Molecular and functional analyses of rice NHX-type Na+/H+ antiporter genes

Exogenous Eugenol Alleviates Salt Stress in Tobacco Seedlings by Regulating the Antioxidant System and Hormone Signaling

Salt stress seriously affects crop growth, leading to a decline in crop quality and yield. Application of exogenous substances to improve the salt tolerance of crops and promote their growth under salt stress has become a widespread and effective means. Eugenol is a small molecule of plant origin with medicinal properties such as antibacterial, antiviral, and antioxidant properties. In this study, tobacco seedlings were placed in Hoagland's solution containing NaCl in the presence or absence of eugenol, and physiological indices related to stress tolerance were measured along with transcriptome sequencing. The results showed that eugenol improved the growth of tobacco seedlings under salt stress. It promoted carbon and nitrogen metabolism, increased the activities of nitrate reductase (NR), sucrose synthase (SS), and glutamine synthetase (GS) by 31.03, 5.80, and 51.06%. It also activated the enzymatic and non-enzymatic antioxidant systems, reduced the accumulation of reactive oxygen species in the tobacco seedlings, and increased the activities of superoxide dismutase (SOD), peroxidase (POD), catalase (CAT), and ascorbate peroxidase (APX) by 24.38%, 18.22%, 21.60%, and 28.8%, respectively. The content of glutathione (GSH) was increased by 29.49%, and the content of superoxide anion (O2-) and malondialdehyde (MDA) were reduced by 29.83 and 33.86%, respectively. Promoted osmoregulation, the content of Na+ decreased by 34.34, K+ increased by 41.25%, and starch and soluble sugar increased by 7.72% and 25.42%, respectively. It coordinated hormone signaling in seedlings; the content of abscisic acid (ABA) and gibberellic acid 3 (GA3) increased by 51.93% and 266.28%, respectively. The transcriptome data indicated that the differentially expressed genes were mainly enriched in phenylpropanoid biosynthesis, the MAPK signaling pathway, and phytohormone signal transduction pathways. The results of this study revealed the novel role of eugenol in regulating plant resistance and provided a reference for the use of exogenous substances to alleviate salt stress.

Role of plant neurotransmitters in salt stress: A critical review

Neurotransmitters are naturally found in many plants, but the molecular processes that govern their actions still need to be better understood. Acetylcholine, γ-Aminobutyric acid, histamine, melatonin, serotonin, and glutamate are the most common neurotransmitters in animals, and they all play a part in the development and information processing. It is worth noting that all these chemicals have been found in plants. Although much emphasis has been placed on understanding how neurotransmitters regulate mood and behaviour in humans, little is known about how they regulate plant growth and development. In this article, the information was reviewed and updated considering current thinking on neurotransmitter signaling in plants' metabolism, growth, development, salt tolerance, and the associated avenues for underlying research. The goal of this study is to advance neurotransmitter signaling research in plant biology, especially in the area of salt stress physiology.

Identification and Functional Analysis of KH Family Genes Associated with Salt Stress in Rice

Salinity stress has a great impact on crop growth and productivity and is one of the major factors responsible for crop yield losses. The K-homologous (KH) family proteins play vital roles in regulating plant development and responding to abiotic stress in plants. However, the systematic characterization of the KH family in rice is still lacking. In this study, we performed genome-wide identification and functional analysis of KH family genes and identified a total of 31 KH genes in rice. According to the homologs of KH genes in Arabidopsis thaliana, we constructed a phylogenetic tree with 61 KH genes containing 31 KH genes in Oryza sativa and 30 KH genes in Arabidopsis thaliana and separated them into three major groups. In silico tissue expression analysis showed that the OsKH genes are constitutively expressed. The qRT-PCR results revealed that eight OsKH genes responded strongly to salt stresses, and OsKH12 exhibited the strongest decrease in expression level, which was selected for further study. We generated the Oskh12-knockout mutant via the CRISPR/Cas9 genome-editing method. Further stress treatment and biochemical assays confirmed that Oskh12 mutant was more salt-sensitive than Nip and the expression of several key salt-tolerant genes in Oskh12 was significantly reduced. Taken together, our results shed light on the understanding of the KH family and provide a theoretical basis for future abiotic stress studies in rice.

Potassium transporter OsHAK17 may contribute to saline-alkaline tolerant mechanisms in rice (Oryza sativa)

Rice production is seriously affected by saline-alkaline stress worldwide. To elucidate the saline-alkaline tolerance mechanisms in a novel tolerant rice variety, Shwe Nang Gyi (SNG), we investigated ion accumulation in SNG and Koshihikari (KSH), which is a saline-alkaline sensitive rice variety, and the candidates for saline-alkaline inducible genes in SNG using RNA-seq. SNG had superior ion accumulation capacity, such as K and Zn, compared to KSH. In contrast, SNG accumulated the same level of Na content in its leaf blades as KSH despite the higher dry weight of the SNG leaf blades. We further found that the expression of numerous genes, including several K+ transporter/high-affinity K+ transporter/K+ uptake protein/K+ transporter (HAK/KUP/KT) family members, were upregulated in SNG, and that OsHAK17 and OsHAK21 expression levels in the roots were significantly higher in SNG than in KSH. Moreover, yeast complementation analysis revealed that OsHAK17 was involved in K+ uptake under high-Na conditions. These results suggested that SNG has an effective K+ acquisition system supported by OsHAK17 functioning in saline-alkaline environments.

Transcriptomic and Lipidomic Analysis Reveals Complex Regulation Mechanisms Underlying Rice Roots' Response to Salt Stress

Rice (Oryza sativa L.), a crucial food crop that sustains over half the world's population, is often hindered by salt stress during various growth stages, ultimately causing a decrease in yield. However, the specific mechanism of rice roots' response to salt stress remains largely unknown. In this study, transcriptomics and lipidomics were used to analyze the changes in the lipid metabolism and gene expression profiles of rice roots in response to salt stress. The results showed that salt stress significantly inhibited rice roots' growth and increased the roots' MDA content. Furthermore, 1286 differentially expressed genes including 526 upregulated and 760 downregulated, were identified as responding to salt stress in rice roots. The lipidomic analysis revealed that the composition and unsaturation of membrane lipids were significantly altered. In total, 249 lipid molecules were differentially accumulated in rice roots as a response to salt stress. And most of the major phospholipids, such as phosphatidic acid (PA), phosphatidylcholine (PC), and phosphatidylserine (PS), as well as major sphingolipids including ceramide (Cer), phytoceramide (CerP), monohexose ceramide (Hex1Cer), and sphingosine (SPH), were significantly increased, while the triglyceride (TG) molecules decreased. These results suggested that rice roots mitigate salt stress by altering the fluidity and integrity of cell membranes. This study enhances our comprehension of salt stress, offering valuable insights into changes in the lipids and adaptive lipid remodeling in rice's response to salt stress.

The potassium transporter TaNHX2 interacts with TaGAD1 to promote drought tolerance via modulating stomatal aperture in wheat

Drought is a major global challenge in agriculture that decreases crop production. γ-Aminobutyric acid (GABA) interfaces with drought stress in plants; however, a mechanistic understanding of the interaction between GABA accumulation and drought response remains to be established. Here we showed the potassium/proton exchanger TaNHX2 functions as a positive regulator in drought resistance in wheat by mediating cross-talk between the stomatal aperture and GABA accumulation. TaNHX2 interacted with glutamate decarboxylase TaGAD1, a key enzyme that synthesizes GABA from glutamate. Furthermore, TaNHX2 targeted the C-terminal auto-inhibitory domain of TaGAD1, enhanced its activity, and promoted GABA accumulation under drought stress. Consistent with this, the tanhx2 and tagad1 mutants showed reduced drought tolerance, and transgenic wheat with enhanced TaNHX2 expression had a yield advantage under water deficit without growth penalty. These results shed light on the plant stomatal movement mechanism under drought stress and the TaNHX2-TaGAD1 module may be harnessed for amelioration of negative environmental effects in wheat as well as other crops.

A novel maize F-bZIP member, ZmbZIP76, functions as a positive regulator in ABA-mediated abiotic stress tolerance by binding to ACGT-containing elements

The group F-bZIP transcription factors (TFs) in Arabidopsis are involved in nutrient deficiency or salt stress responses. Nevertheless, our learning about the functions of group F-bZIP genes in maize remains limited. Here, we cloned a new F-bZIP gene (ZmbZIP76) from maize inbred line He344. The expression of ZmbZIP76 in maize was dramatically induced by high salt, osmotic stress and abscisic acid. Accordingly, overexpression of ZmbZIP76 increased tolerance of transgenic plants to salt and osmotic stress. In addition, ZmbZIP76 functions as a nuclear transcription factor and upregulates the expression of a range of abiotic stress-responsive genes by binding to the ACGT-containing elements, leading to enhanced reactive oxygen species (ROS) scavenging capability, increased abscisic acid level, proline content, and ratio of K+/Na+, reduced water loss rate, and membrane damage. These physiological changes caused by ZmbZIP76 ultimately enhanced tolerance of transgenic plants to salt and osmotic stress.

Meta-analysis of identified genomic regions and candidate genes underlying salinity tolerance in rice (Oryza sativa L.)

Rice output has grown globally, yet abiotic factors are still a key cause for worry. Salinity stress seems to have the more impact on crop production out of all abiotic stresses. Currently one of the most significant challenges in paddy breeding for salinity tolerance with the help of QTLs, is to determine the QTLs having the best chance of improving salinity tolerance with the least amount of background noise from the tolerant parent. Minimizing the size of the QTL confidence interval (CI) is essential in order to primarily include the genes responsible for salinity stress tolerance. By considering that, a genome-wide meta-QTL analysis on 768 QTLs from 35 rice populations published from 2001 to 2022 was conducted to identify consensus regions and the candidate genes underlying those regions responsible for the salinity tolerance, as it reduces the confidence interval (CI) to many folds from the initial QTL studies. In the present investigation, a total of 65 MQTLs were extracted with an average CI reduced from 17.35 to 1.66 cM including the smallest of 0.01 cM. Identification of the MQTLs for individual traits and then classifying the target traits into correlated morphological, physiological and biochemical aspects, resulted in more efficient interpretation of the salinity tolerance, identifying the candidate genes and to understand the salinity tolerance mechanism as a whole. The results of this study have a huge potential to improve the rice genotypes for salinity tolerance with the help of MAS and MABC.

A B-box transcription factor OsBBX17 regulates saline-alkaline tolerance through the MAPK cascade pathway in rice

Rice OsBBX17 encodes a B-box zinc finger transcription factor in which the N-terminal B-box structural domain interacts with OsMPK1. In addition, it directly binds to the G-box of OsHAK2 and OsHAK7 promoters and represses their transcription. Under saline-alkaline conditions, the expression of OsBBX17 was inhibited. Meanwhile, activation of the OsMPK1-mediated mitogen-activated protein kinase cascade pathway caused OsMPK1 to interact with OsBBX17 and phosphorylate OsBBX17 at the Thr-95 site. It reduced OsBBX17 DNA-binding activity and enhanced saline-alkaline tolerance by deregulating transcriptional repression of OsHAK2 and OsHAK7. Genetic assays showed that the osbbx17-KO had an excellent saline-alkaline tolerance, whereas the opposite was in OsBBX17-OE. In addition, overexpression of OsMPK1 significantly improved saline-alkaline tolerance, but knockout of OsMPK1 caused an increased sensitivity. Further overexpression of OsBBX17 in the osmpk1-KO caused extreme saline-alkaline sensitivity, even a quick death. OsBBX17 was validated in saline-alkaline tolerance from two independent aspects, transcriptional level and post-translational protein modification, unveiling a mechanistic framework by which OsMPK1-mediated phosphorylation of OsBBX17 regulates the transcription of OsHAK2 and OsHAK7 to enhance the Na+ /K+ homeostasis, which partially explains light on the molecular mechanisms of rice responds to saline-alkaline stress via B-box transcription factors for the genetic engineering of saline-alkaline tolerant crops.

Genome-wide characterization of the CPA gene family in potato and a preliminary functional analysis of its role in NaCl tolerance

BACKGROUND

The cation/proton antiporter (CPA) superfamily plays a crucial role in regulating ion homeostasis and pH in plant cells, contributing to stress resistance. However, in potato (Solanum tuberosum L.), systematic identification and analysis of CPA genes are lacking.

RESULTS

A total of 33 StCPA members were identified and classified into StNHX (n = 7), StKEA (n = 6), and StCHX (n = 20) subfamilies. StCHX owned the highest number of conserved motifs, followed by StKEA and StNHX. The StNHX and StKEA subfamilies owned more exons than StCHX. NaCl stress induced the differentially expression of 19 genes in roots or leaves, among which StCHX14 and StCHX16 were specifically induced in leaves, while StCHX2 and StCHX19 were specifically expressed in the roots. A total of 11 strongly responded genes were further verified by qPCR. Six CPA family members, StNHX1, StNHX2, StNHX3, StNHX5, StNHX6 and StCHX19, were proved to transport Na+ through yeast complementation experiments.

CONCLUSIONS

This study provides comprehensive insights into StCPAs and their response to NaCl stress, facilitating further functional characterization.

Exogenous riboflavin (vitamin B2) application enhances salinity tolerance through the activation of its biosynthesis in rice seedlings under salinity stress

Salinity stress triggers the accumulation of reactive oxygen species (ROS), leading to impaired plant growth. Riboflavin (RIB; vitamin B2) is synthesized by plants, fungi, and microorganisms and is a precursor of the coenzymes, flavin adenine dinucleotide (FAD) and flavin mononucleotide (FMN), which are important for cellular metabolism. In this study, we aimed to elucidate the mechanistic basis of the RIB-mediated alleviation of salinity stress in rice. We observed higher biomass accumulation and lower concentrations of malondialdehyde (MDA) and hydrogen peroxide (H2O2) in RIB-pretreated seedlings under salinity stress. In vitro assays showed that H2O2 was scavenged as the RIB concentration increased, implying that RIB may function as a non-enzymatic antioxidant in ROS detoxification. RIB-pretreated seedlings accumulated more Na+ in the roots than in the leaf blades because of the contributions of OsHKT2;1, OsNHX1, and OsHKT1;4 in the roots and leaf sheaths, respectively. Liquid chromatography-mass spectrometry (LC-MS/MS) analysis revealed increased RIB concentration in roots and shoots and upregulation of key genes (OsRIBA1, OsGCHI, OsLS, and OsRS) involved in RIB biosynthesis in the roots of RIB-pretreated seedlings. Taken together, our findings suggest that RIB pretreatment ameliorates salinity stress in rice by improving (1) oxidative stress tolerance, as increased RIB concentration may function as a non-enzymatic antioxidant, and (2) ionic stress tolerance, as RIB pretreatment limits Na+ accumulation in the leaf blades and maintains a favorable Na+/K+ balance.

Rice Seed Protrusion Quantitative Trait Loci Mapping through Genome-Wide Association Study

The germination of seeds is a prerequisite for crop production. Protrusion is important for seed germination, and visible radicle protrusion through seed covering layers is the second phase of the process of seed germination. Analyzing the mechanism of protrusion is important for the cultivation of rice varieties. In this study, 302 microcore germplasm populations were used for the GWAS of the protrusion percentage (PP). The frequency distribution of the PP at 48 h and 72 h is continuous, and six PP-associated QTLs were identified, but only qPP2 was detected repeatedly two times. The candidate gene analysis showed that LOC_Os02g57530 (ETR3), LOC_Os01g57610 (GH3.1) and LOC_Os04g0425 (CTB2) were the candidate genes for qPP2, qPP1 and qPP4, respectively. The haplotype (Hap) analysis revealed that Hap1 of ETR3, Hap1 and 3 of GH3.1 and Hap2 and 5 of CTB2 are elite alleles for the PP. Further validation of the germination phenotype of these candidate genes showed that Hap1 of ETR3 is a favorable allele for the germination percentage; Hap3 of GH3.1 is an elite allele for seed germination; and Hap5 of CTB2 is an elite allele for the PP, the germination percentage and the vigor index. The results of this study identified three putative candidate genes that provide valuable information for understanding the genetic control of seed protrusion in rice.

Comparison of the Morpho-Physiological and Molecular Responses to Salinity and Alkalinity Stresses in Rice

Rice is a major food crop that has a critical role in ensuring food security for the global population. However, major abiotic stresses such as salinity and alkalinity pose a major threat to rice farming worldwide. Compared with salinity stress, there is limited progress in elucidating the molecular mechanisms associated with alkalinity tolerance in rice. Since both stresses coexist in coastal and arid regions, unraveling of the underlying molecular mechanisms will help the breeding of high-yielding stress-tolerant rice varieties for these areas. This study examined the morpho-physiological and molecular response of four rice genotypes to both salinity and alkalinity stresses. Geumgangbyeo was highly tolerant and Mermentau was the least tolerant to both stresses, while Pokkali and Bengal were tolerant to only salinity and alkalinity stress, respectively. A set of salinity and alkalinity stress-responsive genes showed differential expression in the above rice genotypes under both stress conditions. The expression patterns were consistent with the observed morphological responses in these rice genotypes, suggesting the potential role of these genes in regulating tolerance to these abiotic stresses. Overall, this study suggested that divergence in response to alkalinity and salinity stresses among rice genotypes could be due to different molecular mechanisms conferring tolerance to each stress. In addition to providing a basis for further investigations into differentiating the molecular bases underlying tolerance, this study also emphasizes the possibilities of developing climate-resilient rice varieties using donors that are tolerant to both abiotic stresses.

Ion Changes and Signaling under Salt Stress in Wheat and Other Important Crops

High concentrations of sodium (Na+), chloride (Cl-), calcium (Ca2+), and sulphate (SO42-) are frequently found in saline soils. Crop plants cannot successfully develop and produce because salt stress impairs the uptake of Ca2+, potassium (K+), and water into plant cells. Different intracellular and extracellular ionic concentrations change with salinity, including those of Ca2+, K+, and protons. These cations serve as stress signaling molecules in addition to being essential for ionic homeostasis and nutrition. Maintaining an appropriate K+:Na+ ratio is one crucial plant mechanism for salt tolerance, which is a complicated trait. Another important mechanism is the ability for fast extrusion of Na+ from the cytosol. Ca2+ is established as a ubiquitous secondary messenger, which transmits various stress signals into metabolic alterations that cause adaptive responses. When plants are under stress, the cytosolic-free Ca2+ concentration can rise to 10 times or more from its resting level of 50-100 nanomolar. Reactive oxygen species (ROS) are linked to the Ca2+ alterations and are produced by stress. Depending on the type, frequency, and intensity of the stress, the cytosolic Ca2+ signals oscillate, are transient, or persist for a longer period and exhibit specific "signatures". Both the influx and efflux of Ca2+ affect the length and amplitude of the signal. According to several reports, under stress Ca2+ alterations can occur not only in the cytoplasm of the cell but also in the cell walls, nucleus, and other cell organelles and the Ca2+ waves propagate through the whole plant. Here, we will focus on how wheat and other important crops absorb Na+, K+, and Cl- when plants are under salt stress, as well as how Ca2+, K+, and pH cause intracellular signaling and homeostasis. Similar mechanisms in the model plant Arabidopsis will also be considered. Knowledge of these processes is important for understanding how plants react to salinity stress and for the development of tolerant crops.

Genome-wide identification and expression analysis of the NHX gene family under salt stress in wheat (Triticum aestivum L)

Salt stress affects plant growth and development, resulting in the loss of crop yield across the world, and sodium-proton antiporters (NHXs) are one of the genes known to promote salt tolerance in transgenic plants. In this study, we conducted a comprehensive genome-wide analysis and expression profile of NHX genes in wheat under salinity stress. We identified 30 TaNHX genes in wheat based on the Na+/H+ exchanger domain, with all genes containing an amiloride motif except one, a known for inhibiting Na+ ions in plants. Phylogenetic analysis classified these genes into three classes with subfamilies: 12 were localized in vacuoles, while 18 were in the endoplasmic reticulum and plasma membrane. Promoter analysis revealed stress-related cis-acting elements, indicating their potential role in abiotic stress tolerance. The non-synonymous (Ka)/synonymous (Ks) ratios highlighted that the majority of TaNHX genes experienced robust purifying selection throughout their evolutionary history. Transcriptomis data analysis and qRT-PCR demonstrated distinct expression patterns for TaNHX genes across various tissues when subjected to salt stress. Additionally, we predicted 20 different miRNA candidates targeting the identified TaNHX genes. Protein-protein interaction prediction revealed NHX6's involvement in the SOS1 pathway, while NHX1 gene exhibit proton antiporter activity. Molecular dynamics (MD) simulations were also conducted to examine the interactions of TaNHX1, TaNHX2, and TaNHX3. These results represent a significant advancement in our understanding of the molecular mechanisms governing Na+ transporters. This may also offer promising avenues for future studies aimed at unraveling the intricate details of their biological roles and applications.

The Molecular Mechanism of Potassium Absorption, Transport, and Utilization in Rice

Potassium is essential for plant growth and development and stress adaptation. The maintenance of potassium homeostasis involves a series of potassium channels and transporters, which promote the movement of potassium ions (K+) across cell membranes and exhibit complex expression patterns and regulatory mechanisms. Rice is a major food crop in China. The low utilization rate of potassium fertilizer limits the yield and quality of rice. Elucidating the molecular mechanisms of potassium absorption, transport, and utilization is critical in improving potassium utilization efficiency in rice. Although some K+ transporter genes have been identified from rice, research on the regulatory network is still in its infancy. Therefore, this review summarizes the relevant information on K+ channels and transporters in rice, covering the absorption of K+ in the roots, transport to the shoots, the regulation pathways, the relationship between K+ and the salt tolerance of rice, and the synergistic regulation of potassium, nitrogen, and phosphorus signals. The related research on rice potassium nutrition has been comprehensively reviewed, the existing research foundation and the bottleneck problems to be solved in this field have been clarified, and the follow-up key research directions have been pointed out to provide a theoretical framework for the cultivation of potassium-efficient rice.

Genetic Databases and Gene Editing Tools for Enhancing Crop Resistance against Abiotic Stress

Abiotic stresses extensively reduce agricultural crop production globally. Traditional breeding technology has been the fundamental approach used to cope with abiotic stresses. The development of gene editing technology for modifying genes responsible for the stresses and the related genetic networks has established the foundation for sustainable agriculture against environmental stress. Integrated approaches based on functional genomics and transcriptomics are now expanding the opportunities to elucidate the molecular mechanisms underlying abiotic stress responses. This review summarizes some of the features and weblinks of plant genome databases related to abiotic stress genes utilized for improving crops. The gene-editing tool based on clustered, regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) has revolutionized stress tolerance research due to its simplicity, versatility, adaptability, flexibility, and broader applications. However, off-target and low cleavage efficiency hinder the successful application of CRISPR/Cas systems. Computational tools have been developed for designing highly competent gRNA with better cleavage efficiency. This powerful genome editing tool offers tremendous crop improvement opportunities, overcoming conventional breeding techniques' shortcomings. Furthermore, we also discuss the mechanistic insights of the CRISPR/Cas9-based genome editing technology. This review focused on the current advances in understanding plant species' abiotic stress response mechanism and applying the CRISPR/Cas system genome editing technology to develop crop resilience against drought, salinity, temperature, heavy metals, and herbicides.

Overexpression of a C3HC4-type E3-ubiquitin ligase contributes to salinity tolerance by modulating Na+ homeostasis in rice

Soil salinity has a negative effect on crop yield. Therefore, plants have evolved many strategies to overcome decreases in yield under saline conditions. Among these, E3-ubiquitin ligase regulates salt tolerance. We characterized Oryza sativa Really Interesting New Gene (RING) Finger C3HC4-type E3 ligase (OsRFPHC-4), which plays a positive role in improving salt tolerance. The expression of OsRFPHC-4 was downregulated by high NaCl concentrations and induced by abscisic acid (ABA) treatment. GFP-fused OsRFPHC-4 was localized to the plasma membrane of rice protoplasts. OsRFPHC-4 encodes a cellular protein with a C3HC4-RING domain with E3 ligase activity. However, its variant OsRFPHC-4C161A does not possess this activity. OsRFPHC-4-overexpressing plants showed enhanced salt tolerance due to low accumulation of Na+ in both roots and leaves, low Na+ transport in the xylem sap, high accumulation of proline and soluble sugars, high activity of reactive oxygen species (ROS) scavenging enzymes, and differential regulation of Na+ /K+ transporter expression compared to wild-type (WT) and osrfphc-4 plants. In addition, OsRFPHC-4-overexpressing plants showed higher ABA sensitivity under exogenous ABA treatment than WT and osrfphc-4 plants. Overall, these results suggest that OsRFPHC-4 contributes to the improvement of salt tolerance and Na+ /K+ homeostasis via the regulation of changes in Na+ /K+ transporters.

Halotolerant endophytic bacteria alleviate salinity stress in rice (oryza sativa L.) by modulating ion content, endogenous hormones, the antioxidant system and gene expression

Excessive salinity reduces crop production and negatively impacts agriculture worldwide. We previously isolated endophytic bacterial strains from two halophytic species: Artemisia princeps and Chenopodium ficifolium. We used three bacterial isolates: ART-1 (Lysinibacillus fusiformis), ART-10 (Lysinibacillus sphaericus), and CAL-8 (Brevibacterium pityocampae) to alleviate the impact of salinity stress on rice. The impact of 160 mM NaCl salinity on rice was significantly mitigated following inoculation with these bacterial strains, resulting in increased growth and chlorophyll content. Furthermore, OsNHX1, OsAPX1, OsPIN1 and OsCATA expression was increased, but OsSOS expression was decreased. Inductively coupled plasma mass spectrometry (ICP-MS) revealed reduced K+ and Na+ levels in shoots of bacteria-inoculated plants, whereas that of Mg2+ was increased. Bacterial inoculation reduced the content of total flavonoids in rice leaves. Salinized plants inoculated with bacteria showed reduced levels of endogenous salicylic acid (SA) and abscisic acid (ABA) but increased levels of jasmonic acid (JA). In conclusion, the bacterial isolates ART-1, ART-10, and CAL-8 alleviated the adverse effect of salinity on rice growth, which justifies their use as an eco-friendly agricultural practice.

NtLTPI.38, a plasma membrane-localized protein, mediates lipid metabolism and salt tolerance in Nicotiana tabacum

Non-specific lipid transfer proteins (nsLTPs) typically have conserved structural resemblance, low sequence identity, and broad biological functions in plant growth and stress resistance. Here, a plasma membrane-localized nsLTP, NtLTPI.38, was identified in tobacco plants. Multi-omics integrated analysis revealed that NtLTPI.38 overexpression or knock out significantly changed glycerophospholipid and glycerolipid metabolism pathways. NtLTPI.38 overexpression remarkably increased phosphatidylcholine, phosphatidylethanolamine, triacylglycerol, and flavonoid levels, but decreased ceramides compared to wild type and mutant lines. Differentially expressed genes were associated with lipid metabolite and flavonoid synthesis. Many genes related to Ca²⁺ channels, abscisic acid (ABA) signal transduction, and ion transport pathways were upregulated in overexpressing plants. NtLTPI.38 overexpression in salt-stressed tobacco triggered a Ca²⁺ and K⁺ influx in leaves, increased the contents of chlorophyll, proline, flavonoids, and osmotic tolerance, and raised enzymatic antioxidant activities as well as the expression level of related genes. However, mutants accumulated more O₂^- and H₂O_2, exhibited ionic imbalance, gathered excess Na⁺, Cl^-, and malondialdehyde, with more severe ion leakage. Therefore, NtLTPI.38 enhanced salt tolerance in tobacco by regulating lipid and flavonoid synthesis, antioxidant activity, ion homeostasis, and ABA signaling pathways.

Seed priming with NaCl helps to improve tissue tolerance, potassium retention ability of plants, and protects the photosynthetic ability in two different legumes, chickpea and lentil, under salt stress

MAIN CONCLUSION

Seed priming with NaCl mimicked the conditions of natural priming to improve the tissue tolerance nature of sensitive legumes, which helps to maintain survivability and yield in mildly saline areas. Seed priming with NaCl is a seed invigoration technique that helps to improve plant growth by altering Na⁺ and K⁺ content under salt stress. Legumes are overall sensitive to salt and salinity hampers their growth and yield. Therefore, a priming (50 mM NaCl) experiment was performed with two different legume members [Cicer arietinum cv. Anuradha and Lens culinaris cv. Ranjan] and different morpho-physiological, biochemical responses at 50 mM, 100 mM, and 150 mM NaCl and molecular responses at 150 mM NaCl were studied in hydroponically grown nonprimed and primed members. Similarly, a pot experiment was performed at 80 mM Na⁺, to check the yield. Tissue Na⁺ and K⁺ content suggested NaCl-priming did not significantly alter the accumulation of Na⁺ among nonprimed and primed members but retained more K⁺ in cells, thus maintaining a lower cellular Na⁺/K⁺ ratio. Low osmolyte content (e.g., proline) in primed members suggested priming could minimize their overall osmolytic requirement. Altogether, these implied tissue tolerance (TT) nature might have improved in case of NaCl-priming as was also reflected by a better TT score (LC₅₀ value). An improved TT nature enabled the primed plants to maintain a significantly higher photosynthetic rate through better stomatal conductance. Along with this, a higher level of chlorophyll content and competent functioning of the photosynthetic subunits improved photosynthetic performance that ensured yield under stress. Overall, this study explores the potential of NaCl-priming and creates possibilities for considerably sensitive members; those in their nonprimed forms have no prospect in mildly saline agriculture.

OsMBTB32, a MATH-BTB domain-containing protein that interacts with OsCUL1s to regulate salt tolerance in rice

MATH-BTB proteins are involved in a variety of cellular processes that regulate cell homeostasis and developmental processes. Previous studies reported the involvement of BTB proteins in the development of various organs in plants; however, the function of BTB proteins in salt stress is less studied. Here, we found a novel MATH-BTB domain-containing OsMBTB32 protein that was highly expressed in leaf, root, and shoot. The up-regulation of the OsMBTB32 transcript in 2-week-old seedlings under salt stress suggests the significant role of the OsMBTB32 gene in salinity. The OsMBTB32 transgenic seedlings (OE and RNAi) exhibited significant differences in various phenotypes, including plumule, radical, primary root, and shoot length, compared to WT seedlings. We further found that OsCUL1 proteins, particularly OsCUL1-1 and OsCUL1-3, interact with OsMBTB32 and may suppress the function of OsMBTB32 during salt stress. Moreover, OsWRKY42, a homolog of ZmWRKY114 which negatively regulates salt stress in rice, directly binds to the W-box of OsCUL1-1 and OsCUL1-3 promoters to promote the interaction of OsCUL1-1 and OsCUL1-3 with OsMBTB32 protein in rice. The overexpression of OsMBTB32 and OsCUL1-3 further confirmed the function of OsMBTB32 and OsCUL1s in salt tolerance in Arabidopsis. Overall, the findings of the present study provide promising knowledge regarding the MATH-BTB domain-containing proteins and their role in enhancing the growth and development of rice under salt stress.MATH-BTB proteins are involved in a variety of cellular processes that regulate cell homeostasis and developmental processes. Previous studies reported the involvement of BTB proteins in the development of various organs in plants; however, the function of BTB proteins in salt stress is less studied. Here, we found a novel MATH-BTB domain-containing OsMBTB32 protein that was highly expressed in leaf, root, and shoot. The up-regulation of the OsMBTB32 transcript in 2-week-old seedlings under salt stress suggests the significant role of the OsMBTB32 gene in salinity. The OsMBTB32 transgenic seedlings (OE and RNAi) exhibited significant differences in various phenotypes, including plumule, radical, primary root, and shoot length, compared to WT seedlings. We further found that OsCUL1 proteins, particularly OsCUL1-1 and OsCUL1-3, interact with OsMBTB32 and may suppress the function of OsMBTB32 during salt stress. Moreover, OsWRKY42, a homolog of ZmWRKY114 which negatively regulates salt stress in rice, directly binds to the W-box of OsCUL1-1 and OsCUL1-3 promoters to promote the interaction of OsCUL1-1 and OsCUL1-3 with OsMBTB32 protein in rice. The overexpression of OsMBTB32 and OsCUL1-3 further confirmed the function of OsMBTB32 and OsCUL1s in salt tolerance in Arabidopsis. Overall, the findings of the present study provide promising knowledge regarding the MATH-BTB domain-containing proteins and their role in enhancing the growth and development of rice under salt stress.

Novel Salinity-Tolerant Third-Generation Hybrid Rice Developed via CRISPR/Cas9-Mediated Gene Editing

Climate change has caused high salinity in many fields, particularly in the mud flats in coastal regions. The resulting salinity has become one of the most significant abiotic stresses affecting the world's rice crop productivity. Developing elite cultivars with novel salinity-tolerance traits is regarded as the most cost-effective and environmentally friendly approach for utilizing saline-alkali land. To develop a highly efficient green strategy and create novel rice germplasms for salt-tolerant rice breeding, this study aimed to improve rice salinity tolerance by combining targeted CRISPR/Cas9-mediated editing of the OsRR22 gene with heterosis utilization. The novel alleles of the genic male-sterility (GMS) and elite restorer line (733S^rr22-T1447-1 and HZ^rr22-T1349-3) produced 110 and 1 bp deletions at the third exon of OsRR22 and conferred a high level of salinity tolerance. Homozygous transgene-free progeny were identified via segregation in the T2 generation, with osrr22 showing similar agronomic performance to wild-type (733S and HZ). Furthermore, these two osrr22 lines were used to develop a new promising third-generation hybrid rice line with novel salinity tolerance. Overall, the results demonstrate that combining CRISPR/Cas9 targeted gene editing with the "third-generation hybrid rice system" approach allows for the efficient development of novel hybrid rice varieties that exhibit a high level of salinity tolerance, thereby ensuring improved cultivar stability and enhanced rice productivity.

OsJRL40, a Jacalin-Related Lectin Gene, Promotes Salt Stress Tolerance in Rice

High salinity is a major stress factor affecting the quality and productivity of rice (Oryza sativa L.). Although numerous salt tolerance-related genes have been identified in rice, their molecular mechanisms remain unknown. Here, we report that OsJRL40, a jacalin-related lectin gene, confers remarkable salt tolerance in rice. The loss of function of OsJRL40 increased sensitivity to salt stress in rice, whereas its overexpression enhanced salt tolerance at the seedling stage and during reproductive growth. β-glucuronidase (GUS) reporter assays indicated that OsJRL40 is expressed to higher levels in roots and internodes than in other tissues, and subcellular localization analysis revealed that the OsJRL40 protein localizes to the cytoplasm. Further molecular analyses showed that OsJRL40 enhances antioxidant enzyme activities and regulates Na⁺-K⁺ homeostasis under salt stress. RNA-seq analysis revealed that OsJRL40 regulates salt tolerance in rice by controlling the expression of genes encoding Na⁺/K⁺ transporters, salt-responsive transcription factors, and other salt response-related proteins. Overall, this study provides a scientific basis for an in-depth investigation of the salt tolerance mechanism in rice and could guide the breeding of salt-tolerant rice cultivars.

Identification of Candidate Genes for Salt Tolerance at the Seedling Stage Using Integrated Genome-Wide Association Study and Transcriptome Analysis in Rice

Salt stress is a major constraint in rice production worldwide. Salt stress is estimated to cause annual losses of 30-50% in rice production. Discovering and deploying salt-resistance genes are the most effective ways to control salt stress. We performed a genome-wide association study (GWAS) to detect QTLs related to salt tolerance at the seedling stage using the japonica-multiparent advanced generation intercross (MAGIC) population. Four QTLs (qDTS1-1, qDTS1-2, qDTS2, and qDTS9) associated with salt tolerance were identified on chromosomes 1, 2, and 9. Among these QTLs, a novel QTL, qDTS1-2, was located between flanking SNPs (1354576 and id1028360) on chromosome 1, with the largest -log10(P) value of 5.81 and a total phenotypic variance of 15.2%. RNA-seq analysis revealed that among the seven differentially expressed genes (DEGs) commonly identified in both P6 and JM298 showing salt tolerance, two upregulated genes, Os01g0963600 (ASR transcription factor) and Os01g0975300 (OsMYB48), related to salt and drought tolerance, were also involved in the target region of qDTS1-2. The results of this study can provide insights into further understanding of salt tolerance mechanisms and developing DNA markers for marker-assisted selection (MAS) breeding to improve the salt tolerance of cultivars in rice breeding programs.

Natural variations of chlorophyll fluorescence and ion transporter genes influenced the differential response of japonica rice germplasm with different salt tolerances

Soil salinity seriously restricts rice growth, development, and production globally. Chlorophyll fluorescence and ion content reflect the level of injury and resistance of rice under salt stress. To understand the differences in the response mechanisms of japonica rice with varying degrees of salt tolerance, we analyzed the chlorophyll fluorescence characteristics and ion homeostasis of 12 japonica rice germplasm accessions by comprehensive evaluation of phenotype, haplotype, and expression of salt tolerance-related genes. The results revealed that salt-sensitive accessions were rapidly affected by the damage due to salinity. Salt tolerance score (STS) and relative chlorophyll relative content (RSPAD) were extremely significantly reduced (p<0.01), and chlorophyll fluorescence and ion homeostasis were influenced by various degrees under salt stress. The STS, RSPAD, and five chlorophyll fluorescence parameters of salt-tolerant accessions (STA) were significantly higher than that of salt-sensitive accessions (SSA). Principal component analysis (PCA) with 13 indices suggested three principal components (PCs), with a cumulative contribution rate of 90.254%, which were used to screen Huangluo (typical salt-tolerant germplasm) and Shanfuliya (typical salt-sensitive germplasm) based on the comprehensive evaluation D-value (D_CI ). The expression characteristics of chlorophyll fluorescence genes (OsABCI7 and OsHCF222) and ion transporter protein genes (OsHKT1;5, OsHKT2;1, OsHAK21, OsAKT2, OsNHX1, and OsSOS1) were analyzed. The expressions of these genes were higher in Huangluo than in Shanfuliya under salt stress. Haplotype analysis revealed four key variations associated with salt tolerance, including an SNP (+1605 bp) within OsABCI7 exon, an SSR (-1231 bp) within OsHAK21 promoter, an indel site at OsNHX1 promoter (-822 bp), and an SNP (-1866 bp) within OsAKT2 promoter. Variation in OsABCI7 protein structure and differential expression of these three ion-transporter genes may contribute to the differential response of japonica rice to salt stress.

Improvement of Salinity Tolerance in Water-Saving and Drought-Resistance Rice (WDR)

Rice is one of the most economically important staple food crops in the world. Soil salinization and drought seriously restrict sustainable rice production. Drought aggravates the degree of soil salinization, and, at the same time, increased soil salinity also inhibits water absorption, resulting in physiological drought stress. Salt tolerance in rice is a complex quantitative trait controlled by multiple genes. This review presents and discusses the recent research developments on salt stress impact on rice growth, rice salt tolerance mechanisms, the identification and selection of salt-tolerant rice resources, and strategies to improve rice salt tolerance. In recent years, the increased cultivation of water-saving and drought-resistance rice (WDR) has shown great application potential in alleviating the water resource crisis and ensuring food and ecological security. Here, we present an innovative germplasm selection strategy of salt-tolerant WDR, using a population that is developed by recurrent selection based on dominant genic male sterility. We aim to provide a reference for efficient genetic improvement and germplasm innovation of complex traits (drought and salt tolerance) that can be translated into breeding all economically important cereal crops.

OsBBX11 on qSTS4 links to salt tolerance at the seeding stage in Oryza sativa L. ssp. Japonica

Rice has been reported to be highly sensitive to salt stress at the seedling stage. However, the lack of target genes that can be used for improving salt tolerance has resulted in several saline soils unsuitable for cultivation and planting. To characterize new salt-tolerant genes, we used 1,002 F_2:3 populations derived from Teng-Xi144 and Long-Dao19 crosses as the phenotypic source to systematically characterize seedlings' survival days and ion concentration under salt stress. Utilizing QTL-seq resequencing technology and a high-density linkage map based on 4,326 SNP markers, we identified qSTS4 as a major QTL influencing seedling salt tolerance, which accounted for 33.14% of the phenotypic variation. Through functional annotation, variation detection and qRT-PCR analysis of genes within 46.9 Kb of qSTS4, it was revealed that there was one SNP in the promoter region of OsBBX11, which resulted in a significant response difference between the two parents to salt stress. Transgenic plants using knockout-based technology and demonstrated that Na⁺ and K⁺ in the roots of the functional-loss-type OsBBX11 were translocated largely to the leaves under 120 mmol/L NaCl compared with the wild-type, causing osbbx11 leaves to die after 12 days of salt stress due to an imbalance in osmotic pressure. In conclusion, this study identified OsBBX11 as a salt-tolerance gene, and one SNPs in the OsBBX11 promoter region can be used to identify its interacting transcription factors. This provides a theoretical basis for finding the molecular mechanism of OsBBX11 upstream and downstream regulation of salt tolerance and molecular design breeding in the future.

Endophytic Fungi Regulate HbNHX1 Expression and Ion Balance in Hordeum bogdanii under Alkaline Stress

Plants cope with abiotic stress in several ways, including by collaborating with microorganisms. Epichloë, an endophytic fungus, has been shown to improve plant tolerance to extreme external environments. Hordeum bogdanii is a known salt-tolerant plant with the potential to improve alkaline lands. NHX1 plays a key role in the transport of ions in the cell and is overexpressed in plants with increased salt tolerance. However, the expression levels of HbNHX1 in Epichloë endophytic fungal symbionts in H. bogdanii have not been elucidated. We used Hordeum bogdanii (E+) with the endophytic fungi Epichloë bromicola and H. bogdanii (E-) without the endophytic fungi and compared the differences in the ion content and HbNHX1 expression between the shoots and roots of E+ and E- plants under alkaline stress. The absorption capacity of both K⁺ and Na⁺ of H. bogdanii with endophytic fungi was higher than that without endophytic fungi. In the absence of alkaline stress, endophytic fungi significantly reduced the Cl^- content in the host H. bogdanii. Alkaline stress reduced SO₄^2- content in H. bogdanii; however, compared with E-, endophytic fungi increased the content of SO₄^2- in E+ plants. With an increase in the alkaline concentration, the expression of HbNHX1 in the roots of H. bogdanii with endophytic fungus exhibited an upward trend, whereas the expression in the shoots exhibited a downward trend first and then an upward trend. Under 100 mmol·L^-1 mixed alkaline stress, the expression of HbNHX1 in E+ was significantly higher than that in E-, indicating that endophytic fungi could increase the Na⁺ region in vacuoles. The external environment affects the regulation of endophytic fungi in H. bogdanii and that endophytic fungi can play a key role in soil salinization. Therefore, the findings of this study will provide technical support and a theoretical basis for better utilization of endophytic fungi from H. bogdanii in saline land improvement.

Integrated Transcriptome and Metabolome Analysis of Rice Leaves Response to High Saline-Alkali Stress

Rice (Oryza sativa) is one of the most important crops grown worldwide, and saline-alkali stress seriously affects the yield and quality of rice. It is imperative to elucidate the molecular mechanisms underlying rice response to saline-alkali stress. In this study, we conducted an integrated analysis of the transcriptome and metabolome to elucidate the effects of long-term saline-alkali stress on rice. High saline-alkali stress (pH > 9.5) induced significant changes in gene expression and metabolites, including 9347 differentially expressed genes (DEGs) and 693 differentially accumulated metabolites (DAMs). Among the DAMs, lipids and amino acids accumulation were greatly enhanced. The pathways of the ABC transporter, amino acid biosynthesis and metabolism, glyoxylate and dicarboxylate metabolism, glutathione metabolism, TCA cycle, and linoleic acid metabolism, etc., were significantly enriched with DEGs and DAMs. These results suggest that the metabolites and pathways play important roles in rice's response to high saline-alkali stress. Our study deepens the understanding of mechanisms response to saline-alkali stress and provides references for molecular design breeding of saline-alkali resistant rice.

Unfolding molecular switches for salt stress resilience in soybean: recent advances and prospects for salt-tolerant smart plant production

The increasing sodium salts (NaCl, NaHCO3, NaSO4 etc.) in agricultural soil is a serious global concern for sustainable agricultural production and food security. Soybean is an important food crop, and their cultivation is severely challenged by high salt concentration in soils. Classical transgenic and innovative breeding technologies are immediately needed to engineer salt tolerant soybean plants. Additionally, unfolding the molecular switches and the key components of the soybean salt tolerance network are crucial for soybean salt tolerance improvement. Here we review our understandings of the core salt stress response mechanism in soybean. Recent findings described that salt stress sensing, signalling, ionic homeostasis (Na⁺/K⁺) and osmotic stress adjustment might be important in regulating the soybean salinity stress response. We also evaluated the importance of antiporters and transporters such as Arabidopsis K⁺ Transporter 1 (AKT1) potassium channel and the impact of epigenetic modification on soybean salt tolerance. We also review key phytohormones, and osmo-protectants and their role in salt tolerance in soybean. In addition, we discuss the progress of omics technologies for identifying salt stress responsive molecular switches and their targeted engineering for salt tolerance in soybean. This review summarizes recent progress in soybean salt stress functional genomics and way forward for molecular breeding for developing salt-tolerant soybean plant.

Melatonin-mediated endogenous nitric oxide coordinately boosts stability through proline and nitrogen metabolism, antioxidant capacity, and Na+/K+ transporters in tomato under NaCl stress

The interactions between nitric oxide (NO) and melatonin in alleviating sodium chloride (NaCl) toxicity in plants are poorly comprehended. Here, the associations between the exogenous application of melatonin and endogenous NO levels in inducing tomato seedlings' defense response during NaCl toxicity were investigated. The results indicated that the application of melatonin (150 μM) increased height (23.7%) and biomass (32.2%), improved chlorophyll (a (137%) and b (92.8%)), and proline metabolisms, and reduced the contents of superoxide anion radicals (49.6%), hydrogen peroxide (31.4%), malondialdehyde (38%), and electrolyte leakage (32.6%) in 40-day-old tomato seedlings grown under NaCl (150 mM) treatment. Melatonin increased the antioxidant defense system in NaCl-stressed seedlings by increasing the activity of the antioxidant enzymes. Melatonin also improved N metabolism and endogenous NO content in NaCl-stressed seedlings by upregulating the activity of enzymes implicated in N assimilation. Furthermore, melatonin improved ionic balance and reduced Na content in NaCl-exposed seedlings by upregulating the expression of genes involved in K/Na ratio homeostasis (NHX1-4) and increasing the accumulation of mineral nutrients (P, N, Ca, and Mg). However, the addition of cPTIO (100 μM; an NO scavenger) reversed the beneficial impacts of melatonin, indicating the effective function of NO in melatonin-induced defense mechanisms in NaCl-stressed tomato seedlings. Therefore, our results revealed that melatonin improves the tolerance of tomato plants during NaCl toxicity by mediating internal NO.

The WRKY Transcription Factor OsWRKY54 Is Involved in Salt Tolerance in Rice

Salt stress is a critical limiting factor for rice growth and production. Although numerous salt-tolerant genes have been identified, the mechanism underlying salt stress tolerance in rice remains unclear. This study reports the need for an uncharacterized WRKY transcription factor OsWRKY54 for rice salt-tolerance. Salt stress resulted in a rapid induction of OsWRKY54 expression in roots. Immunostaining analysis showed that it was mainly expressed in the stele. The loss of OsWRKY54 resulted in greater Na accumulation in shoots and enhanced sensitivity of rice plants to salt stress. The real-time quantitative PCR (qRT-PCR) and transcriptome analysis revealed that OsWRKY54 regulated the expression of some essential genes related to salt tolerance, such as OsNHX4 and OsHKT1;5. Furthermore, OsWRKY54 was found to regulate OsHKT1;5 expression by directly binding to the W-box motif in its promoter. Thus, these results indicated that OsWRKY54 was a critical regulatory factor in salt tolerance in rice.

A Novel mechanisms of the signaling cascade associated with the SAPK10-bZIP20-NHX1 synergistic interaction to enhance tolerance of plant to abiotic stress in rice (Oryza sativa L.)

The bzip transcription factors can modulate the transcriptional expressions of target genes by binding specifically to cis-regulatory elements in the promoter region of stress-related genes, hence regulating plant stress resistance. Here, we investigated a stress-responsive transcription factor Osbzip20 under abiotic stresses. The OsbZIP20-GFP fusion protein predominantly aggregated in the nucleus, in accordance with our subcellular localization. OsbZIP20 transcript was observed in all vegetative tissues with highest levels being detected in the seed. Transcription of Osbzip20 was induced by salinity, exsiccation, and abscisic acid. Overexpression of OsbZIP20 in transgenic rice considerably improved tolerance to salt and drought stresses, as well as increased sensitivity to ABA. Furthermore, abiotic stress responsive genes transcript were found to be remarkably elevated in transgenic rice overexpressing OsbZIP20 than in wild-type plants. SAPK10 was discovered to directly interact with and phosphorylate OsbZIP20. Yeast one-hybrid and luciferase assay revealed that OsbZIP20 acted as a transcriptional stimulator. Interestingly, gel shift assay showed that phosphorylated bZIP20 augmented its DNA-binding affinity to the ABRE element of the NHX1 promoter and induced its transcription. In sum, our findings establish a novel signaling pathway associated with the SAPK10-bZIP20-NHX1 synergistic interaction, as well as a new strategy for enhancing rice drought and salt tolerance.

Sodium Accumulation in Infected Cells and Ion Transporters Mistargeting in Nodules of Medicago truncatula: Two Ugly Items That Hinder Coping with Salt Stress Effects

The maintenance of intracellular nitrogen-fixing bacteria causes changes in proteins’ location and in gene expression that may be detrimental to the host cell fitness. We hypothesized that the nodule’s high vulnerability toward salt stress might be due to alterations in mechanisms involved in the exclusion of Na+ from the host cytoplasm. Confocal and electron microscopy immunolocalization analyses of Na+/K+ exchangers in the root nodule showed the plasma membrane (MtNHX7) and endosome/tonoplast (MtNHX6) signal in non-infected cells; however, in mature infected cells the proteins were depleted from their target membranes and expelled to vacuoles. This mistargeting suggests partial loss of the exchanger’s functionality in these cells. In the mature part of the nodule 7 of the 20 genes encoding ion transporters, channels, and Na+/K+ exchangers were either not expressed or substantially downregulated. In nodules from plants subjected to salt treatments, low temperature-scanning electron microscopy and X-ray microanalysis revealed the accumulation of 5–6 times more Na+ per infected cell versus non-infected one. Hence, the infected cells’ inability to withstand the salt may be the integral result of preexisting defects in the localization of proteins involved in Na+ exclusion and the reduced expression of key genes of ion homeostasis, resulting in premature senescence and termination of symbiosis.

OsABT Is Involved in Abscisic Acid Signaling Pathway and Salt Tolerance of Roots at the Rice Seedling Stage

Rice is a staple cereal crop worldwide, and increasing its yields is vital to ensuring global food security. Salinity is a major factor that affects rice yield. Therefore, it is necessary to investigate salt tolerance mechanisms in rice. Proteins containing WD40 repeats play important roles in eukaryotic development and environmental adaptation. Here, we showed that overexpression of OsABT, a gene encoding a WD40-repeat protein, enhanced salt tolerance in rice seedlings by regulating root activity, relative conductivity, malondialdehyde and H₂O₂ content, and O₂^•− production rate. Root ion concentrations indicated that OsABT overexpression lines could maintain lower Na⁺ and higher K⁺/Na⁺ ratios and upregulated expression of salt-related genes OsSOS1 and OsHAK5 compared with the wild-type (WT) Nipponbare plants. Furthermore, Overexpression of OsABT decreased the abscisic acid (ABA) content, while downregulating the ABA synthesis genes OsNCED3 and OsNCED4 and upregulating the ABA catabolic gene OsABA8ox2. The yeast two-hybrid and bimolecular fluorescence complementation analyses showed that OsABT interacted with the ABA receptor proteins OsPYL4, OsPYL10, and PP2C phosphatase OsABIL2. A transcriptome analysis revealed that the differentially expressed genes between OsABT overexpression lines and WT plants were enriched in plant hormone signal transduction, including ABA signaling pathway under salt stress. Thus, OsABT can improve the salt tolerance in rice seedling roots by inhibiting reactive oxygen species accumulation, thereby regulating the intracellular Na⁺/K⁺ balance, ABA content, and ABA signaling pathway.

Effects of Exogenous Melatonin on Root Physiology, Transcriptome and Metabolome of Cotton Seedlings under Salt Stress

Root systems are the key organs through which plants absorb water and nutrients and perceive the soil environment and thus are easily damaged by salt stress. Melatonin can alleviate stress-induced damage to roots. The present study investigated the effects of exogenous melatonin on the root physiology, transcriptome and metabolome of cotton seedlings under salt stress. Salt stress was observed to damage the cell structure and disorder the physiological system of cotton seedling roots. After subjecting melatonin-soaked seeds to salt stress, the activities of SOD, CAT and POD in cotton seedling roots increased by 10–25%, 50–60% and 50–60%, respectively. The accumulation of H₂O₂ and MDA were significantly decreased by 30–60% and 30–50%, respectively. The contents of soluble sugar, soluble protein and K⁺ increased by 15–30%, 15–30% and 20–50%, respectively, while the Na⁺ content was significantly reduced. Melatonin also increased auxin (by 20–40%), brassinosteroids (by 5–40%) and gibberellin (by 5–35%) and promoted melatonin content and root activity. Exogenous melatonin maintained the integrity of root cells and increased the number of organelles. Transcriptomic and metabolomic results showed that exogenous melatonin could mitigate the salt-stress-induced inhibition of plant root development by regulating the reactive oxygen species scavenging system; ABC transporter synthesis; plant hormone signal transduction, endogenous melatonin gene expression; and the expression of the transcription factors MYB, TGA and WRKY33. These results provide a new direction and empirical basis for improving crop salt tolerance with melatonin.

OsUGE3-mediated cell wall polysaccharides accumulation improves biomass production, mechanical strength, and salt tolerance

Cell walls constitute the majority of plant biomass and are essential for plant resistance to environmental stresses. It is promising to improve both plant biomass production and stress resistance simultaneously by genetic modification of cell walls. Here, we report the functions of a UDP-galactose/glucose epimerase 3 (OsUGE3) in rice growth and salt tolerance by characterizing its overexpressing plants (OsUGE3-OX) and loss-of-function mutants (uge3). The OsUGE3-OX plants showed improvements in biomass production and mechanical strength, whereas uge3 mutants displayed growth defects. The OsUGE3 exhibits UDP-galactose/glucose epimerase activity that provides substrates for polysaccharides polymerization, consistent with the increased biosynthesis of cellulose and hemicelluloses and strengthened walls in OsUGE3-OX plants. Notably, the OsUGE3 is ubiquitously expressed and induced by salt treatment. The uge3 mutants were hypersensitive to salt and osmotic stresses, whereas the OsUGE3-OX plants showed improved tolerance to salt and osmotic stresses. Moreover, OsUGE3 overexpression improves the homeostasis of Na⁺ and K⁺ and induces a higher accumulation of hemicelluloses and soluble sugars during salt stress. Our results suggest that OsUGE3 improves biomass production, mechanical strength, and salt stress tolerance by reinforcement of cell walls with polysaccharides and it could be targeted for genetic modification to improve rice growth under salt stress.

Effect of Different Salts on Nutrients Uptake, Gene Expression, Antioxidant, and Growth Pattern of Selected Rice Genotypes

Climate change leads to soil salinization, and the dynamic scarcity of freshwater has negatively affected crop production worldwide, especially Oryza sativa. The association among ion uptake, gene expression, antioxidant, biomass, and root and shoot development under different salt stress are not fully understood. Many studies are related to the effect of NaCl only. This study used two salts (CaCl₂ and MgCl₂) along with NaCl and analyzed their effects on mineral uptake (macronutrients and micronutrients), gene expression, seed germination, antioxidants, plant growth, and biomass in different rice genotypes. CaCl₂ (up to 200 mM) slightly increased the germination percentage and seedling growth, whereas, 150 mM MgCl₂ in the soil increased the root, shoot length, and fresh and dry weight in cultivars IR 28 and Cheongcheong. All agronomic traits among rice genotypes were drastically reduced by NaCl stress compared to other salts. Different salt stress differentially regulated ion uptake in the roots and shoots among different rice genotypes. Under different salt stress, a consistent decrease in Ca²⁺, Mn²⁺, and Fe²⁺ ions was observed in the roots of Cheongcheong, Nagdong, and IR 28. Similarly, under different salts, the stress in the shoots of Cheongcheong (Ca²⁺, Na⁺, and Zn²⁺) and Nagdong (Ca²⁺, Mg²⁺, Na⁺, and Zn²⁺) and the shoots of IR 28 (Ca²⁺ and Mg²⁺) consistently increased. Under different salts, a salt stress-related gene was expressed differentially in the roots of rice genotypes. However, after 6 and 12 h, there was consistent OsHKT1, OsNHX1, and OsSOS1 gene upregulation in the shoots of Nagdong and roots and shoots of the salt-tolerant cultivar Pokkali. Under different salt stress, glutathione (GSH) content increased in the shoot of IR 28 and Nagdong by NaCl, and MgCl₂ salt, whereas, POD activity increased significantly by CaCl₂ and MgCl₂ in cultivar Cheongcheong and IR 28 shoot. Therefore, this study suggested that Pokkali responded well to NaCl stress only, whereas, the plant molecular breeding lab cultivar Nagdong showed more salt tolerance to different salts (NaCl, CaCl₂, and MgCl₂). This can potentially be used by agriculturists to develop the new salt-tolerant cultivar "Nagdong"-like Pokkali.

Transcriptomic analysis of OsRUS1 overexpression rice lines with rapid and dynamic leaf rolling morphology

Moderate leaf rolling helps to form the ideotype of rice. In this study, six independent OsRUS1-GFP overexpression (OsRUS1-OX) transgenic rice lines with rapid and dynamic leaf rolling phenotype in response to sunlight were constructed. However, the mechanism is unknown. Here, RNA-Seq approach was utilized to identify differentially expressed genes between flag leaves of OsRUS1-OX and wildtype under sunlight. 2920 genes were differentially expressed between OsRUS1-OX and WT, of which 1660 upregulated and 1260 downregulated. Six of the 16 genes in GO: 0009415 (response to water stimulus) were significantly upregulated in OsRUS1-OX. The differentially expressed genes between WT and OsRUS1-OX were assigned to 110 KEGG pathways. 42 of the 222 genes in KEGG pathway dosa04075 (Plant hormone signal transduction) were differentially expressed between WT and OsRUS1-OX. The identified genes in GO:0009415 and KEGG pathway dosa04075 were good candidates to explain the leaf rolling phenotype of OsRUS1-OX. The expression patterns of the 15 genes identified by RNA-Seq were verified by qRT-PCR. Based on transcriptomic and qRT-PCR analysis, a mechanism for the leaf rolling phenotype of OsRUS1-OX was proposed. The differential expression profiles between WT and OsRUS1-OX established by this study provide important insights into the molecular mechanism behind the leaf rolling phenotype of OsRUS1-OX.

Evolutionary Significance of NHX Family and NHX1 in Salinity Stress Adaptation in the Genus Oryza

Rice (Oryza sativa), a staple crop for a substantial part of the world’s population, is highly sensitive to soil salinity; however, some wild Oryza relatives can survive in highly saline environments. Sodium/hydrogen antiporter (NHX) family members contribute to Na⁺ homeostasis in plants and play a major role in conferring salinity tolerance. In this study, we analyzed the evolution of NHX family members using phylogeny, conserved domains, tertiary structures, expression patterns, and physiology of cultivated and wild Oryza species to decipher the role of NHXs in salt tolerance in Oryza. Phylogenetic analysis showed that the NHX family can be classified into three subfamilies directly related to their subcellular localization: endomembrane, plasma membrane, and tonoplast (vacuolar subfamily, vNHX1). Phylogenetic and structural analysis showed that vNHX1s have evolved from streptophyte algae (e.g., Klebsormidium nitens) and are abundant and highly conserved in all major land plant lineages, including Oryza. Moreover, we showed that tissue tolerance is a crucial trait conferring tolerance to salinity in wild rice species. Higher Na⁺ accumulation and reduced Na⁺ effluxes in leaf mesophyll were observed in the salt-tolerant wild rice species O. alta, O. latifolia, and O. coarctata. Among the key genes affecting tissue tolerance, expression of NHX1 and SOS1/NHX7 exhibited significant correlation with salt tolerance among the rice species and cultivars. This study provides insights into the evolutionary origin of plant NHXs and their role in tissue tolerance of Oryza species and facilitates the inclusion of this trait during the development of salinity-tolerant rice cultivars.

Reduced apoplastic barriers in tissues of shoot-proximal rhizomes of Oryza coarctata are associated with Na+ sequestration

Oryza coarctata is the only wild rice species with significant salinity tolerance. The present work examines the role of the substantial rhizomatous tissues of O. coarctata in conferring salinity tolerance. Transition to an erect phenotype (shoot emergence) from prostrate growth of rhizome tissues is characterized by marked lignification and suberization of supporting sclerenchymatous tissue, epidermis, and bundle sheath cells in aerial shoot-proximal nodes and internodes in O. coarctata. With salinity, however, aerial shoot-proximal internodal tissues show reductions in lignification and suberization, most probably related to re-direction of carbon flux towards synthesis of the osmporotectant proline. Concurrent with hypolignification and reduced suberization, the aerial rhizomatous biomass of O. coarctata appears to have evolved mechanisms to store Na+ in these specific tissues under salinity. This was confirmed by histochemical staining, quantitative real-time reverse transcription-PCR expression patterns of genes involved in lignification/suberization, Na+ and K+ contents of internodal tissues, as well as non-invasive microelectrode ion flux measurements of NaCl-induced net Na+, K+, and H+ flux profiles of aerial nodes were determined. In O. coarctata, aerial proximal internodes appear to act as 'traffic controllers', sending required amounts of Na+ and K+ into developing leaves for osmotic adjustment and turgor-driven growth, while more deeply positioned internodes assume a Na+ buffering/storage role.

Genome-Wide Identification, Primary Functional Characterization of the NHX Gene Family in Canavalia rosea, and Their Possible Roles for Adaptation to Tropical Coral Reefs

Canavalia rosea, distributed in the coastal areas of tropical and subtropical regions, is an extremophile halophyte with good adaptability to high salinity/alkaline and drought tolerance. Plant sodium/hydrogen (Na⁺/H⁺) exchanger (NHX) genes encode membrane transporters involved in sodium ion (Na⁺), potassium ion (K⁺), and lithium ion (Li⁺) transport and pH homeostasis, thereby playing key roles in salinity tolerance. However, the NHX family has not been reported in this leguminous halophyte. In the present study, a genome-wide comprehensive analysis was conducted and finally eight CrNHXs were identified in C. rosea genome. Based on the bioinformatics analysis about the chromosomal location, protein domain, motif organization, and phylogenetic relationships of CrNHXs and their coding proteins, as well as the comparison with plant NHXs from other species, the CrNHXs were grouped into three major subfamilies (Vac-, Endo-, and PM-NHX). Promoter analyses of cis-regulatory elements indicated that the expression of different CrNHXs was affected by a series of stress challenges. Six CrNHXs showed high expression levels in five tested tissues of C. rosea in different levels, while CrNHX1 and CrNHX3 were expressed at extremely low levels, indicating that CrNHXs might be involved in regulating the development of C. rosea plant. The expression analysis based on RNA-seq showed that the transcripts of most CrNHXs were obviously decreased in mature leaves of C. rosea plant growing on tropical coral reefs, which suggested their involvement in this species' adaptation to reefs and specialized islands habitats. Furthermore, in the single-factor stress treatments mimicking the extreme environments of tropical coral reefs, the RNA-seq data also implied CrNHXs holding possible gene-specific regulatory roles in the environmental adaptation. The qRT-PCR based expression profiling exhibited that CrNHXs responded to different stresses to varying degrees, which further confirmed the specificity of CrNHXs' in responding to abiotic stresses. Moreover, the yeast functional complementation test proved that some CrNHXs could partially restore the salt tolerance of the salt-sensitive yeast mutant AXT3. This study provides comprehensive bio-information and primary functional identification of NHXs in C. rosea, which could help improve the salt/alkaline tolerance of genetically modified plants for further studies. This research also contributes to our understanding of the possible molecular mechanism whereby NHXs maintain the ion balance in the natural ecological adaptability of C. rosea to tropical coral islands and reefs.

NHX Gene Family in Camellia sinensis: In-silico Genome-Wide Identification, Expression Profiles, and Regulatory Network Analysis

Salt stress affects the plant growth and productivity worldwide and NHX is one of those genes that are well known to improve salt tolerance in transgenic plants. It is well characterized in several plants, such as Arabidopsis thaliana and cotton; however, not much is known about NHXs in tea plant. In the present study, NHX genes of tea were obtained through a genome-wide search using A. thaliana as reference genome. Out of the 9 NHX genes in tea, 7 genes were localized in vacuole while the remaining 2 genes were localized in the endoplasmic reticulum (ER; CsNHX8) and plasma membrane (PM; CsNHX9), respectively. Furthermore, phylogenetic relationships along with structural analysis which includes gene structure, location, and protein-conserved motifs and domains were systematically examined and further, predictions were validated by the expression analysis. The dN/dS values show that the majority of tea NHX genes is subjected to strong purifying selection under the course of evolution. Also, functional interaction was carried out in Camellia sinensis based on the orthologous genes in A. thaliana. The expression profiles linked to various stress treatments revealed wide involvement of NHX genes from tea in response to various abiotic factors. This study provides the targets for further comprehensive identification, functional study, and also contributed for a better understanding of the NHX regulatory network in C. sinensis.

Transcript profiling of stress-responsive genes and metabolic changes during salinity in indica and japonica rice exhibit distinct varietal difference

In the present study, we carried out comprehensive transcript profiling of diverse genes under salinity (200 mM NaCl) at different time points, accompanied by certain biochemical alterations of the indica (IR-64 and Pokkali) and japonica (Nipponbare and M-202) rice. The higher susceptibility of Nipponbare and IR-64 was reflected by lower relative water content, chlorophyll loss, higher malondialdehyde content, and accumulation of H₂ O₂ , and reduced nitrate reductase activity, compared to M-202 and Pokkali, where such changes were less pronounced. Enhanced levels of anthocyanins and reduced glutathione, together with elevated phenylalanine ammonia lyase activity, mainly conferred protection to Nipponbare and IR-64, while metabolites like phenolics, flavonoids, proline, and polyamines were more induced in M-202 and Pokkali. Varietal differences in the expression pattern of diverse groups of genes during different durations (6, 24, and 48 h) of stress were striking. A gene showing early induction for a particular variety exhibited a delayed induction in another variety or a gradually decreased expression with treatment time. Pokkali was clearly identified as the salt-tolerant genotype among the examined varieties based on increased antioxidant potential and enhanced expression of genes encoding for PAL, CHS, and membrane transporters like SOS3, NHX-1, and HKT-1. The results presented in this work provide insight into the complex varying regulation patterns for different genes across the investigated rice varieties in providing salt tolerance and highlights distinct differences in expression patterns between susceptible and tolerant indica and japonica rice.

Rice Cultivars Under Salt Stress Show Differential Expression of Genes Related to the Regulation of Na+/K+ Balance

Soil salinity is a major problem in agriculture because high accumulation of Na⁺ ions in plants causes toxicity that can result in yield reduction. Na⁺/K⁺ homeostasis is known to be important for salt tolerance in plants. Na⁺/K⁺ homeostasis in rice (Oryza sativa L.) involves nine high-affinity K⁺ transporter (HKT) encoding Na⁺-K⁺ symporter, five OsNHX Na⁺/H⁺ antiporters, and OsSOS1 Na⁺/K⁺ antiporter genes. In the present study, we investigated various molecular and physiological processes to evaluate germination rate, growth pattern, ion content, and expression of OsHKT, OsNHX, and OsSOS1genes related to Na⁺/K⁺ homeostasis in different rice genotypes under salt stress. We found a significant increase in the germination percentage, plant vigor, Na⁺/K⁺ ratio, and gene expression of the OsHKT family in both the roots and shoots of the Nagdong cultivar and salt-tolerant cultivar Pokkali. In the roots of Cheongcheong and IR28 cultivars, Na⁺ ion concentrations were found to be higher than K⁺ ion concentrations. Similarly, high expression levels of OsHKT1, OsHKT3, and OsHKT6 were observed in Cheongcheong, whereas expression levels of OsHKT9 was high in IR28. The expression patterns of OsNHX and OsSOS1 and regulation of other micronutrients differed in the roots and shoots regions of rice and were generally increased by salt stress. The OsNHX family was also expressed at high levels in the roots of Nagdong and in the roots and shoots of Pokkali; in contrast, comparatively low expression levels were observed in the roots and shoots of Cheongcheong and IR28 (with the exception of high OsNHX1 expression in the roots of IR28). Furthermore, the OsSOS1 gene was highly expressed in the roots of Nagdong and shoots of Cheongcheong. We also observed that salt stress decreases chlorophyll content in IR28 and Pokkali but not in Cheongcheong and Nagdong. This study suggests that under salt stress, cultivar Nagdong has more salt-tolerance than cultivar Cheongcheong.

Genome-wide association mapping of sodium and potassium concentration in rice grains and shoots under alternate wetting and drying and continuously flooded irrigation

Identification of a large number of QTL and candidate genes for sodium accumulation in a field grown population of rice derived from the aus subpopulation. Rice (Oryza sativa L.) is a globally important cereal crop. Sodium (Na⁺) and potassium (K⁺) are the major monovalent ions which affect rice growth, and exploring their uptake mechanisms will be useful for understanding rice biology. Since the balance of Na⁺ and K⁺ plays a significant role in adaptation of rice to salinity, that biology might inform the search for tolerance. In this study, the Na⁺ and K⁺ concentration and Na⁺/K⁺ ratio in grains and shoots were analyzed in the Bengal and Assam Aus Panel grown in field conditions under continuously flooded (CF) and alternate wetting and drying (AWD) irrigation. Overall, AWD irrigation significantly reduced the Na⁺ concentration and increased the K⁺ concentration in shoots and grains compared to the plants grown under CF. Genome-wide association mapping was conducted on Na⁺, K⁺ concentration and Na⁺/K⁺ ratio with 2 million SNPs using an efficient mixed model. Only QTLs which contained more than two significant SNPs (p < 0.0001) and where at least one of these significant SNPs passed a 10% false discovery rate were reported. A total of 106 QTLs were identified as being associated with Na⁺ concentration and Na⁺/K⁺ ratio across all traits and field conditions, with 48 QTLs found in multiple traits and/or water conditions. Four notable QTLs (one each on chromosomes 1 and 11, two on chromosome 2) and the haplotype variants of four candidate genes (OsHKT1;5, OsNHX2, LOC_Os02g32490 and OsFAD2_1) are discussed. The QTLs/candidate genes identified here could be useful for breeding rice that accumulates lower concentrations of sodium.

Identification and characterisation of monovalent cation/proton antiporters (CPAs) in Phyllostachys edulis and the functional analysis of PheNHX2 in Arabidopsis thaliana

Plant monovalent cation/proton antiporters (CPAs), types of transmembrane transporters, play important roles in resistance to salt stress. In this study, 37 CPA genes from moso bamboo (Phyllostachys edulis) were identified and characterised. The expression profiles of 10 CPA1 genes (PheNHXs) of moso bamboo were detected by qRT-PCR, which showed that they were specifically expressed in six tissues. In addition, the expression of 10 PheNHXs in leaves and roots changed significantly under 150/200 mM NaCl and 100 μM ABA treatments. In particular, the expression of PheNHX2 in leaves and roots was significantly upregulated under NaCl treatment, thus, we cloned PheNHX2 and analysed its function. Subcellular localisation analysis showed that PheNHX2 was located on the vacuolar membrane. Overexpression of PheNHX2 reduced seed germination and root growth of Arabidopsis thaliana under salt stress, as well as severely affecting cellular Na⁺ and K⁺ content, which in turn reduced the salt tolerance of transgenic Arabidopsis. Measurements of physiological indicators, including chlorophyll content, malondialdehyde content, peroxidase and catalase enzyme activities and relative electrical conductivity, all supported this conclusion. Under salt stress, PheNHX2 also inhibited the expression of some stress-related and ion transport-related genes in transgenic Arabidopsis. Overall, these results indicate that overexpression of PheNHX2 reduces the salt tolerance of transgenic Arabidopsis. This investigation establishes a foundation for subsequent functional studies of moso bamboo CPA genes, and it provides a deeper understanding of PheNHX2 regulation in relation to the salt tolerance of moso bamboo.