Nitrate-responsive OsMADS27 promotes salt tolerance in rice

Integrative RNA-seq and ATAC-seq analysis unveils antioxidant defense mechanisms in salt-tolerant rice variety Pokkali

BACKGROUND

Salt stress is one of the most significant environmental challenges, severely impacting rice growth and yield. While different rice varieties exhibit varying levels of tolerance to salinity, Pokkali, a traditional salt-tolerant variety, stands out for its ability to thrive in saline conditions. Understanding the molecular and physiological mechanisms that underpin this tolerance is essential for breeding and developing rice varieties with enhanced resilience to salt stress.

METHODS

In this study, we selected the salt-tolerant rice variety Pokkali and the salt-sensitive variety IR29 for a controlled saline stress experiment. Plants were subjected to a 150 mM NaCl treatment for 7 days, after which leaf samples were collected from both varieties. Antioxidant physiological parameters were measured, and RNA-seq and ATAC-seq analyses were conducted to explore gene expression and chromatin accessibility. Key genes identified through sequencing were validated using RT-qPCR.

RESULTS

Under salt stress, Pokkali demonstrated strong tolerance and a higher antioxidant capacity compared to IR29, as evidenced by increased survival rates and fresh weight. Pokkali also showed elevated activity of antioxidant enzymes such as superoxide dismutase, peroxidase, and catalase, along with reduced accumulation of hydrogen peroxide. Transcriptomic and ATAC-seq analyses revealed that Pokkali's upregulated genes were significantly enriched in pathways related to redox homeostasis. These genes were also involved in metabolic processes such as glycan biosynthesis, amino acid metabolism, carbohydrate metabolism, and energy production. Furthermore, ATAC-seq analysis indicated increased chromatin accessibility in the promoter regions of key antioxidant genes under salt stress in Pokkali, reflecting enhanced transcriptional activity. Four key antioxidant-related genes-MnSOD1, OsAPx7, OsGR1, and Osppc3-were identified and validated by qPCR, showing significant upregulation in Pokkali. ATAC-seq data further supported that these genes had increased promoter accessibility under salt stress, aligning with the RNA-seq findings.

CONCLUSION

This study underscores the critical role of antioxidant defense mechanisms in conferring salt tolerance in Pokkali. The identification of key genes involved in redox regulation provides valuable insights into the molecular basis of salt tolerance, offering potential targets for the genetic improvement of salt-sensitive rice varieties through breeding programs.

Auxin-responsive OsMADS60 negatively mediates rice tillering and grain yield by modulating OsPIN5b expression

Rice tillering determines grain yield, yet the molecular regulatory network is still limited. In this study, we demonstrated that the transcription factor OsMADS60 promotes the expression of the auxin transporter OsPIN5b to affect auxin distribution and inhibit rice tillering and grain yield. Natural variation was observed in the promoter region of OsMADS60, with its expression level negatively correlated with tiller number and inducible by auxin. Overexpression of OsMADS60 resulted in reduced tillers and grain yield, whereas CRISPR-mediated knockouts of OsMADS60 led to increased tillering and yield. OsMADS60 was found to directly bind the CArG motif [CATTTAC] in the OsPIN5b promoter, thereby upregulating its expression. Moreover, we found that auxin content in various tissues of OsMADS60 and OsPIN5b overexpression lines increased relative to the wild-type ZH11, whereas the auxin levels in mutant lines showed the opposite trend. Genetic analysis further confirmed that OsPIN5b acted downstream of OsMADS60, coregulating the expression of genes involved in hormone pathways. Our findings reveal that OsMADS60 modulates auxin distribution by promoting OsPIN5b expression, thereby influencing rice tillering. This regulatory mechanism holds significant potential for the genetic improvement of rice architecture and grain yield.

Nitrate reductase-dependent nitric oxide production mediates nitrate-conferred salt tolerance in rice seedlings

Soil salinity is a destructive environmental factor that inhibits plant growth and crop yield. Applying nitrogen fertilizer is a practical method to enhance salt tolerance. However, the underlying mechanisms remain largely unknown. Here, we demonstrated that NO3--enhanced salt tolerance in rice (Oryza sativa L.) seedlings is mediated by nitrate reductase (NR)-dependent nitric oxide (NO) production. Seedlings grown in nitrate condition (N) exhibited much greater salt tolerance compared with those grown in ammonium nitrate and ammonium (A) conditions, a pattern also observed in the MADS-box transcription factor 27 (mads27) mutant. NR activity was highly induced by NO3- under both normal and salt stress conditions. Only the double mutant nr1/2 and the triple mutant nr1/2/3 displayed a dramatic reduction in salt tolerance. Application of tungstate suppressed salt tolerance of wild-type seedlings but not the triple mutants. Furthermore, both NO3--enhanced salt tolerance and salt-induced NO production were totally blocked in triple mutants. However, treatment with exogenous sodium nitroprusside (an NO donor) significantly enhanced salt tolerance in both Nipponbare (NIP) and the triple mutants. Antioxidant enzyme activities in shoots were significantly inhibited in the triple mutants when compared with NIP. Furthermore, expression of OsAKT1 was specifically induced by NO3- but was inhibited in the roots of triple mutants, resulting in a lower potassium/sodium ratio in NR triple mutants. Our results revealed that NO3--conferred salt tolerance is mediated by NR-dependent NO production in rice seedlings.

Improvement in Nitrogen-Use Efficiency Increases Salt Stress Tolerance in Rice Seedlings and Grain Yield in Salinized Soil

Salt stress has become a major limiting factor of rice (Oryza sativa L.) yield worldwide. Appropriate nitrogen application contributes to improvement in the salt tolerance of rice. Here, we show that improvement in nitrogen-use efficiency increases salt stress tolerance in rice. Rice varieties with different nitrogen-use efficiencies were subjected to salt stress; they were stimulated with 50, 100, and 150 mmol/L of NaCl solution at the seedling stage and subjected to salinities of 0.2, 0.4%, and 0.6% at the reproductive growth stage. Compared with nitrogen-inefficient rice varieties, the nitrogen-efficient rice varieties showed significant increases in the expression levels of nitrogen-use-efficiency-related genes (TOND1 and OsNPF6.1), nitrogen content (5.1-12.1%), and nitrogen-use enzyme activities (11.7-36.4%) when under salt stress conditions. The nitrogen-efficient rice varieties showed a better adaptation to salt stress, as shown by the decrease in leaf-withering rate (4.7-10.3%), the higher chlorophyll (3.8-9.7%) and water contents (1.1-9.2%), and the better root status (7.3-9.1%) found in the rice seedlings under salt stress conditions. Analysis of physiological indexes revealed that the nitrogen-efficient rice varieties accumulated higher osmotic adjustment substances (9.7-79.9%), lower ROS (23.1-190.8%) and Na+ (15.9-97.5%) contents, higher expression levels of salt stress-related genes in rice seedlings under salt stress conditions. Furthermore, the nitrogen-efficient rice varieties showed higher yield under salt stress, as shown by a lower salt-induced decrease in 1000-grain weight (2.1-6.2%), harvest index (1.4-4.9%), and grain yield (2.8-4.1%) at the reproductive growth stage in salinized soil. Conversely, the nitrogen-efficient rice varieties showed better growth and physiological metabolism statuses under severe salt stress conditions. Our results suggest that nitrogen-efficient rice varieties could improve nitrogen-use and transport efficiency; accordingly, their use can improve the gene expression network, alleviating salt damage and improving grain yield under severe salt stress conditions.

OsWNK9 mitigates salt stress by promoting root growth and stomatal closure in rice

Salinity stress severely affects rice growth and reduces its productivity. With No Lysine Kinases (WNKs) are serine/threonine kinases emerging as potential candidate genes due to their involvement in various abiotic stress tolerance responses. However, studies providing mechanistic insights into the roles of WNKs in plants remain scarce. In the present study, OsWNK9-overexpressing rice lines showed strong tolerance to salinity stress. Overexpression of OsWNK9 also triggered the accumulation of abscisic acid (ABA) and restored indole-3-acetic acid (IAA) concentrations in roots, triggering stomatal closure in shoots and maintaining cell expansion of the root epidermal cells when challenged with salt treatment. The overexpression lines showed increased activity of antioxidant enzymes, which further mitigated ROS-mediated cellular damage under salinity stress. We also identified that OsWNK9 interacts with Receptor for Activated Kinase C1A (RACK1A), ABA-8'-hydroxylase, and (Vacuolar Type ATPase) V-Type ATPase. Taken together, our findings suggest that OsWNK9 expression is warranted under salinity stress and exerts its effects by interacting with its downstream targets and by increased accumulation of ABA and IAA, thereby regulating seed germination, stomatal activity, improved root growth, and ionic homeostasis, which all contribute to significantly higher yield produced per plant under long term salinity stress.

A loss-of-function mutation in OsTZF5 confers sensitivity to low temperature and effects the growth and development in rice

Rice (Oryza sativa L.) is highly sensitive to low temperatures, which can significantly reduce its production. Cold tolerance in rice is a complex trait regulated by multiple mechanisms. OsTZF5, a member of the CCCH-type zinc finger gene family in rice, has been previously reported that overexpressing OsTZF5 under the stress-responsive promoter can confer drought resistance. In this study, we showed that the loss of function mutants of OsTZF5 decreased seed germination rate and chilling tolerance in rice, and influencing normal growth and development. OsTZF5 is expressed in various parts of the rice plant, including roots, stems, leaves and inflorescences, with the highest expression levels observed in leaves. Additionally, the expression of OsTZF5 gene was influenced by various stress conditions and hormone treatments. OsTZF5 knock-out mutants exhibited significantly lower survival rates compared to the wild type (Zhonghua11, ZH11) after cold stress, as well as fewer tillers, lower thousand-grain weight, and reduced grain yield under normal conditions. Transcriptomic analyses revealed that the expression of cold stress-related genes was significantly down-regulated in OsTZF5 knock-out mutants compared to ZH11 after cold stress. This down-regulation likely contributes to the reduced cold stress tolerance observed in OsTZF5 knock-out mutants. Our findings suggest that OsTZF5 is a multifunctional gene that plays a crucial role in regulating cold stress in rice.

Physiological and transcriptomic analyses reveal the molecular mechanism of PsAMT1.2 in salt tolerance

Soil salinization has become a global problem and high salt concentration in soil negatively affects plant growth. In our previous study, we found that overexpression of PsAMT1.2 from Populus simonii could improve the salt tolerance of poplar, but the physiological and molecular mechanism was not well understood. To explore the regulation pathway of PsAMT1.2 in salt tolerance, we investigated the morphological, physiological and transcriptome differences between the PsAMT1.2 overexpression transgenic poplar and the wild type under salt stress. The PsAMT1.2 overexpression transgenic poplar showed better growth with increased net photosynthetic rate and higher chlorophyll content compared with wild type under salt stress. The overexpression of PsAMT1.2 increased the catalase, superoxide dismutase, peroxidase and ascorbate peroxidase activities, and therefore probably enhanced the reactive oxygen species clearance ability, which also reduced the degree of membrane lipid peroxidation under salt stress. Meanwhile, the PsAMT1.2 overexpression transgenic poplar maintained a relatively high K+/Na+ ratio under salt stress. RNA-seq analysis indicated that PsAMT1.2 might improve plant salt tolerance by regulating pathways related to the photosynthetic system, chloroplast structure, antioxidant activity and anion transport. Among the 1056 differentially expressed genes, genes related to photosystem I and photosystem II were up-regulated and genes related to chloride channel protein-related were down-regulated. The result of the present study would provide new insight into regulation mechanism of PsAMT1.2 in improving salt tolerance of poplar.

Loss of OsSPL8 Function Confers Improved Resistance to Glufosinate and Abiotic Stresses in Rice

Weeds are among the most significant factors contributing to decreases in crop yield and quality. Glufosinate, a nonselective, broad-spectrum herbicide, has been extensively utilized for weed control in recent decades. However, crops are usually sensitive to glufosinate. Therefore, the development of glufosinate-resistant crops is crucial for effective weed management in agriculture. In this study, we characterized a SQUAMOSA promoter-binding-like (SPL) factor, OsSPL8, which acts as a negative regulator of glufosinate resistance by inhibiting the transcription of OsGS1;1 and OsGS2 and consequently reducing GS activity. Furthermore, the loss of OsSPL8 function enhanced tolerance to drought and salt stresses. Transcriptomic comparisons between the gar18-3 mutant and wild type revealed that OsSPL8 largely downregulates stress-responsive genes and upregulates growth-related genes. We demonstrated that OsSPL8 directly regulates OsOMTN6 and OsNAC17, which influence drought tolerance. In addition, OsSPL8 directly represses the expression of salt stress tolerance-related genes such as OsHKT1.1 and OsTPP1. Collectively, our results demonstrate that OsSPL8 is a negative regulator of both glufosinate resistance and abiotic stress tolerance.

Physiological and Molecular Mechanisms of Rice Tolerance to Salt and Drought Stress: Advances and Future Directions

Rice, a globally important food crop, faces significant challenges due to salt and drought stress. These abiotic stresses severely impact rice growth and yield, manifesting as reduced plant height, decreased tillering, reduced biomass, and poor leaf development. Recent advances in molecular biology and genomics have uncovered key physiological and molecular mechanisms that rice employs to cope with these stresses, including osmotic regulation, ion balance, antioxidant responses, signal transduction, and gene expression regulation. Transcription factors such as DREB, NAC, and bZIP, as well as plant hormones like ABA and GA, have been identified as crucial regulators. Utilizing CRISPR/Cas9 technology for gene editing holds promise for significantly enhancing rice stress tolerance. Future research should integrate multi-omics approaches and smart agriculture technologies to develop rice varieties with enhanced stress resistance, ensuring food security and sustainable agriculture in the face of global environmental changes.

A novel OsHB5-OsAPL-OsMADS27/OsWRKY102 regulatory module regulates grain size in rice

Grain size, a crucial trait that determines rice yield and quality, is typically regulated by multiple genes. Although numerous genes controlling grain size have been identified, the precise and dynamic regulatory network governing grain size is still not fully understood. In this study, we unveiled a novel regulatory module composed of OsHB5, OsAPL and OsMADS27/OsWRKY102, which plays a crucial role in modulating grain size in rice. As a positive regulator of grain size, OsAPL has been found to interact with OsHB5 both in vitro and in vivo. Through chromatin immunoprecipitation-sequencing, we successfully mapped two potential targets of OsAPL, namely OsMADS27, a positive regulator in grain size and OsWRKY102, a negative regulator in lignification that is also associated with grain size control. Further evidence from EMSA and chromatin immunoprecipitation-quantitative PCR experiments has shown that OsAPL acts as an upstream transcription factor that directly binds to the promoters of OsMADS27 and OsWRKY102. Moreover, EMSA and dual-luciferase reporter assays have indicated that the interaction between OsAPL and OsHB5 enhances the repressive effect of OsAPL on OsMADS27 and OsWRKY102. Collectively, our findings discovered a novel regulatory module, OsHB5-OsAPL-OsMADS27/OsWRKY102, which plays a significant role in controlling grain size in rice. These discoveries provide potential targets for breeding high-yield and high-quality rice varieties.

Genome-wide analysis of MADS-box transcription factor gene family in wild emmer wheat (Triticum turgidum subsp. dicoccoides)

The members of MADS-box gene family have important roles in regulating the growth and development of plants. MADS-box genes are highly regarded for their potential to enhance grain yield and quality under shifting global conditions. Wild emmer wheat (Triticum turgidum subsp. dicoccoides) is a progenitor of common wheat and harbors valuable traits for wheat improvement. Here, a total of 117 MADS-box genes were identified in the wild emmer wheat genome and classified to 90 MIKCC, 3 MIKC*, and 24 M-type. Furthermore, a phylogenetic analysis and expression profiling of the emmer wheat MADS-box gene family was presented. Although some MADS-box genes belonging to SOC1, SEP1, AGL17, and FLC groups have been expanded in wild emmer wheat, the number of MIKC-type MADS-box genes per subgenome is similar to that of rice and Arabidopsis. On the other hand, M-type genes of wild emmer wheat is less frequent than that of Arabidopsis. Gene expression patterns over different tissues and developmental stages agreed with the subfamily classification of MADS-box genes and was similar to common wheat and rice, indicating their conserved functionality. Some TdMADS-box genes are also differentially expressed under drought stress. The promoter region of each of the TdMADS-box genes harbored 6 to 48 responsive elements, mainly related to light, however hormone, drought, and low-temperature related cis-acting elements were also present. In conclusion, the results provide detailed information about the MADS-box genes of wild emmer wheat. The present work could be useful in the functional genomics efforts toward breeding for agronomically important traits in T. dicoccoides.

Joint QTL Mapping and Transcriptome Sequencing Analysis Reveal Candidate Genes for Salinity Tolerance in Oryza sativa L. ssp. Japonica Seedlings

Salinity stress is one of the major abiotic stresses affecting crop growth and production. Rice is an important food crop in the world, but also a salt-sensitive crop, and the rice seedling stage is the most sensitive to salt stress, which directly affects the final yield formation. In this study, two RIL populations derived from the crosses of CD (salt-sensitive)/WD (salt-tolerant) and KY131 (salt-sensitive)/XBJZ (salt-tolerant) were used as experimental materials, and the score of salinity toxicity (SST), the relative shoot length (RSL), the relative shoot fresh weight (RSFW), and the relative shoot dry weight (RSDW) were used for evaluating the degree of tolerance under salt stress in different lines. The genetic linkage map containing 978 and 527 bin markers were constructed in two RIL populations. A total of 14 QTLs were detected on chromosomes 1, 2, 3, 4, 7, 9, 10, 11, and 12. Among them, qSST12-1, qSST12-2, and qRSL12 were co-localized in a 140-kb overlap interval on chromosome 12, which containing 16 candidate genes. Furthermore, transcriptome sequencing and qRT-PCR were analyzed in CD and WD under normal and 120 mM NaCl stress. LOC_Os12g29330, LOC_Os12g29350, LOC_Os12g29390, and LOC_Os12g29400 were significantly induced by salt stress in both CD and WD. Sequence analysis showed that LOC_Os12g29400 in the salt-sensitive parents CD and KY131 was consistent with the reference sequence (Nipponbare), whereas the salt-tolerant parents WD and XBJZ differed significantly from the reference sequence both in the promoter and exon regions. The salt-tolerant phenotype was identified by using two T3 homozygous mutant plants of LOC_Os12g29400; the results showed that the score of salinity toxicity (SST) of the mutant plants (CR-3 and CR-5) was significantly lower than that of the wild type, and the seedling survival rate (SSR) was significantly higher than that of the wild type, which indicated that LOC_Os12g29400 could negatively regulate the salinity tolerance of rice at the seedling stage. The results lay a foundation for the analysis of the molecular mechanism of rice salinity tolerance and the cultivation of new rice varieties.

Nuclear translocation of OsMADS25 facilitated by OsNAR2.1 in reponse to nitrate signals promotes rice root growth by targeting OsMADS27 and OsARF7

Nitrate is an important nitrogen source and signaling molecule that regulates plant growth and development. Although several components of the nitrate signaling pathway have been identified, the detailed mechanisms are still unclear. Our previous results showed that OsMADS25 can regulate root development in response to nitrate signals, but the mechanism is still unknown. Here, we try to answer two key questions: how does OsMADS25 move from the cytoplasm to the nucleus, and what are the direct target genes activated by OsMADS25 to regulate root growth after it moves to the nucleus in response to nitrate? Our results demonstrated that OsMADS25 moves from the cytoplasm to the nucleus in the presence of nitrate in an OsNAR2.1-dependent manner. Chromatin immunoprecipitation sequencing, chromatin immunoprecipitation qPCR, yeast one-hybrid, and luciferase experiments showed that OsMADS25 directly activates the expression of OsMADS27 and OsARF7, which are reported to be associated with root growth. Finally, OsMADS25-RNAi lines, the Osnar2.1 mutant, and OsMADS25-RNAi Osnar2.1 lines exhibited significantly reduced root growth compared with the wild type in response to nitrate supply, and expression of OsMADS27 and OsARF7 was significantly suppressed in these lines. Collectively, these results reveal a new mechanism by which OsMADS25 interacts with OsNAR2.1. This interaction is required for nuclear accumulation of OsMADS25, which promotes OsMADS27 and OsARF7 expression and root growth in a nitrate-dependent manner.

Finding Balance in Adversity: Nitrate Signaling as the Key to Plant Growth, Resilience, and Stress Response

To effectively adapt to changing environments, plants must maintain a delicate balance between growth and resistance or tolerance to various stresses. Nitrate, a significant inorganic nitrogen source in soils, not only acts as an essential nutrient but also functions as a critical signaling molecule that regulates multiple aspects of plant growth and development. In recent years, substantial advancements have been made in understanding nitrate sensing, calcium-dependent nitrate signal transmission, and nitrate-induced transcriptional cascades. Mounting evidence suggests that the primary response to nitrate is influenced by environmental conditions, while nitrate availability plays a pivotal role in stress tolerance responses. Therefore, this review aims to provide an overview of the transcriptional and post-transcriptional regulation of key components in the nitrate signaling pathway, namely, NRT1.1, NLP7, and CIPK23, under abiotic stresses. Additionally, we discuss the specificity of nitrate sensing and signaling as well as the involvement of epigenetic regulators. A comprehensive understanding of the integration between nitrate signaling transduction and abiotic stress responses is crucial for developing future crops with enhanced nitrogen-use efficiency and heightened resilience.

Sustaining nitrogen dynamics: A critical aspect for improving salt tolerance in plants

In the current changing environment, salt stress has become a major concern for plant growth and food production worldwide. Understanding the mechanisms of how plants function in saline environments is critical for initiating efforts to mitigate the detrimental effects of salt stress. Agricultural productivity is linked to nutrient availability, and it is expected that the judicious metabolism of mineral nutrients has a positive impact on alleviating salt-induced losses in crop plants. Nitrogen (N) is a macronutrient that contributes significantly to sustainable agriculture by maintaining productivity and plant growth in both optimal and stressful environments. Significant progress has been made in comprehending the fundamental physiological and molecular mechanisms associated with N-mediated plant responses to salt stress. This review provided an (a) overview of N-sensing, transportation, and assimilation in plants; (b) assess the salt stress-mediated regulation of N dynamics and nitrogen use- efficiency; (c) critically appraise the role of N in plants exposed to salt stress. Furthermore, the existing but less explored crosstalk between N and phytohormones has been discussed that may be utilized to gain a better understanding of plant adaptive responses to salt stress. In addition, the shade of a small beam of light on the manipulation of N dynamics through genetic engineering with an aim of developing salt-tolerant plants is also highlighted.