Salt-responsive ERF1 regulates reactive oxygen species-dependent signaling during the initial response to salt stress in rice

Transcriptome Analysis of the Regulatory Mechanisms of Holly (Ilex dabieshanensis) under Salt Stress Conditions

The holly Ilex dabieshanensis K. Yao & M. B. Deng, a tree endemic to the Dabieshan Mountains region in China, is a commonly used landscaping plant. Like other crops, its growth is affected by salt stress. The molecular mechanism underlying salt tolerance in holly is still unclear. In this study, we used NaCl treatment and RNA sequencing (RNA-seq) at different times to identify the salt stress response genes of holly. A total of 4775 differentially expressed genes (DEGs) were identified. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of the DEGs obtained at different salt treatment times (3, 6, 9, 12, and 24 h), as compared to control (ck, 0 h), showed that plant hormone signal transduction and carotenoid biosynthesis were highly enriched. The mechanism by which holly responds to salt stress involves many plant hormones, among which the accumulation of abscisic acid (ABA) and its signal transduction may play an important role. In addition, ion homeostasis, osmotic metabolism, accumulation of antioxidant enzymes and nonenzymatic antioxidant compounds, and transcription factors jointly regulate the physiological balance in holly, providing important guarantees for its growth and development under conditions of salt stress. These results lay the foundation for studying the molecular mechanisms of salt tolerance in holly and for the selection of salt-tolerant varieties.

C-terminal frameshift mutations generate viable knockout mutants with developmental defects for three essential protein kinases

Loss-of-function mutants are fundamental resources for gene function studies. However, it is difficult to generate viable and heritable knockout mutants for essential genes. Here, we show that targeted editing of the C-terminal sequence of the embryo lethal gene MITOGEN-ACTIVATED PROTEIN KINASES 1 (OsMPK1) results in weak mutants. This C-terminal-edited osmpk1 mutants displayed severe developmental defects and altered disease resistance but generated tens of viable seeds that inherited the mutations. Using the same C-terminal editing approach, we also obtained viable mutants for a wall-associated protein kinase (Os07g0493200) and a leucine-rich repeat receptor-like protein kinase (Os01g0239700), while the null mutations of these genes were lethal. These data suggest that protein kinase activity could be reduced by introducing frameshift mutations adjacent to the C-terminus, which could generate valuable resources for gene function studies and tune protein kinase activity for signaling pathway engineering.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42994-024-00165-5.

OsMGD1-Mediated Membrane Lipid Remodeling Improves Salt Tolerance in Rice

Salt stress severely reduces photosynthetic efficiency, resulting in adverse effects on crop growth and yield production. Two key thylakoid membrane lipid components, monogalactosyldiacylglycerol (MGDG) and digalactosyldiacylglycerol (DGDG), were perturbed under salt stress. MGDG synthase 1 (MGD1) is one of the key enzymes for the synthesis of these galactolipids. To investigate the function of OsMGD1 in response to salt stress, the OsMGD1 overexpression (OE) and RNA interference (Ri) rice lines, and a wild type (WT), were used. Compared with WT, the OE lines showed higher chlorophyll content and biomass under salt stress. Besides this, the OE plants showed improved photosynthetic performance, including light absorption, energy transfer, and carbon fixation. Notably, the net photosynthetic rate and effective quantum yield of photosystem II in the OE lines increased by 27.5% and 25.8%, respectively, compared to the WT. Further analysis showed that the overexpression of OsMGD1 alleviated the negative effects of salt stress on photosynthetic membranes and oxidative defense by adjusting membrane lipid composition and fatty acid levels. In summary, OsMGD1-mediated membrane lipid remodeling enhanced salt tolerance in rice by maintaining membrane stability and optimizing photosynthetic efficiency.

Potential molecular mechanism of photosynthesis regulation by PeMPK7 in poplar under para-hydroxybenzoic acid stress

Due to continuous plantation of poplar, its growth and biomass accumulation may be negatively affected by the accumulation of allelochemicals such as para-hydroxybenzoic acid (pHBA) in soil. As photosynthesis is the most fundamental process in plants, it can be negatively impacted by pHBA stress. Therefore, it is crucial to improve photosynthetic capacity under pHBA stress to facilitate poplar plant growth. The mitogen-activated protein kinase (MAPK) cascade pathway is widely involved in environmental stress responses in plants. However, the regulation mechanisms of photosynthesis-related pathways by MAPK pathway genes under pHBA stress are still unclear. In this study, through transcriptome analysis and weighted gene co-expression network analysis, we observed that PeMPK7 overexpression in poplar can regulate the expression of photosynthesis-related genes and transcription factor genes, namely, WRKY1, WRKY33, and ERF3, during the early stage of pHBA stress. In addition, PeMPK7 can improve photosynthesis in poplar under long-term pHBA stress. Moreover, yeast two-hybrid and pull-down assays confirmed the interaction between PeMPK7 and PeMKK7/10. Based on these results, a schematic diagram of the pathways involved in the regulation of photosynthesis by PeMPK7 was constructed. This study provided novel insights into the molecular mechanisms of regulation of pHBA stress via MAPK cascade pathway.

Significance of phosphorus deficiency for the mitigation of mercury toxicity in the Robinia pseudoacacia L.- rhizobia symbiotic association

Nitrogen (N2)-fixing legumes can be used for phytoremediation of toxic heavy metal Mercury (Hg) contaminated soil, but N2-fixation highly relies on phosphorus (P) availability for nodule formation and functioning. Here, we characterized the significance of P deficiency for Hg accumulation and toxicity in woody legume plants. Consequences for foliar and root traits of rhizobia inoculation, Hg exposure (+Hg) and low P (-P) supply, individually and in combination were characterized at both the metabolite and transcriptome levels in seedlings of two Robinia pseudoacacia L. provenances originating from contrasting climate and soil backgrounds, i.e., GS in northwest and the DB in northeast China. Our results reveal that depleted P mitigates the toxicity of Hg at the transcriptional level. In leaves of Robinia depleted P reduced oxidative stress and improved the utilization strategy of C, N and P nutrition; in roots depleted P regulated the expression of genes scavenging oxidative stress and promoting cell membrane synthesis. Rhizobia inoculation significantly improved the performance of both Robinia provenances under individual and combined +Hg and -P by promoting photosynthesis, increasing foliar N and P content and reducing H2O2 and MDA accumulation despite enhanced Hg uptake. DB plants developed more nodules, had higher biomass and accumulated higher Hg amounts than GS plants and thus are suggested as the high potential Robinia provenance for future phytoremediation of Hg contaminated soils with P deficiency.

The zinc finger protein DHHC09 S-acylates the kinase STRK1 to regulate H2O2 homeostasis and promote salt tolerance in rice

Soil salinity results in oxidative stress and heavy losses to crop production. The S-acylated protein SALT TOLERANCE RECEPTOR-LIKE CYTOPLASMIC KINASE 1 (STRK1) phosphorylates and activates CATALASE C (CatC) to improve rice (Oryza sativa L.) salt tolerance, but the molecular mechanism underlying its S-acylation involved in salt signal transduction awaits elucidation. Here, we show that the DHHC-type zinc finger protein DHHC09 S-acylates STRK1 at Cys5, Cys10, and Cys14 and promotes salt and oxidative stress tolerance by enhancing rice H2O2-scavenging capacity. This modification determines STRK1 targeting to the plasma membrane or lipid nanodomains and is required for its function. DHHC09 promotes salt signaling from STRK1 to CatC via transphosphorylation, and its deficiency impairs salt signal transduction. Our findings demonstrate that DHHC09 S-acylates and anchors STRK1 to the plasma membrane to promote salt signaling from STRK1 to CatC, thereby regulating H2O2 homeostasis and improving salt stress tolerance in rice. Moreover, overexpression of DHHC09 in rice mitigates grain yield loss under salt stress. Together, these results shed light on the mechanism underlying the role of S-acylation in RLK/RLCK-mediated salt signal transduction and provide a strategy for breeding highly salt-tolerant rice.

Comparison of the genetic basis of salt tolerance at germination, seedling, and reproductive stages in an introgression line population of rice

BACKGROUND

Salinity is a major limitation for rice farming due to climate change. Since salt stress adversely impact rice plants at germination, seedling, and reproductive stages resulting in poor crop establishment and reduced grain yield, enhancing salt tolerance at these vulnerable growth stages will enhance rice productivity in salinity prone areas.

METHODS AND RESULTS

An introgression line (ILs) population from a cross between a high yielding cultivar 'Cheniere' and a salt tolerant donor 'TCCP' was evaluated to map quantitative trait loci (QTLs) for traits associated with salt tolerance at germination, seedling, and reproductive stages. Using a genotyping-by-sequencing based high density SNP linkage map, a total of 7, 16, and 30 QTLs were identified for five germination traits, seven seedling traits, and ten reproductive traits, respectively. There was overlapping of QTLs for some traits at different stages indicating the pleiotropic effects of these QTLs or clustering of linked genes. Candidate genes identified for salt tolerance were OsSDIR1 and SERF for the seedling stage, WRKY55 and OsUBC for the reproductive stage, and MYB family transcription factors for all three stages. Gene ontology analysis revealed significant GO terms related to nucleotide binding, protein binding, protein kinase activity, antiporter activity, active transmembrane transporter activity, calcium-binding protein, and F- box protein interaction domain containing protein.

CONCLUSIONS

The colocalized QTLs for traits at different growth stages would be helpful to improve multiple traits simultaneously using marker-assisted selection. The salt tolerant ILs have the potential to be released as varieties or as pre-breeding lines for developing salt tolerant rice varieties.

Exogenous melatonin induces salt and drought stress tolerance in rice by promoting plant growth and defense system

Due to global climate change, crops are certainly confronted with a lot of abiotic and biotic stress factors during their growth that cause a serious threat to their development and overall productivity. Among different abiotic stresses, salt and drought are considered the most devastating stressors with serious impact on crop's yield stability. Here, the current study aimed to elucidate how melatonin works in regulating plant biomass, oxidative stress, antioxidant defense system, as well as the expression of genes related to salt and drought stress in rice plants. Eight groups of rice plants (3 replicates, 5 plants each) underwent varied treatments: control, melatonin, salt, drought, salt + drought, salt + melatonin, drought + melatonin, and salt + drought + melatonin. Melatonin (100 µM) was alternately applied a week before stress exposure; salt stress received 100 mM NaCl every 3 days for 3 weeks, and drought stress involved 10% PEG. Young leaves were randomly sampled from each group. The results showed that melatonin treatment markedly reduces salt and drought stress damage by promoting root, shoot length, fresh and dry weight, increasing chlorophyll contents, and inhibiting excessive production of oxidative stress markers. Salt and drought stress significantly decreased the water balance, and damaged cell membrane by reducing relative water contents and increasing electrolyte leakage. However, melatonin treated rice plants showed high relative water contents and low electrolyte leakage. Under salt and drought stress conditions, exogenous application of melatonin boosted the expression level of salt and drought stress responsive genes like OsSOS, OsNHX, OsHSF and OsDREB in rice plants. Taken together, our results reveal that melatonin treatment significantly increases salt and drought tolerance of rice plants, by increasing plant biomass, suppressing ROS accumulation, elevating antioxidants defense efficiency, and up-regulating the expression of salt and drought stress responsive genes.

Comparative Transcriptome Analysis Provides Insights into the Effect of Epicuticular Wax Accumulation on Salt Stress in Coconuts

The coconut is an important tropical economical crop and exhibits high tolerance to various types of salinity stress. However, little is known about the molecular mechanism underlying its salt tolerance. In this study, RNA-Seq was applied to examine the different genes expressed in four coconut varieties when exposed to a salt environment, resulting in the generation of data for 48 transcriptomes. Comparative transcriptome analysis showed that some genes involved in cutin and wax biosynthesis were significantly upregulated in salt treatment compared to the control, including CYP86A4, HTH, CER1, CER2, CER3, DCR, GPAT4, LTP3, LTP4, and LTP5. In particular, the expression of CER2 was induced more than sixfold, with an RPKM value of up to 205 ten days after salt treatment in Hainan Tall coconut, demonstrating superior capacity in salt tolerance compared to dwarf coconut varieties. However, for yellow dwarf and red dwarf coconut varieties, the expression level of the CER2 gene was low at four different time points after exposure to salt treatment, suggesting that this gene may contribute to the divergence in salt tolerance between tall and dwarf coconut varieties. Cytological evidence showed a higher abundance of cuticle accumulation in tall coconut and severe damage to cuticular wax in dwarf coconut.

The ERF transcription factor LTF1 activates DIR1 to control stereoselective synthesis of antiviral lignans and stress defense in Isatis indigotica roots

Lignans are a powerful weapon for plants to resist stresses and have diverse bioactive functions to protect human health. Elucidating the mechanisms of stereoselective biosynthesis and response to stresses of lignans is important for the guidance of plant improvement. Here, we identified the complete pathway to stereoselectively synthesize antiviral (-)-lariciresinol glucosides in Isatis indigotica roots, which consists of three-step sequential stereoselective enzymes DIR1/2, PLR, and UGT71B2. DIR1 was further identified as the key gene in respoJanuary 2024nse to stresses and was able to trigger stress defenses by mediating the elevation in lignan content. Mechanistically, the phytohormone-responsive ERF transcription factor LTF1 colocalized with DIR1 in the cell periphery of the vascular regions in mature roots and helped resist biotic and abiotic stresses by directly regulating the expression of DIR1. These systematic results suggest that DIR1 as the first common step of the lignan pathway cooperates with PLR and UGT71B2 to stereoselectively synthesize (-)-lariciresinol derived antiviral lignans in I. indigotica roots and is also a part of the LTF1-mediated regulatory network to resist stresses. In conclusion, the LTF1-DIR1 module is an ideal engineering target to improve plant Defenses while increasing the content of valuable lignans in plants.

Autophagy receptor OsNBR1 modulates salt stress tolerance in rice

KEY MESSAGE

Autophagy receptor OsNBR1 modulates salt stress tolerance by affecting ROS accumulation in rice. The NBR1 (next to BRCA1 gene 1), as important selective receptors, whose functions have been reported in animals and plants. Although the function of NBR1 responses to abiotic stress has mostly been investigated in Arabidopsis thaliana, the role of NBR1 under salt stress conditions remains unclear in rice (Oryza sativa). In this study, by screening the previously generated activation-tagged line, we identified a mutant, activation tagging 10 (AC10), which exhibited salt stress-sensitive phenotypes. TAIL-PCR (thermal asymmetric interlaced PCR) showed that the AC10 line carried a loss-of-function mutation in the OsNBR1 gene. OsNBR1 was found to be a positive regulator of salt stress tolerance and was localized in aggregates. A loss-of-function mutation in OsNBR1 increased salt stress sensitivity, whereas overexpression of OsNBR1 enhanced salt stress resistance. The osnbr1 mutants showed higher ROS (reactive oxygen species) production, whereas the OsNBR1 overexpression (OsNBR1OE) lines showed lower ROS production, than Kitaake plants under normal and salt stress conditions. Furthermore, RNA-seq analysis revealed that expression of OsRBOH9 (respiratory burst oxidase homologue) was increased in osnbr1 mutants, resulting in increased ROS accumulation in osnbr1 mutants. Together our results established that OsNBR1 responds to salt stress by influencing accumulation of ROS rather than by regulating transport of Na+ and K+ in rice.

Rice OsANN9 Enhances Drought Tolerance through Modulating ROS Scavenging Systems

Drought is a critical abiotic stress which leads to crop yield and a decrease in quality. Annexins belong to a multi-gene family of calcium- and lipid-binding proteins and play diverse roles in plant growth and development. Herein, we report a rice annexin protein, OsANN9, which in addition to regular annexin repeats and type-II Ca2+ binding sites, also consists of a C2H2-type zinc-finger domain. We found that the expression of OsANN9 was upregulated by polyethylene glycol (PEG) or water-deficient treatment. Moreover, plants that overexpressed OsANN9 had increased survival rates under drought stress, while both OsANN9-RNAi and osann9 mutants showed sensitivity to drought. In addition, the overexpression of OsANN9 increased superoxide dismutase (SOD), peroxidase (POD) and catalase (CAT) activities, which regulate reactive oxygen species homeostasis. Collectively, these findings indicate that OsANN9 may function as a positive regulator in response to drought stress by modulating antioxidant accumulation. Interestingly, the setting rates of osann9 mutant rice plants significantly decreased in comparison to wild-type plants, suggesting that OsANN9 might be involved in other molecular mechanisms in the rice seed development stage.

A comprehensive investigation of the regulatory roles of OsERF096, an AP2/ERF transcription factor, in rice cold stress response

KEY MESSAGE

OsERF096 negatively regulates rice cold tolerance and mediates IAA biosynthesis and signaling under cold stress. The APETALA2/ethylene-responsive factor (AP2/ERF) transcription factors play important roles in regulating plant tolerance to abiotic stress. OsERF096 was previously identified as a direct target of miR1320, and was suggested to negatively regulate rice cold tolerance. In this study, we performed RNA-sequencing and targeted metabolomics assays to reveal the regulatory roles of OsERF096 in cold stress response. GO and KEGG analysis of differentially expressed genes showed that the starch and sucrose metabolism, plant-pathogen interaction, and plant hormone signal transduction pathways were significantly enriched. Quantification analysis confirmed a significant difference in sugar contents among WT and OsERF096 transgenic lines under cold treatment. Targeted metabolomics analysis uncovered that IAA accumulation and signaling were modified by OsERF096 in response to cold stress. Expectedly, qRT-PCR assays confirmed significant OsIAAs and OsARFs expression changes in OsERF096 transgenic lines. Finally, we identified three targets of OsERF096 based on RNA-seq, qRT-PCR, and dual-LUC assays. In summary, these results revealed the multiple regulatory roles of OsERF096 in cold stress response.

Co-Expression Network Analysis of the Transcriptome Identified Hub Genes and Pathways Responding to Saline-Alkaline Stress in Sorghum bicolor L

Soil salinization, an intractable problem, is becoming increasingly serious and threatening fragile natural ecosystems and even the security of human food supplies. Sorghum (Sorghum bicolor L.) is one of the main crops growing in salinized soil. However, the tolerance mechanisms of sorghum to saline-alkaline soil are still ambiguous. In this study, RNA sequencing was carried out to explore the gene expression profiles of sorghum treated with sodium bicarbonate (150 mM, pH = 8.0, treated for 0, 6, 12 and 24 h). The results show that 6045, 5122, 6804, 7978, 8080 and 12,899 differentially expressed genes (DEGs) were detected in shoots and roots after 6, 12 and 24 h treatments, respectively. GO, KEGG and weighted gene co-expression analyses indicate that the DEGs generated by saline-alkaline stress were primarily enriched in plant hormone signal transduction, the MAPK signaling pathway, starch and sucrose metabolism, glutathione metabolism and phenylpropanoid biosynthesis. Key pathway and hub genes (TPP1, WRKY61, YSL1 and NHX7) are mainly related to intracellular ion transport and lignin synthesis. The molecular and physiological regulation processes of saline-alkali-tolerant sorghum are shown by these results, which also provide useful knowledge for improving sorghum yield and quality under saline-alkaline conditions.

Metabolomics-mediated elucidation of rice responses to salt stress

MAIN CONCLUSION

Role of salinity responsive metabolites of rice and its wild species has been discussed. Salinity stress is one of the important environmental stresses that severely affects rice productivity. Although, several vital physio-biochemical and molecular responses have been activated in rice under salinity stress which were well described in literatures, the mechanistic role of salt stress and microbes-induced metabolites to overcome salt stress in rice are less studied. Nevertheless, over the years, metabolomic studies have allowed a comprehensive analyses of rice salt stress responses. Hence, we review the salt stress-triggered alterations of various metabolites in rice and discuss their significant roles toward salinity tolerance. Some of the metabolites such as serotonin, salicylic acid, ferulic acid and gentisic acid may act as signaling molecules to activate different downstream salt-tolerance mechanisms; whereas, the other compounds such as amino acids, sugars and organic acids directly act as protective agents to maintain osmotic balance and scavenger of reactive oxygen species during the salinity stress. The quantity, type, tissues specificity and time of accumulation of metabolites induced by salinity stress vary between salt-sensitive and tolerant rice genotypes and thus, contribute to their different degrees of salt tolerance. Moreover, few tolerance metabolites such as allantoin, serotonin and melatonin induce unique pathways for activation of defence mechanisms in salt-tolerant varieties of rice, suggesting their potential roles as the universal biomarkers for salt tolerance. Therefore, these metabolites can be applied exogenously to the sensitive genotypes of rice to enhance their performance under salt stress. Furthermore, the microbes of rhizosphere also participated in rice salt tolerance either directly or indirectly by regulating their metabolic pathways. Thus, this review for the first time offers valuable and comprehensive insights into salt-induced spatio-temporal and genotype-specific metabolites in different genotypes of rice which provide a reference point to analyze stress-gene-metabolite relationships for the biomarker designing in rice. Further, it can also help to decipher several metabolic systems associated with salt tolerance in rice which will be useful in developing salt-tolerance cultivars by conventional breeding/genetic engineering/exogenous application of metabolites.

Desalination brine effects beyond excess salinity: Unravelling specific stress signaling and tolerance responses in the seagrass Posidonia oceanica

Desalination has been proposed as a global strategy for tackling freshwater shortage in the climate change era. However, there is a concern regarding the environmental effects of high salinity brines discharged from desalination plants on benthic communities. In this context, seagrasses such as the Mediterranean endemic and ecologically important Posidonia oceanica have shown high vulnerability to elevated salinities. Most ecotoxicological studies regarding desalination effects are based on salinity increments using artificial sea salts, although it has been postulated that certain additives within the industrial process of desalination may exacerbate a negative impact beyond just the increased salinities of the brine. To assess the potential effect of whole effluent brines on P. oceanica, mesocosm experiments were conducted within 10 days, simulating salinity increment with either artificial sea salts or brines from a desalination plant (at 43 psμ, 6 psμ over the natural 37 psμ). Morphometrical (growth and necrosis), photochemical (PSII chlorophyll a fluorometry), metabolic, such as hydrogen peroxide (H2O2), thiobarbituric reactive substances (TBARS) and ascorbate/dehydroascorbate (ASC/DHA), and molecular (expression of key tolerance genes) responses were analyzed in each different treatment. Although with a still positive leaf growth, associated parameters decreased similarly for both artificial sea salt and brine treatments. Photochemical parameters did not show general patterns, although only P. oceanica under brines demonstrated greater energy release through heat (NPQ). Lipid peroxidation and upregulation of genes related to oxidative stress (GR, MnSOD, and FeSOD) or ion exclusion (SOS3 and AKT2/3) were similarly incremented on both hypersalinity treatments. Conversely, the ASC/DHA ratio was significantly lower, and the expression of SOS1, CAT, and STRK1 was increased under brine influence. This study revealed that although metabolic and photochemical differences occurred under both hypersalinity treatments, growth (the last sign of physiological detriment) was similarly compromised, suggesting that the potential effects of desalination are mainly caused by brine-associated salinities and are not particularly related to other industrial additives.

GhDof1.7, a Dof Transcription Factor, Plays Positive Regulatory Role under Salinity Stress in Upland Cotton

Salt stress is a major abiotic stressor that can severely limit plant growth, distribution, and crop yield. DNA-binding with one finger (Dof) is a plant-specific transcription factor that plays a crucial role in plant growth, development, and stress response. In this study, the function of a Dof transcription factor, GhDof1.7, was investigated in upland cotton. The GhDof1.7 gene has a coding sequence length of 759 base pairs, encoding 252 amino acids, and is mainly expressed in roots, stems, leaves, and inflorescences. Salt and abscisic acid (ABA) treatments significantly induced the expression of GhDof1.7. The presence of GhDof1.7 in Arabidopsis may have resulted in potential improvements in salt tolerance, as suggested by a decrease in H2O2 content and an increase in catalase (CAT) and superoxide dismutase (SOD) activities. The GhDof1.7 protein was found to interact with GhCAR4 (C2-domain ABA-related 4), and the silencing of either GhDof1.7 or GhCAR4 resulted in reduced salt tolerance in cotton plants. These findings demonstrate that GhDof1.7 plays a crucial role in improving the salt tolerance of upland cotton and provide insight into the regulation of abiotic stress response by Dof transcription factors.

OsSTS, a Novel Allele of Mitogen-Activated Protein Kinase Kinase 4 (OsMKK4), Controls Grain Size and Salt Tolerance in Rice

Soil salinization is one of the most common abiotic stresses of rice, which seriously affects the normal growth of rice. Breeding salt-tolerant varieties have become one of the important ways to ensure food security and sustainable agricultural development. However, the mechanisms underlying salt tolerance control still need to be clarified. In this study, we identified a mutant, termed salt-tolerant and small grains(sts), with salt tolerance and small grains. Gene cloning and physiological and biochemical experiments reveal that sts is a novel mutant allele of Mitogen-activated protein Kinase Kinase 4 (OsMKK4), which controls the grain size, and has recently been found to be related to salt tolerance in rice. Functional analysis showed that OsSTS is constitutively expressed throughout the tissue, and its proteins are localized to the nucleus, cell membrane, and cytoplasm. It was found that the loss of OsSTS function enhanced the salt tolerance of rice seedlings, and further studies showed that the loss of OsSTS function increased the ROS clearance rate of rice seedlings, independent of ionic toxicity. In order to explore the salt tolerance mechanism of sts, we found that the salt tolerance of sts is also regulated by ABA through high-throughput mRNA sequencing. Salt and ABA treatment showed that ABA might alleviate the inhibitory effect of salt stress on root length in sts. These results revealed new functions of grain size gene OsMKK4, expanded new research ideas related to salt tolerance mechanism and hormone regulation network, and provided a theoretical basis for salt-tolerant rice breeding.

Genome-wide analysis of the AP2/ERF gene family in Tritipyrum and the response of TtERF_B2-50 in salt-tolerance

The AP2/ERF transcription factor is widely distributed across the plant kingdom and plays a crucial role in various abiotic stress responses in plants. Tritipyrum, an octoploid resulting from an intergeneric cross between Triticum aestivum (AABBDD) and Thinopyrum elongatum (EE), is a valuable source of germplasm for incorporating superior traits of Th. elongatum into T. aestivum. With the recent availability of whole -genome sequences for T. aestivum and Th. elongatum, we explored the organization and expression profiling of Tritipyrum AP2/ERF genes across the entire genome. Our investigation identified 543 Tritipyrum AP2/ERF genes, which evolutionary analysis categorized into four major groups (AP2, DREB, ERF, and RAV), whose members share a conserved motif composition. These 543 TtAP2/ERF genes were distributed throughout 28 chromosomes, with 132 duplications. Synteny analysis suggests that the AP2/ERF gene family may have a common ancestor. Transcriptome data and Real-Time PCR expression profiles revealed 43 TtAP2/ERF genes with high expression levels in response to various salt stressors and recovery regimens. Tel2E01T236300 (TtERF_B2-50) was particularly salt stress-sensitive and evolutionarily related to the salt-tolerant gene AtERF7 in A. thaliana. Pearson correlation analysis identified 689 genes positively correlated (R > 0.9) with TtERF_B2-50 expression, enriched in metabolic activities, cellular processes, stimulus response, and biological regulation. Real-time PCR showed that TtERF_B2-50 was highly expressed in roots, stems, and leaves under salt stress. These findings suggest that TtERF_B2-50 may be associated with salt stress tolerance and may serve as a valuable foreign gene for enhancing salt tolerance in wheat.

Proline Metabolism Process and Antioxidant Potential of Lycium ruthenicum Murr. in Response to NaCl Treatments

Salinity influences the level of antioxidants and proline content, which are both involved in the regulation of stress responses in plants. To examine the interplay between the antioxidant system and proline metabolism in plant stress acclimation, explants of Lycium ruthenicum were subjected to NaCl treatments, and the growth characteristics, antioxidant enzyme activities, proline accumulation, and metabolic enzyme content were analyzed. The results revealed that NaCl concentrations between 50 to 150 mM have a positive effect on the growth of L. ruthenicum explants. Increasing NaCl concentrations elevated the activities of superoxide dismutase (SOD) and catalase (CAT), while hydrogen peroxide (H2O2) content was inhibited, suggesting that the elevated antioxidants play a central protective role in superoxide anion (O2•-) and H2O2 scavenging processes in response to NaCl treatments. Also, high proline levels also protect antioxidant enzyme machinery, thus protecting the plants from oxidative damage and enhancing osmotic adjustment. Increasing levels of pyrroline-5-carboxylate synthetase (P5CS), pyrroline-5-carboxylate reductase (P5CR), and ornithine-δ-aminotransferase (δ-OAT) were observed, resulting in elevated level of proline. In addition, the expression levels of LrP5CS1, -2, -3, LrOAT-1, and -2 were promoted in NaCl treatments. According to the combined analysis of metabolic enzyme activities and their relative expression, it is confirmed that the glutamate (Glu) pathway is activated in L. ruthenicum faced with different levels of NaCl concentrations. However, Glu supplied by δ-OAT is fed back into the main pathway for proline metabolism.

The protein phosphatase PC1 dephosphorylates and deactivates CatC to negatively regulate H2O2 homeostasis and salt tolerance in rice

Catalase (CAT) is often phosphorylated and activated by protein kinases to maintain hydrogen peroxide (H2O2) homeostasis and protect cells against stresses, but whether and how CAT is switched off by protein phosphatases remains inconclusive. Here, we identified a manganese (Mn2+)-dependent protein phosphatase, which we named PHOSPHATASE OF CATALASE 1 (PC1), from rice (Oryza sativa L.) that negatively regulates salt and oxidative stress tolerance. PC1 specifically dephosphorylates CatC at Ser-9 to inhibit its tetramerization and thus activity in the peroxisome. PC1 overexpressing lines exhibited hypersensitivity to salt and oxidative stresses with a lower phospho-serine level of CATs. Phosphatase activity and seminal root growth assays indicated that PC1 promotes growth and plays a vital role during the transition from salt stress to normal growth conditions. Our findings demonstrate that PC1 acts as a molecular switch to dephosphorylate and deactivate CatC and negatively regulate H2O2 homeostasis and salt tolerance in rice. Moreover, knockout of PC1 not only improved H2O2-scavenging capacity and salt tolerance but also limited rice grain yield loss under salt stress conditions. Together, these results shed light on the mechanisms that switch off CAT and provide a strategy for breeding highly salt-tolerant rice.

OsAAI1 Increases Rice Yield and Drought Tolerance Dependent on ABA-Mediated Regulatory and ROS Scavenging Pathway

In this study, we investigated the function of OsAAI1 in yield and drought tolerance by constructing overexpression line OE-OsAAI1 and mutant line osaai1. Bioinformatics analysis showed that the AAI gene-OsAAI1- belongs to the HPS_like subfamily of the AAI_LTSS superfamily, and OsAAI1 was localized in the nucleus. The expression of OsAAI1 was significantly induced by ABA and drought stress. OsAAI1 overexpression (OE19) significantly increased, and gene mutant (osaai1-1) repressed plant height, primary root length, lateral root number, grain size and yield in rice. Moreover, physiological and biochemical analyses showed that osaai1 was sensitive to drought stress, while OE19 enhanced the drought tolerance in rice. DAB and NBT staining revealed that under drought treatment, osaai1 accumulated a large amount of ROS compared with the wild type, while OE19 accumulated the least, and CAT, APX, GPX, GR activities were higher in OE19 and lower in osaai1, suggesting that OE19 improves rice tolerance to drought stress by enhancing ROS scavenging ability. OE19 also induce the expression of ABA-mediated regulatory pathway genes and enhance accumulation of ABA content in rice seedling. Predictably, OE19 displayed enhanced sensitivity to ABA, and ROS accumulation was significantly higher than in wild type and osaai1 under 3 µM ABA treatment. Thus, these results suggest that OsAAI1 is a positive regulator of rice yield and drought tolerance dependent on the ABA-mediated regulatory and ROS scavenging pathway.

Catalase Gene Family in Durum Wheat: Genome-Wide Analysis and Expression Profiling in Response to Multiple Abiotic Stress Conditions

Catalase (CAT) is an antioxidant enzyme expressed by the CAT gene family and exists in almost all aerobic organisms. In fact, the CAT enzyme modulates the hydrogen peroxide (H₂O₂) contents in cells by translating this toxic compound into water (H₂O) and O₂^- to reduce reactive oxygen species (ROS) contents in cells. ROS are produced as a result of biotic and abiotic environmental stressors. To avoid ROS toxicity, plants are armed with different enzymatic and non-enzymatic systems to decompose ROS. Among the enzymatic system, CAT proteins are well studied. CAT not only controls growth and development in plants but is also involved in plant defense against different stresses. So far, the CAT gene family has not been reported in durum wheat (Triticum turgidum ssp. durum L.). Therefore, a genome-wide comprehensive analysis was conducted to classify the CAT genes in the durum wheat genome. Here, six TdCAT genes were identified. Based on phylogenetics, the TdCAT genes belong to three groups (Groups I-III) which is explainable by their comparable structural characteristics. Using bio-informatic analysis, we found that the secondary and tertiary structures were conserved among plants and present similar structures among durum wheat CATs. Two conserved domains (pfam00199 and pfam06628) are also present in all identified proteins, which have different subcellular localizations: peroxisome and mitochondrion. By analyzing their promoters, different cis-elements were identified, such as hormone-correlated response and stress-related responsive elements. Finally, we studied the expression pattern of two catalase genes belonging to two different sub-classes under different abiotic stresses. Expression profiling revealed that TdCAT2 and TdCAT3 presented a constitutive expression pattern. Moreover, both genes are induced in response to salt, mannitol, cold, heat and ABA. Thus, we speculate that those genes are activated by different stresses, such as oxygen deficiency, light, cold, abscisic acid and methyl jasmonate. Further, this study will help in understanding the behavior of CAT genes during environmental stress in durum wheat and in Triticeae species in general.

A Review of Potato Salt Tolerance

Potato is the world's fourth largest food crop. Due to limited arable land and an ever-increasing demand for food from a growing population, it is critical to increase crop yields on existing acreage. Soil salinization is an increasing problem that dramatically impacts crop yields and restricts the growing area of potato. One possible solution to this problem is the development of salt-tolerant transgenic potato cultivars. In this work, we review the current potato planting distribution and the ways in which it overlaps with salinized land, in addition to covering the development and utilization of potato salt-tolerant cultivars. We also provide an overview of the current progress toward identifying potato salt tolerance genes and how they may be deployed to overcome the current challenges facing potato growers.

PeMPK17 interacts with PeMKK7 and participates in para-hydroxybenzoic acid stress resistance by removing reactive oxygen species

Mitogen-activated protein kinase (MAPK) plays a crucial role in plant stress response. Poplar is one of the most important afforestation and timber species and inevitably encounters allelopathy effects during continuous cropping. para-hydroxybenzoic acid (pHBA) is a primary soil allelochemical, which can restrict the growth and biomass of poplar. However, the involvement of MAPKs in the underlying physiological and molecular regulatory mechanisms in response to pHBA stress remains unclear. In this study, PeMPK17, a gene encoding a group D MAPK, was cloned from Populus × euramericana. PeMPK17 protein was localized in both nucleus and plasma membrane. Quantitative real-time polymerase chain reaction analysis demonstrated that PeMPK17 expression in poplar increased when treated with pHBA, PEG, and H₂O₂. Exogenous pHBA and H₂O₂ induced PeMPK17 expression mediated by reactive oxygen species (ROS). The transgenic poplar plants overexpressing PeMPK17 demonstrated attenuated phenotypic injury, higher relative water content in leaves, and lower ion leakage under pHBA stress. In transgenic poplar, the activity and expression of antioxidant enzymes including superoxide dismutase, peroxidase, and catalase increased, while the content of H₂O₂, O₂·^-, and malondialdehyde decreased. These results suggested that PeMPK17 protects cell membranes from oxidative damage by removing excess ROS. In addition, overexpression of PeMPK17 promoted osmoprotectant accumulation including soluble sugar and free proline, which may aid in the regulation of ROS balance under pHBA treatment. Furthermore, the interaction between PeMPK17 and PeMKK7 was confirmed. Collectively, these data identify the molecular mechanisms and signal pathways associated with PeMPK17 that regulate pHBA response in poplar.

Twenty years of mining salt tolerance genes in soybean

Current combined challenges of rising food demand, climate change and farmland degradation exert enormous pressure on agricultural production. Worldwide soil salinization, in particular, necessitates the development of salt-tolerant crops. Soybean, being a globally important produce, has its genetic resources increasingly examined to facilitate crop improvement based on functional genomics. In response to the multifaceted physiological challenge that salt stress imposes, soybean has evolved an array of defences against salinity. These include maintaining cell homeostasis by ion transportation, osmoregulation, and restoring oxidative balance. Other adaptations include cell wall alterations, transcriptomic reprogramming, and efficient signal transduction for detecting and responding to salt stress. Here, we reviewed functionally verified genes that underly different salt tolerance mechanisms employed by soybean in the past two decades, and discussed the strategy in selecting salt tolerance genes for crop improvement. Future studies could adopt an integrated multi-omic approach in characterizing soybean salt tolerance adaptations and put our existing knowledge into practice via omic-assisted breeding and gene editing. This review serves as a guide and inspiration for crop developers in enhancing soybean tolerance against abiotic stresses, thereby fulfilling the role of science in solving real-life problems.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-023-01383-3.

Receptor-Like Cytoplasmic Kinase STK Confers Salt Tolerance in Rice

BACKGROUND

Soil salinization is a major abiotic environmental stress factor threatening crop production throughout the world. Salt stress drastically affects the growth, development, and grain yield of rice (Oryza sativa L.), and the improvement of rice tolerance to salt stress is a desirable approach for meeting increasing food demand. Receptor-like cytoplasmic kinases (RLCKs) play essential roles in plant growth, development and responses to environmental stresses. However, little is known about their functions in salt stress. Previous reports have demonstrated that overexpression of an RLCK gene SALT TOLERANCE KINASE (STK) enhances salt tolerance in rice, and that STK may regulate the expression of GST (Glutathione S-transferase) genes.

RESULTS

The expression of STK was rapidly induced by ABA. STK was highest expressed in the stem at the heading stage. STK was localized at the plasma membrane. Overexpression of STK in rice increased tolerance to salt stress and oxidative stress by increasing ROS scavenging ability and ABA sensitivity. In contrast, CRISPR/Cas9-mediated knockout of STK increased the sensitivity of rice to salt stress and oxidative stress. Transcriptome sequencing analysis suggested that STK increased the expression of GST genes (LOC_Os03g17480, LOC_Os10g38140 and LOC_Os10g38710) under salt stress. Reverse transcription quantitative PCR (RT-qPCR) suggested that four stress-related genes may be regulated by STK including OsABAR1, Os3BGlu6, OSBZ8 and OsSIK1.

CONCLUSIONS

These findings suggest that STK plays a positive regulatory role in salt stress tolerance by inducing antioxidant defense and associated with the ABA signaling pathway in rice.

Physiological and transcriptome analysis of response of soybean (Glycine max) to cadmium stress under elevated CO2 concentration

The continuous accumulation of Cd has long-lasting detrimental effects on plant growth and food safety. Although elevated CO₂ concentration (EC) has been reported to reduce Cd accumulation and toxicity in plants, evidence on the functions of elevated CO₂ concentration and its mechanisms in the possible alleviation of Cd toxicity in soybean are limited. Here, we used physiological and biochemical methods together with transcriptomic comparison to explore the effects of EC on Cd-stressed soybean. Under Cd stress, EC significantly increased the weight of roots and leaves, promoted the accumulations of proline, soluble sugars, and flavonoid. In addition, the enhancement of GSH activity and GST gene expressions promoted Cd detoxification. These defensive mechanisms reduced the contents of Cd²⁺, MDA, and H₂O₂ in soybean leaves. The up-regulation of genes encoding phytochelatin synthase, MTPs, NRAMP, and vacuoles protein storage might play vital roles in the transportation and compartmentalization process of Cd. The MAPK and some transcription factors such as bHLH, AP2/ERF, and WRKY showed changed expressions and might be engaged in mediation of stress response. These findings provide a boarder view on the regulatory mechanism of EC on Cd stress and provide numerous potential target genes for future engineering of Cd-tolerant cultivars in soybean breeding programs under climate changes scenarios.

Growth-regulating factor 15-mediated gene regulatory network enhances salt tolerance in poplar

Soil salinity is an important determinant of crop productivity and triggers salt stress response pathways in plants. The salt stress response is controlled by transcriptional regulatory networks that maintain regulatory homeostasis through combinations of transcription factor (TF)-DNA and TF-TF interactions. We investigated the transcriptome of poplar 84 K (Populus alba × Populus glandulosa) under salt stress using samples collected at 4- or 6-h intervals within 2 days of salt stress treatment. We detected 24,973 differentially expressed genes, including 2,231 TFs that might be responsive to salt stress. To explore these interactions and targets of TFs in perennial woody plants, we combined gene regulatory networks, DNA affinity purification sequencing, yeast two-hybrid-sequencing, and multi-gene association approaches. Growth-regulating factor 15 (PagGRF15) and its target, high-affinity K+ transporter 6 (PagHAK6), were identified as an important regulatory module in the salt stress response. Overexpression of PagGRF15 and PagHAK6 in transgenic lines improved salt tolerance by enhancing Na+ transport and modulating H2O2 accumulation in poplar. Yeast two-hybrid assays identified more than 420 PagGRF15-interacting proteins, including ETHYLENE RESPONSE FACTOR TFs and a zinc finger protein (C2H2) that are produced in response to a variety of phytohormones and environmental signals and are likely involved in abiotic stress. Therefore, our findings demonstrate that PagGRF15 is a multifunctional TF involved in growth, development, and salt stress tolerance, highlighting the capability of a multifaceted approach in identifying regulatory nodes in plants.

Salinity Alleviation and Reduction in Oxidative Stress by Endophytic and Rhizospheric Microbes in Two Rice Cultivars

Increased soil salinity poses serious limitations in crop yield and quality; thus, an attempt was made to explore microbial agents to mitigate the ill effects of salinity in rice. The hypothesis was mapping of microbial induction of stress tolerance in rice. Since the rhizosphere and endosphere are two different functional niches directly affected by salinity, it could be very crucial to evaluate them for salinity alleviation. In this experiment, endophytic and rhizospheric microbes were tested for differences in salinity stress alleviation traits in two rice cultivars, CO51 and PB1. Two endophytic bacteria, Bacillus haynesii 2P2 and Bacillus safensis BTL5, were tested with two rhizospheric bacteria, Brevibacterium frigoritolerans W19 and Pseudomonas fluorescens 1001, under elevated salinity (200 mM NaCl) along with Trichoderma viride as an inoculated check. The pot study indicated towards the presence of variable salinity mitigation mechanisms among these strains. Improvement in the photosynthetic machinery was also recorded. These inoculants were evaluated for the induction of antioxidant enzymes viz. CAT, SOD, PO, PPO, APX, and PAL activity along with the effect on proline levels. Modulation of the expression of salt stress responsive genes OsPIP1, MnSOD1, cAPXa, CATa, SERF, and DHN was assessed. Root architecture parameters viz. cumulative length of total root, projection area, average diameter, surface area, root volume, fractal dimension, number of tips, and forks were studied. Confocal scanning laser microscopy indicated accumulation of Na⁺ in leaves using cell impermeant Sodium Green™, Tetra (Tetramethylammonium) Salt. It was found that each of these parameters were induced differentially by endophytic bacteria, rhizospheric bacteria, and fungus, indicating different paths to complement one ultimate plant function. The biomass accumulation and number of effective tillers were highest in T4 (Bacillus haynesii 2P2) plants in both cultivars and showed the possibility of cultivar specific consortium. These strains and their mechanisms could form the basis for further evaluating microbial strains for climate-resilient agriculture.

Membrane Proteins in Plant Salinity Stress Perception, Sensing, and Response

Plants have several mechanisms to endure salinity stress. The degree of salt tolerance varies significantly among different terrestrial crops. Proteins at the plant's cell wall and membrane mediate different physiological roles owing to their critical positioning between two distinct environments. A specific membrane protein is responsible for a single type of activity, such as a specific group of ion transport or a similar group of small molecule binding to exert multiple cellular effects. During salinity stress in plants, membrane protein functions: ion homeostasis, signal transduction, redox homeostasis, and solute transport are essential for stress perception, signaling, and recovery. Therefore, comprehensive knowledge about plant membrane proteins is essential to modulate crop salinity tolerance. This review gives a detailed overview of the membrane proteins involved in plant salinity stress highlighting the recent findings. Also, it discusses the role of solute transporters, accessory polypeptides, and proteins in salinity tolerance. Finally, some aspects of membrane proteins are discussed with potential applications to developing salt tolerance in crops.

MKKK20 works as an upstream triple-kinase of MKK3-MPK6-MYC2 module in Arabidopsis seedling development

The mitogen-activated protein kinase (MAPK) cascade is involved in several signal transduction processes in eukaryotes. Here, we report a mechanistic function of MAP kinase kinase kinase 20 (MKKK20) in light signal transduction pathways. We show that MKKK20 acts as a negative regulator of photomorphogenic growth at various wavelengths of light. MKKK20 not only regulates the expression of light signaling pathway regulatory genes but also gets regulated by the same pathway genes. The atmyc2 mkkk20 double mutant analysis shows that MYC2 works downstream to MKKK20 in the regulation of photomorphogenic growth. MYC2 directly binds to the promoter of MKKK20 to modulate its expression. The protein-protein interaction study indicates that MKKK20 physically interacts with MYC2, and this interaction likely suppresses the MYC2-mediated promotion of MKKK20 expression. Further, the protein phosphorylation studies demonstrate that MKKK20 works as the upstream kinase of MKK3-MPK6-MYC2 module in photomorphogenesis.

Identification of a DEAD-box RNA Helicase BnRH6 Reveals Its Involvement in Salt Stress Response in Rapeseed (Brassica napus)

Rapeseed (Brassica napus) is one of the most important vegetable oil crops worldwide. Abiotic stresses such as salinity are great challenges for its growth and productivity. DEAD-box RNA helicase 6 (RH6) is a subfamily member of superfamily 2 (SF2), which plays crucial roles in plant growth and development. However, no report is available on RH6 in regulating plant abiotic stress response. This study investigated the function and regulatory mechanism for BnRH6. BnRH6 was targeted to the nucleus and cytoplasmic processing body (P-body), constitutively expressed throughout the lifespan, and induced by salt stress. Transgenic overexpressing BnRH6 in Brassica and Arabidopsis displayed salt hypersensitivity, manifested by lagging seed germination (decreased to 55−85% of wild-type), growth stunt, leaf chlorosis, oxidative stress, and over-accumulation of Na ions with the K+/Na+ ratio being decreased by 18.3−28.6%. Given the undesirable quality of knockout Brassica plants, we utilized an Arabidopsis T-DNA insertion mutant rh6-1 to investigate downstream genes by transcriptomics. We constructed four libraries with three biological replicates to investigate global downstream genes by RNA sequencing. Genome-wide analysis of differentially expressed genes (DEGs) (2-fold, p < 0.05) showed that 41 genes were upregulated and 66 genes were downregulated in rh6-1 relative to wild-type under salt stress. Most of them are well-identified and involved in transcription factors, ABA-responsive genes, and detoxified components or antioxidants. Our research suggests that BnRH6 can regulate a group of salt-tolerance genes to negatively promote Brassica adaptation to salt stress.

Suppression of microRNA168 enhances salt tolerance in rice (Oryza sativa L.)

BACKGROUND

Rice is a salt-sensitive crop. Complex gene regulatory cascades are likely involved in salinity stress in rice roots. microRNA168 (miR168) is a conserved miRNA among different plant species. It in-directly regulates the expression of all miRNAs by targeting gene ARGONAUTE1(AGO1). Short Tandem Target Mimic (STTM) technology is an ideal approach to study miRNA functions by in-activating mature miRNA in plants.

RESULTS

In this study, rice miR168 was inactivated by STTM. The T3 generation seedlings of STTM168 exhibited significantly enhanced salt resistance. Direct target genes of rice miR168 were obtained by in silico prediction and further confirmed by degradome-sequencing. PINHEAD (OsAGO1), which was previously suggested to be a plant abiotic stress response regulator. RNA-Seq was performed in root samples of 150mM salt-treated STTM168 and control seedlings. Among these screened 481 differentially expressed genes within STTM168 and the control, 44 abiotic stress response related genes showed significant difference, including four known salt-responsive genes.

CONCLUSION

Based on sequencing and qRT-PCR, a "miR168-AGO1-downstream" gene regulation model was proposed to be responsible for rice salt stress response. The present study proved miR168-AGO1 cascade to play important role in rice salinity stress responding, as well as to be applied in agronomic improvement in further.

Role of Melatonin and Nitrogen Metabolism in Plants: Implications under Nitrogen-Excess or Nitrogen-Low

Melatonin is a new plant hormone involved in multiple physiological functions in plants such as germination, photosynthesis, plant growth, flowering, fruiting, and senescence, among others. Its protective role in different stress situations, both biotic and abiotic, has been widely demonstrated. Melatonin regulates several routes in primary and secondary plant metabolism through the up/down-regulation of many enzyme/factor genes. Many of the steps of nitrogen metabolism in plants are also regulated by melatonin and are presented in this review. In addition, the ability of melatonin to enhance nitrogen uptake under nitrogen-excess or nitrogen-low conditions is analyzed. A model that summarizes the distribution of nitrogen compounds, and the osmoregulation and redox network responses mediated by melatonin, are presented. The possibilities of using melatonin in crops for more efficient uptake, the assimilation and metabolization of nitrogen from soil, and the implications for Nitrogen Use Efficiency strategies to improve crop yield are also discussed.

Impact of OsBadh2 Mutations on Salt Stress Response in Rice

Mutations in the Betaine aldehyde dehydrogenase 2 (OsBadh2) gene resulted in aroma, which is a highly preferred grain quality attribute in rice. However, research on naturally occurring aromatic rice has revealed ambiguity and controversy regarding aroma emission, stress tolerance, and response to salinity. In this study, mutant lines of two non-aromatic varieties, Huaidao#5 (WT_HD) and Jiahua#1 (WT_JH), were generated by targeted mutagenesis of OsBadh2 using CRISPR/Cas9 technology. The mutant lines of both varieties became aromatic; however, WT_HD mutants exhibited an improved tolerance, while those of WT_JH showed a reduced tolerance to salt stress. To gain insight into the molecular mechanism leading to the opposite effects, comparative analyses of the physiological activities and expressions of aroma- and salinity-related genes were investigated. The WT_HD mutants had a lower mean increment rate of malondialdehyde, superoxide dismutase, glutamate, and proline content, with a higher mean increment rate of γ-aminobutyric acid, hydrogen peroxide, and catalase than the WT_JH mutants. Fluctuations were also detected in the salinity-related gene expression. Thus, the response mechanism of OsBadh2 mutants is complicated where the genetic makeup of the rice variety and interactions of several genes are involved, which requires more in-depth research to explore the possibility of producing highly tolerant aromatic rice genotypes.

Improving the Tolerance to Salinity Stress in Lettuce Plants (Lactuca sativa L.) Using Exogenous Application of Salicylic Acid, Yeast, and Zeolite

Salinity is among the most limiting factors of crop production worldwide. This study aims to investigate the influence of the exogenous application of zeolite, yeast, and salicylic acid in alleviating the negative effect of salt stress under field conditions. Lettuce plants (Lactuca sativa L. cv. Batavia) were tested in a split-plot arrangement replicated three times. The salt stress was applied as a whole-plot factor in the concentrations (0 mM, 50 mM, 100 mM, and 150 mM NaCl). After 28 days of sowing, the plants were sprayed twice during the foliage growth with (control, salicylic acid 0.02%, yeast extract 3%, and zeolite 0.5%) as a split-plot factor. The length of roots and shoots, the number and area of leaves, and the biomass accumulation (dry and fresh weights) were measured 50 days after sowing. The concentrations of total soluble sugars, proline, Chlorophylls a and b in leaves have also been quantified. Salt stress significantly reduced the growth and the total chlorophyll of the lettuce plants (p < 0.05) and increased their proline and sugar contents’. Zeolite application improved the growth of lettuce at 0 and 50 mM NaCl, but at the highest salinity level only the number of leaves was improved by 15%. At a mild salinity stress, the application of salicylic acid has significantly (p < 0.05) increased the root length, height of plant, chlorophyll, and proline contents. Regarding the high stress levels (100 and 150 mM NaCl), yeast application showed the best tolerance to salinity stress by improving significantly most of the growth parameters (p < 0.05) but with lower proline, sugar, and chlorophyll contents. In general, foliar spray of yeast extract may offer a good alternative source of nutrients through leaves, leading to a better tolerance of the high salt stress exerted on roots.

Group IIc WRKY transcription factors regulate cotton resistance to Fusarium oxysporum by promoting GhMKK2-mediated flavonoid biosynthesis

WRKY transcription factors (TFs) are crucial regulators in response to pathogen infection. However, the regulatory mechanisms of WRKY TFs in response to Fusarium oxysporum f. sp. vasinfectum (Fov), the most devastating pathogen of cotton, remain unclear. Here, transcriptome sequencing indicated that the group IIc WRKY TF subfamily was the most important TF subfamily in response to Fov. Gain-of-function and loss-of-function analyses showed that group IIc WRKY TFs positively regulated cotton resistance to Fov. A series of chromatin immunoprecipitation sequencing, yeast one-hybrid assay and electrophoresis mobility shift assay experiments indicated that group IIc WRKY TFs directly bound to the promoter of GhMKK2 and regulated its expression. Importantly, a novel mitogen-activated protein kinase (MAPK) cascade composed of GhMKK2, GhNTF6 and GhMYC2 was identified. The functional analysis indicated that group IIc WRKY TFs induced the GhMKK2-GhNTF6 pathway to increase resistance to Fov by upregulating the GhMYC2-mediated expression of several flavonoid biosynthesis-related genes, which led to flavonoid accumulation. In conclusion, our study demonstrated a novel disease defense mechanism by which the WRKY-MAPK pathway promotes flavonoid biosynthesis to defend against pathogen infection. This pathway improves our understanding of the interaction mode between WRKY TFs and MAPK cascades in plant immunity and the vital role of plant flavonoids in pathogen defense.

TaMPK2B, a member of the MAPK family in T. aestivum, enhances plant low-Pi stress tolerance through modulating physiological processes associated with phosphorus starvation defensiveness

The mitogen-activated protein kinase (MAPK) cascades are present in plant species and modulate plant growth and stress responses. This study characterizes TaMPK2B, a MAPK family gene in T. aestivum that regulates plant adaptation to low-Pi stress. TaMPK2B harbors the conserved domains involving protein phosphorylation and protein-protein interaction. A yeast two-hybrid assay reveals an interaction between TaMPK2B and TaMPKK2 and between the latter and TaMPKKK;A, suggesting that all comprise a MAPK signaling cascade TaMPKKK;A-TaMPKK2-TaMPK2B. TaMPK2B expression levels were elevated in roots and leaves under a Pi starvation (PS) condition. Additionally, the induced TaMPK2B transcripts under PS in tissues were gradually restored following the Pi normal recovery condition. TaMPK2B overexpression conferred on plants improved PS adaptation; the tobacco lines with TaMPK2B overexpression enhanced the plant's dry mass production, Pi uptake capacity, root system architecture (RSA) establishment, and ROS homeostasis relative to wild type under PS treatment. Moreover, the transcripts of genes in phosphate transporter (PT), PIN-FORMED, and antioxidant enzyme (AE) families, including NtPT3 and NtPT4, NtPIN9, and NtMnSOD1 and NtPOD1;7, were elevated in Pi-deprived lines overexpressing TaMPK2B. Transgene analyses validated their functions in regulating Pi uptake, RSA establishment, and AE activities of plants treated by PS. These results suggest that TaMPK2B-mediated plant PS adaptation is correlated with the modified transcription of distinct PT, PIN, and AE genes. Our investigation suggests that TaMPK2B is one of the crucial regulators in plant low-Pi adaptation by improving Pi uptake, RSA formation, and ROS homeostasis via transcriptionally regulating genes associated with the above physiological processes.

De novo transcriptome analysis of high-salinity stress-induced antioxidant activity and plant phytohormone alterations in Sesuvium portulacastrum

Sesuvium portulacastrum has a strong salt tolerance and can grow in saline and alkaline coastal and inland habitats. This study investigated the physiological and molecular responses of S. portulacastrum to high salinity by analyzing the changes in plant phytohormones and antioxidant activity, including their differentially expressed genes (DEGs) under similar high-salinity conditions. High salinity significantly affected proline (Pro) and hydrogen peroxide (H2O2) in S. portulacastrum seedlings, increasing Pro and H2O2 contents by 290.56 and 83.36%, respectively, compared to the control. Antioxidant activities, including superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT), significantly increased by 83.05, 205.14, and 751.87%, respectively, under high salinity. Meanwhile, abscisic acid (ABA) and gibberellic acid (GA3) contents showed the reverse trend of high salt treatment. De novo transcriptome analysis showed that 36,676 unigenes were matched, and 3,622 salt stress-induced DEGs were identified as being associated with the metabolic and biological regulation processes of antioxidant activity and plant phytohormones. POD and SOD were upregulated under high-salinity conditions. In addition, the transcription levels of genes involved in auxin (SAURs and GH3), ethylene (ERF1, ERF3, ERF114, and ABR1), ABA (PP2C), and GA3 (PIF3) transport or signaling were altered. This study identified key metabolic and biological processes and putative genes involved in the high salt tolerance of S. portulacastrum and it is of great significance for identifying new salt-tolerant genes to promote ecological restoration of the coastal strand.

Multiple forms of vitamin B6 regulate salt tolerance by balancing ROS and abscisic acid levels in maize root

Salt stress causes osmotic stress, ion toxicity and oxidative stress, inducing the accumulation of abscisic acid (ABA) and excessive reactive oxygen species (ROS) production, which further damage cell structure and inhibit the development of roots in plants. Previous study showed that vitamin B6 (VB6) plays a role in plant responses to salt stress, however, the regulatory relationship between ROS, VB6 and ABA under salt stress remains unclear yet in plants. In our study, we found that salt stress-induced ABA accumulation requires ROS production, in addition, salt stress also promoted VB6 (including pyridoxamine (PM), pyridoxal (PL), pyridoxine (PN), and pyridoxal 5'-phosphate (PLP)) accumulation, which involved in ROS scavenging and ABA biosynthesis. Furthermore, VB6-deficient maize mutant small kernel2 (smk2) heterozygous is more susceptible to salt stress, and which failed to scavenge excessive ROS effectively or induce ABA accumulation in maize root under salt stress, interestingly, which can be restored by exogenous PN and PLP, respectively. According to these results, we proposed that PN and PLP play an essential role in balancing ROS and ABA levels under salt stress, respectively, it laid a foundation for VB6 to be better applied in crop salt resistance than ABA.

Discovery of cold-resistance genes in Vitis amurensis using bud-based quantitative trait locus mapping and RNA-seq

Background

In cold regions, low temperature is the main limiting factor affecting grape production. As an important breeding resource, V. amurensis Rupr. has played a crucial role in the discovery of genes which confer cold resistance in grapes. Thus far, many cold-resistance genes have been reported based on the study of V. amurensis. In order to identify more candidate genes related to cold resistance in V. amurensis, QTL mapping and RNA-seq was conducted based on the hybrid population and different cold-resistance cultivars in this study.

Results

In this study, highly cold-resistant grape cultivar ‘Shuangyou’ (SY) which belongs to V. amurensis, and cold-sensitive cultivar ‘Red Globe’ (RG) which belongs to Vitis vinifera L. were used to identify cold resistance genes. Cold-resistance quantitative trait locus (QTL) mapping was performed based on genetic population construction through interspecific crossing of ‘Shuangyou’ and ‘Red Globe’. Additionally, transcriptome analysis was conducted for the dormant buds of these two cultivars at different periods. Based on transcriptome analysis and QTL mapping, many new structural genes and transcription factors which relate to V. amurensis cold resistance were discovered, including CORs (VaCOR413IM), GSTs (VaGST-APIC, VaGST-PARB, VaGSTF9 and VaGSTF13), ARFs (VaIAA27 and VaSAUR71), ERFs (VaAIL1), MYBs (VaMYBR2, VaMYBLL and VaMYB3R-1) and bHLHs (VaICE1 and VabHLH30).

Conclusions

This discovery of candidate cold-resistance genes will provide an important theoretical reference for grape cold-resistance mechanisms, research, and cold-resistant grape cultivar breeding in the future.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08788-y.

SbWRKY55 regulates sorghum response to saline environment by its dual role in abscisic acid signaling

SbWRKY55 functions as a key component of the ABA-mediated signaling pathway; transgenic sorghum regulates plant responses to saline environments and will help save arable land and ensure food security. Salt tolerance in plants is triggered by various environmental stress factors and endogenous hormonal signals. Numerous studies have shown that WRKY transcription factors are involved in regulating plant salt tolerance. However, the underlying mechanism for WRKY transcription factors regulated salt stress response and signal transduction pathways remains largely unknown. In this study, the SbWRKY55 transcription factor was found to be the key component for reduced levels of salt and abscisic acid in SbWRKY55 overexpression significantly reduced salt tolerance in sorghum and Arabidopsis. Mutation of the homologous gene AtWRKY55 in A. thaliana significantly enhanced salt tolerance, and SbWRKY55 supplementation in the mutants restored salt tolerance. In the transgenic sorghum with SbWRKY55 overexpression, the expression levels of genes involved in the abscisic acid (ABA) pathway were altered, and the endogenous ABA content decreased. Yeast one-hybrid assays and dual-luciferase reporter assay showed that SbWRKY55 binds directly to the promoter of SbBGLU22 and inhibits its expression level. In addition, both in vivo and in vitro biochemical analyses showed that SbWRKY55 interacts with the FYVE zinc finger protein SbFYVE1, blocking the ABA signaling pathway. This could be an important feedback regulatory pathway to balance the SbWRKY55-mediated salt stress response. In summary, the results of this study provide convincing evidence that SbWRKY55 functions as a key component in the ABA-mediated signaling pathway, highlighting the dual role of SbWRKY55 in ABA signaling. This study also showed that SbWRKY55 could negatively regulate salt tolerance in sorghum.

Natural variation of HTH5 from wild rice, Oryza rufipogon Griff., is involved in conferring high-temperature tolerance at the heading stage

Global warming is a major abiotic stress factor, which limit rice production. Exploiting the genetic basis of the natural variation in heat resistance at different reproductive stages among diverse exotic Oryza germplasms can help breeding heat-resistant rice cultivars. Here, we identified a stable quantitative trait locus (QTL) for heat tolerance at the heading stage on chromosome 5 (qHTH5) in O. rufipogon Griff. The corresponding gene, HTH5, pertains to the pyridoxal phosphate-binding protein PLPBP (formerly called PROSC) family, which is predicted to encode pyridoxal phosphate homeostasis protein (PLPHP) localized to the mitochondrion. Overexpression of HTH5 increased the seed-setting rate of rice plants under heat stress at the heading stage, whereas suppression of HTH5 resulted in greater susceptibility to heat stress. Further investigation indicated that HTH5 reduces reactive oxygen species accumulation at high temperatures by increasing the heat-induced pyridoxal 5'-phosphate (PLP) content. Moreover, we found that two SNPs located in the HTH5 promoter region are involved with its expression level and associated with heat tolerance diversity. These findings suggest that the novel gene HTH5 might have great potential value for heightening rice tolerance to heat stress to the on-going threat of global warming.

Multifaceted roles of zinc finger proteins in regulating various agronomic traits in rice

Rice is an important cereal crop, which provides staple food for more than half of the world's population. To meet the demand of the ever-growing population in the next few decades, an extra increase in rice yield is an urgent need. Given that various agronomic traits contribute to the yield of rice, deciphering the key regulators involved in multiple agronomic trait formation is particularly important. As a superfamily of transcription factors, zinc finger proteins participate in regulating multiple genes in almost every stage of rice growth and development. Therefore, understanding zinc finger proteins underlying regulatory network would provide insights into the regulation of agronomic traits in rice. To this end, we intend to summarize the current advances in zinc finger proteins, with emphasis on C2H2 and CCCH proteins, and then discuss their potential in improving rice yield.

Overexpression VaPYL9 improves cold tolerance in tomato by regulating key genes in hormone signaling and antioxidant enzyme

BACKGROUND

Abscisic acid (ABA) has been reported in controlling plant growth and development, and particularly dominates a role in resistance to abiotic stress. The Pyrabactin Resistance1/PYR1-Like /Regulatory Components of ABA receptors (PYR1/PYL/RCAR) gene family, of which the PYL9 is a positive regulator related to stress response in ABA signaling transduction. Although the family has been identified in grape, detailed VaPYL9 function in cold stress remains unknown.

RESULTS

In order to explore the cold tolerance mechanism in grape, VaPYL9 was cloned from Vitis amurensis. The subcellular localization showed that VaPYL9 was mainly expressed in the plasma membrane. Yeast two-hybrid (Y2H) showed VaPCMT might be a potential interaction protein of VaPYL9. Through the overexpression of VaPYL9 in tomatoes, results indicated transgenic plants had higher antioxidant enzyme activities and proline content, lower malondialdehyde (MDA) and H₂O₂ content, and improving the ability to scavenge reactive oxygen species than wild-type (WT). Additionally, ABA content and the ratio of ABA/IAA kept a higher level than WT. Quantitative real-time PCR (qRT-PCR) showed that VaPYL9, SlNCED3, SlABI5, and antioxidant enzyme genes (POD, SOD, CAT) were up-regulated in transgenic tomatoes. Transcriptome sequencing (RNA-seq) found that VaPYL9 overexpression caused the upregulation of key genes PYR/PYL, PYL4, MAPK17/18, and WRKY in transgenic tomatoes under cold stress.

CONCLUSION

Overexpression VaPYL9 enhances cold resistance of transgenic tomatoes mediated by improving antioxidant enzymes activity, reducing membrane damages, and regulating key genes in plant hormones signaling and antioxidant enzymes.

Mitogen-Activated Protein Kinase Is Involved in Salt Stress Response in Tomato (Solanum lycopersicum) Seedlings

Salt stress impairs plant growth and development, thereby causing low yield and inferior quality of crops. In this study, tomato (Solanum lycopersicum L. ‘Micro-Tom’) seedlings treated with different concentrations of sodium chloride (NaCl) were investigated in terms of decreased plant height, stem diameter, dry weight, fresh weight, leaves relative water content and root activity. To reveal the response mechanism of tomato seedlings to salt stress, the transcriptome of tomato leaves was conducted. A total of 6589 differentially expressed genes (DEGs) were identified and classified into different metabolic pathways, especially photosynthesis, carbon metabolism, biosynthesis of amino acids and mitogen-activated protein kinase (MAPK) signaling pathway. Of these, approximately 42 DEGs were enriched in the MAPK signaling pathway, most of which mainly included plant hormone, hydrogen peroxide (H₂O₂), wounding and pathogen infection signaling pathways. To further explore the roles of MAPK under salt stress, MAPK phosphorylation inhibitor SB203580 (SB) was applied. We found that SB further decreased endogenous jasmonic acid, abscisic acid and ethylene levels under salt stress condition. Additionally, in comparison with NaCl treatment alone, SB + NaCl treatment reduced the content of O²⁻ and H₂O₂ and the activities of antioxidant enzyme and downregulated the expression levels of genes related to pathogen infection. Together, the results revealed that MAPK might be involved in the salinity response of tomato seedlings by regulating hormone balance, ROS metabolism, antioxidant capacity and plant immunity.

Reactive oxygen species signalling in plant stress responses

Reactive oxygen species (ROS) are key signalling molecules that enable cells to rapidly respond to different stimuli. In plants, ROS play a crucial role in abiotic and biotic stress sensing, integration of different environmental signals and activation of stress-response networks, thus contributing to the establishment of defence mechanisms and plant resilience. Recent advances in the study of ROS signalling in plants include the identification of ROS receptors and key regulatory hubs that connect ROS signalling with other important stress-response signal transduction pathways and hormones, as well as new roles for ROS in organelle-to-organelle and cell-to-cell signalling. Our understanding of how ROS are regulated in cells by balancing production, scavenging and transport has also increased. In this Review, we discuss these promising developments and how they might be used to increase plant resilience to environmental stress.

Transcriptomic Analysis of Mature Transgenic Poplar Expressing the Transcription Factor JERF36 Gene in Two Different Environments

During the last several decades, a number of transgenic or genetically modified tree varieties with enhanced characteristics and new traits have been produced. These trees have become associated with generally unsubstantiated concerns over health and environmental safety. We conducted transcriptome sequencing of transgenic Populus alba × P. berolinensis expressing the transcription factor JERF36 gene (ABJ01) and the non-transgenic progenitor line (9#) to compare the transcriptional changes in the apical buds. We found that 0.77% and 1.31% of the total expressed genes were significant differentially expressed in ABJ01 at the Daqing and Qiqihar sites, respectively. Among them, 30%–50% of the DEGs contained cis-elements recognized by JERF36. Approximately 5% of the total number of expressed genes showed significant differential expression between Daqing and Qiqihar in both ABJ01 and 9#. 10 DEGs resulting from foreign gene introduction, 394 DEGs that resulted solely from the environmental differences, and 47 DEGs that resulted from the combination of foreign gene introduction and the environment were identified. The number of DEGs resulting from environmental factors was significantly greater than that resulting from foreign gene introduction, and the combined effect of the environmental effects with foreign gene introduction was significantly greater than resulting from the introduction of JERF36 alone. GO and KEGG annotation showed that the DEGs mainly participate in the photosynthesis, oxidative phosphorylation, plant hormone signaling, ribosome, endocytosis, and plant-pathogen interaction pathways, which play important roles in the responses to biotic and abiotic stresses ins plant. To enhance its adaptability to salt-alkali stress, the transgenic poplar line may regulate the expression of genes that participate in the photosynthesis, oxidative phosphorylation, MAPK, and plant hormone signaling pathways. The crosstalk between biotic and abiotic stress responses by plant hormones may improve the ability of both transgenic and non-transgenic poplars to defend against pathogens. The results of our study provide a basis for further studies on the molecular mechanisms behind improved stress resistance and the unexpected effects of transgenic gene expression in poplars, which will be significant for improving the biosafety evaluation of transgenic trees and accelerating the breeding of new varieties of forest trees resistant to environmental stresses.

Ethylene responsive factor34 mediates stress-induced leaf senescence by regulating salt stress-responsive genes

Leaf senescence proceeds with age but is modulated by various environmental stresses and hormones. Salt stress is one of the most well-known environmental stresses that accelerate leaf senescence. However, the molecular mechanisms that integrate salt stress signalling with leaf senescence programmes remain elusive. In this study, we characterised the role of ETHYLENE RESPONSIVE FACTOR34 (ERF34), an Arabidopsis APETALA2 (AP2)/ERF family transcription factor, in leaf senescence. ERF34 was differentially expressed under various leaf senescence-inducing conditions, and negatively regulated leaf senescence induced by age, dark, and salt stress. ERF34 also promoted salt stress tolerance at different stages of the plant life cycle such as seed germination and vegetative growth. Transcriptome analysis revealed that the overexpression of ERF34 increased the transcript levels of salt stress-responsive genes including COLD-REGULATED15A (COR15A), EARLY RESPONSIVE TO DEHYDRATION10 (ERD10), and RESPONSIVE TO DESICCATION29A (RD29A). Moreover, ERF34 directly bound to ERD10 and RD29A promoters and activated their expression. Our findings indicate that ERF34 plays a key role in the convergence of the salt stress response with the leaf senescence programmes, and is a potential candidate for crop improvement, particularly by enhancing salt stress tolerance.