism of heterosis in rice. Further exploration of the molecular mechanism underlying the salt tolerance of CY1000 can provide a theoretical basis for breeding new salt-tolerant rice varieties.

As a global staple crop, rice production is seriously threatened by biotic and abiotic stresses. OsMYB, which is a core transcriptional regulator in plants, mediates key processes, including secondary metabolism, organ development, and stress responses. In this paper, we systematically describe the mechanisms underlying the synergistic effects of OsMYB family members on developmental plasticity and stress adaptations. Specifically, 1R-MYB transcription factors mainly regulate metabolism and yield formation, R2R3-MYB transcription factors mainly regulate organ development and stress resistance through the bidirectional modulation of the antioxidant system and lignin synthesis, 3R-MYB transcription factors primarily affect cell cycle regulation, and 4R-MYB transcription factors have functions that remain to be characterized. Further elucidating OsMYB-mediated molecular networks may lead to new strategies for developing stress-resistant and high-yielding rice varieties, with positive implications for sustainable agricultural development.

Phosphoenolpyruvate (PEP) plays a key role in the development of plants and exists in a wide variety of species. Research on the metabolic activities of PEP in plants has received increasing attention. PEP regulates multiple processes in plant growth and development. This article provides a comprehensive summary of these pathways, including embryo formation, root development, synthesis of secondary metabolites, and the formation of lignification. We also summarize new findings, including PEP’s role in nodule energy sensing and carbon allocation under the influence of ozone. This review displays the complex and differential regulatory pathways in plant growth and development and provides a reference for basic and applied research on PEP metabolism in plants.

High temperatures accelerate the accumulation of storage material in seeds, often leading to defects in grain filling. However, the mechanisms regulating grain filling at high temperatures remain unknown. Here, we want to explore the quality factors influenced by the environment and have identified a LATE EMBROYGENESIS ABUNDANT gene, OsLEA1b, a heat-stress-responsive gene in rice grain filling. OsLEA1b is highly expressed in the endosperm, and its coding protein localizes to the nucleus and cytoplasm. Knock-out mutants of OsLEA1b had abnormal compound starch granules in endosperm cells and chalky endosperm with significantly decreased grain weight and grain number per panicle. The oslea1b mutants exhibited a lower proportion of short starch chains with degrees of polymerization values from 6 to 13 and a higher proportion of chains with degrees from 14 to 48, as well as significantly lower contents of starch, protein, and lipid compared to the wild type. The difference was exacerbated under high temperature conditions. Moreover, OsLEA1b was induced by drought stress. The survival rate of oslea1b mutants decreased significantly under drought stress treatment, with significant increase in ROS levels. These results indicate that OsLEA1b regulates starch biosynthesis and influences rice grain quality, especially under high temperatures. This provides a valuable resource for genetic improvement in rice grain quality.