Evidence for nuclear interaction of a cytoskeleton protein (OsIFL) with metallothionein and its role in salinity stress tolerance

A cystathionine beta-synthase domain containing protein, OsCBSCBS4, interacts with OsSnRK1A and OsPKG and functions in abiotic stress tolerance in rice

The Cystathionine-β-Synthase (CBS) domain-containing proteins (CDCPs) constitute a functionally diverse protein superfamily, sharing an evolutionary conserved CBS domain either in pair or quad. Rice genome (Oryza sativa subsp. indica) encodes 42 CDCPs; their functions remain largely unexplored. This study examines OsCBSCBS4, a quadruple CBS domain containing protein towards its role in regulating the abiotic stress tolerance in rice. Gene expression analyses revealed upregulation of OsCBSCBS4 in response to diverse abiotic stresses. Further, the cytoplasm-localised OsCBSCBS4 showed interaction with two different kinases, a cytoplasmic localised cGMP-dependant protein kinase (OsPKG) and the nucleo-cytoplasmic catalytic subunit of sucrose-nonfermentation 1-related protein kinase 1 (OsSnRK1A). The interaction with the latter assisted in trafficking of OsCBSCBS4 to the nucleus as well. Overexpression of OsCBSCBS4 in rice resulted in enhanced tolerance to drought and salinity stress, via maintaining better physiological parameters and antioxidant activity. Additionally, OsCBSCBS4-overexpressing rice plants exhibited reduced yield penalty under stress conditions. The in silico docking and in vitro binding analyses of OsCBSCBS4 with ATP suggest its involvement in cellular energy balance. Overall, this study provides novel insight into the unexplored functions of OsCBSCBS4 and demonstrates it as a new promising target for augmenting crop resilience.

Abnormal Degraded Tapetum 1 (ADT1) is required for tapetal cell death and pollen development in rice

The timely degradation of tapetum, the innermost somatic anther cell layer in flowering plants, is critical for pollen development. Although several genes involved in tapetum development have been characterized, the molecular mechanisms underlying tapetum degeneration remain elusive. Here, we showed that mutation in Abnormal Degraded Tapetum 1 (ADT1) resulted in overaccumulation of Reactive Oxygen Species (ROS) and abnormal anther development, causing earlier tapetum Programmed Cell Death (PCD) and pollen abortion. ADT1 encodes a nuclear membrane localized protein, which is strongly expressed in the developing microspores and tapetal cells during early anther development. Moreover, ADT1 could interact with metallothionein MT2b, which was related to ROS scavenging and cell death regulation. These findings indicate that ADT1 is required for proper timing of tapetum PCD by regulating ROS homeostasis, expanding our understanding of the regulatory network of male reproductive development in rice.

Uncovering key salt-tolerant regulators through a combined eQTL and GWAS analysis using the super pan-genome in rice

For sessile plants, gene expression plays a pivotal role in responding to salinity stress by activating or suppressing specific genes. However, our knowledge of genetic variations governing gene expression in response to salt stress remains limited in natural germplasm. Through transcriptome analysis of the Global Mini-Core Rice Collection consisting of a panel of 202 accessions, we identified 22 345 and 27 610 expression quantitative trait loci associated with the expression of 7787 and 9361 eGenes under normal and salt-stress conditions, respectively, leveraging the super pan-genome map. Notably, combined with genome-wide association studies, we swiftly pinpointed the potential candidate gene STG5-a major salt-tolerant locus known as qSTS5. Intriguingly, STG5 is required for maintaining Na+/K+ homeostasis by directly regulating the transcription of multiple members of the OsHKT gene family. Our study sheds light on how genetic variants influence the dynamic changes in gene expression responding to salinity stress and provides a valuable resource for the mining of salt-tolerant genes in the future.

Comparative quantitative trait loci analysis framework reveals relationships between salt stress responsive phenotypes and pathways

Soil salinity is a complex abiotic stress that involves several biological pathways. Hence, focusing on a specific or a few salt-tolerant phenotypes is unlikely to provide comprehensive insights into the intricate and interwinding mechanisms that regulate salt responsiveness. In this study, we develop a heuristic framework for systematically integrating and comprehensively evaluating quantitative trait loci (QTL) analyses from multiple stress-related traits obtained by different studies. Making use of a combined set of 46 salinity-related traits from three independent studies that were based on the same chromosome segment substitution line (CSSL) population of rice (Oryza sativa), we demonstrate how our approach can address technical biases and limitations from different QTL studies and calling methods. This allows us to compile a comprehensive list of trait-specific and multi-trait QTLs, as well as salinity-related candidate genes. In doing so, we discover several novel relationships between traits that demonstrate similar trends of phenotype scores across the CSSLs, as well as the similarities between genomic locations that the traits were mapped to. Finally, we experimentally validate our findings by expression analyses and functional validations of several selected candidate genes from multiple pathways in rice and Arabidopsis orthologous genes, including OsKS7 (ENT-KAURENE SYNTHASE 7), OsNUC1 (NUCLEOLIN 1) and OsFRO1 (FERRIC REDUCTASE OXIDASE 1) to name a few. This work not only introduces a novel approach for conducting comparative analyses of multiple QTLs, but also provides a list of candidate genes and testable hypotheses for salinity-related mechanisms across several biological pathways.

Drought stress tolerance mechanisms and their potential common indicators to salinity, insights from the wild watermelon (Citrullus lanatus): A review

Climate change has escalated the effect of drought on crop production as it has negatively altered the environmental condition. Wild watermelon grows abundantly in the Kgalagadi desert even though the environment is characterized by minimal rainfall, high temperatures and intense sunshine during growing season. This area is also characterized by sandy soils with low water holding capacity, thus bringing about drought stress. Drought stress affects crop productivity through its effects on development and physiological functions as dictated by molecular responses. Not only one or two physiological process or genes are responsible for drought tolerance, but a combination of various factors do work together to aid crop tolerance mechanism. Various studies have shown that wild watermelon possess superior qualities that aid its survival in unfavorable conditions. These mechanisms include resilient root growth, timely stomatal closure, chlorophyll fluorescence quenching under water deficit as key physiological responses. At biochemical and molecular level, the crop responds through citrulline accumulation and expression of genes associated with drought tolerance in this species and other plants. Previous salinity stress studies involving other plants have identified citrulline accumulation and expression of some of these genes (chloroplast APX, Type-2 metallothionein), to be associated with tolerance. Emerging evidence indicates that the upstream of functional genes are the transcription factor that regulates drought and salinity stress responses as well as adaptation. In this review we discuss the drought tolerance mechanisms in watermelons and some of its common indicators to salinity at physiological, biochemical and molecular level.

Nitric oxide: A core signaling molecule under elevated GHGs (CO2, CH4, N2O, O3)-mediated abiotic stress in plants

Nitric oxide (NO), an ancient molecule with multiple roles in plants, has gained momentum and continues to govern plant biosciences-related research. NO, known to be involved in diverse physiological and biological processes, is a central molecule mediating cellular redox homeostasis under abiotic and biotic stresses. NO signaling interacts with various signaling networks to govern the adaptive response mechanism towards stress tolerance. Although diverging views question the role of plants in the current greenhouse gases (GHGs) budget, it is widely accepted that plants contribute, in one way or another, to the release of GHGs (carbon dioxide (CO2), methane (CH4), nitrous oxide (N2O) and ozone (O3)) to the atmosphere, with CH4 and N2O being the most abundant, and occur simultaneously. Studies support that elevated concentrations of GHGs trigger similar signaling pathways to that observed in commonly studied abiotic stresses. In the process, NO plays a forefront role, in which the nitrogen metabolism is tightly related. Regardless of their beneficial roles in plants at a certain level of accumulation, high concentrations of CO2, CH4, and N2O-mediating stress in plants exacerbate the production of reactive oxygen (ROS) and nitrogen (RNS) species. This review assesses and discusses the current knowledge of NO signaling and its interaction with other signaling pathways, here focusing on the reported calcium (Ca2+) and hormonal signaling, under elevated GHGs along with the associated mechanisms underlying GHGs-induced stress in plants.

OsCyp2-P, an auxin-responsive cyclophilin, regulates Ca2+ calmodulin interaction for an ion-mediated stress response in rice

OsCYP2-P is an active cyclophilin (having peptidyl-prolyl cis/trans-isomerase activity, PPIase) isolated from the wild rice Pokkali having a natural capacity to grow and yield seeds in coastal saline regions of India. Transcript abundance analysis in rice seedlings showed the gene is inducible by multiple stresses, including salinity, drought, high temperature, and heavy metals. To dissect the role of OsCYP2-P gene in stress response, we raised overexpression (OE) and knockdown (KD) transgenic rice plants with >2-3 folds higher and approximately 2-fold lower PPIase activity, respectively. Plants overexpressing this gene had more favorable physiological and biochemical parameters (K⁺ /Na⁺ ratio, electrolytic leakage, membrane damage, antioxidant enzymes) than wild type, and the reverse was observed in plants that were knocked down for this gene. We propose that OsCYP2-P contributes to stress tolerance via maintenance of ion homeostasis and thus prevents toxic cellular ion buildup and membrane damage. OE plants were found to have a higher harvest index and higher number of filled grains under salinity and drought stress than wild type. OsCYP2-P interacts with calmodulin, indicating it functions via the Ca-CaM pathway. Compared to the WT, the germinating OE seeds exhibited a substantially higher auxin level, and this hormone was below the detection limits in the WT and KD lines. These observations strongly indicate that OsCyp2-P affects the signaling and transport of auxin in rice.

How salt stress-responsive proteins regulate plant adaptation to saline conditions

An overview is presented of recent advances in our knowledge of candidate proteins that regulate various physiological and biochemical processes underpinning plant adaptation to saline conditions. Salt stress is one of the environmental constraints that restrict plant distribution, growth and yield in many parts of the world. Increased world population surely elevates food demands all over the globe, which anticipates to add a great challenge to humanity. These concerns have necessitated the scientists to understand and unmask the puzzle of plant salt tolerance mechanisms in order to utilize various strategies to develop salt tolerant crop plants. Salt tolerance is a complex trait involving alterations in physiological, biochemical, and molecular processes. These alterations are a result of genomic and proteomic complement readjustments that lead to tolerance mechanisms. Proteomics is a crucial molecular tool that indicates proteins expressed by the genome, and also identifies the functions of proteins accumulated in response to salt stress. Recently, proteomic studies have shed more light on a range of promising candidate proteins that regulate various processes rendering salt tolerance to plants. These proteins have been shown to be involved in photosynthesis and energy metabolism, ion homeostasis, gene transcription and protein biosynthesis, compatible solute production, hormone modulation, cell wall structure modification, cellular detoxification, membrane stabilization, and signal transduction. These candidate salt responsive proteins can be therefore used in biotechnological approaches to improve tolerance of crop plants to salt conditions. In this review, we provided comprehensive updated information on the proteomic data of plants/genotypes contrasting in salt tolerance in response to salt stress. The roles of salt responsive proteins that are potential determinants for plant salt adaptation are discussed. The relationship between changes in proteome composition and abundance, and alterations observed in physiological and biochemical features associated with salt tolerance are also addressed.

Epigenetic regulation of salinity stress responses in cereals

Cereals are important crops and are exposed to various types of environmental stresses that affect the overall growth and yield. Among the various abiotic stresses, salt stress is a major environmental factor that influences the genetic, physiological, and biochemical responses of cereal crops. Epigenetic regulation which includes DNA methylation, histone modification, and chromatin remodelling plays an important role in salt stress tolerance. Recent studies in rice genomics have highlighted that the epigenetic changes are heritable and therefore can be considered as molecular signatures. An epigenetic mechanism under salinity induces phenotypic responses involving modulations in gene expression. Association between histone modification and altered DNA methylation patterns and differential gene expression has been evidenced for salt sensitivity in rice and other cereal crops. In addition, epigenetics also creates stress memory that helps the plant to better combat future stress exposure. In the present review, we have discussed epigenetic influences in stress tolerance, adaptation, and evolution processes. Understanding the epigenetic regulation of salinity could help for designing salt-tolerant varieties leading to improved crop productivity.

Methods for metal chelation in plant homeostasis: Review

Metal uptake, transport and storage in plants depend on specialized ligands with closely related functions. Individual studies differing by species, nutrient availability, tissue type, etc. are not comprehensive enough to understand plant metal homeostasis in its entirety. A thorough review is required that distinguishes the role of ligands directly involved in chelation from the myriad of plant responses to general stress. Distinguishing between the functions of metal chelating compounds is the primary focus of this review; reactive oxygen species mediation and other aspects of metal homeostasis are also discussed. High molecular weight ligands (polysaccharides, phytochelatin, metallothionein), low molecular weight ligands (nicotianamine, histidine, secondary metabolites) and select studies which demonstrate the complex nature of plant metal homeostasis are explored.

Screening and identification of abiotic stress-responsive efficient antifungal Pseudomonas spp. from rice rhizospheric soil

Plant growth-promoting rhizobacteria (PGPR) are a collection of microorganisms often used to support and promote plant development and combat plant infectious diseases with various biological control methods. The most significant restricting factors for agricultural productivity worldwide are abiotic constraints. In the present study, seven bacterial isolates from the rice rhizosphere were selected for detailed tests based on results obtained in experiments determining the ACC deaminase synthesis and drought tolerance at -0.30 MPa PEG level. Screening results of the stress tolerance analysis of the seven isolates for elevated temperature (50°C), alkalinity (10% NaCl), and drought (-1.2 MPa) showed that abiotic stress resistance was less prevalent in DRO2, DRO13, and DRO43 isolates than in DRO17, DRO28, DRO35, and DRO51 isolates. During the study, it was observed that DRO17, DRO28, and DRO51 tended to maintain similar cell density at -0.73 MPa PEG level, as observed at -0.30 MPa stress condition. No bacterial growth was observed at higher PEG level (-1.12 MPa) for any bacterial isolate. Four strains of Pseudomonas (DRO17, DRO28, DRO35, and DRO51) exhibited salinity and temperature tolerance. Antifungal screening using the bangle method showed that DRO35 was highly antagonistic towards Rhizoctonia solani 4633, followed by Fusarium moniliforme 4223, with an inhibition of 64.3% and 48%, respectively. The DRO28 isolate exhibited 72.5% growth inhibition for Fusarium moniliforme 4223, while the DRO51 isolate showed 38.2% growth inhibition for Bipolaris hawaiiensis 2445. DRO17 reduced the growth of Rhizoctonia solani 4633, and Curvularia lunata 350 by 36% and 31%, respectively. In conclusion, the screening of bacterial strains with promising stress tolerance and antifungal characteristics could support farmers to achieve the required positive outcomes in the agriculture field.

Recent progress in understanding salinity tolerance in plants: Story of Na+/K+ balance and beyond

High salt concentrations in the growing medium can severely affect the growth and development of plants. It is imperative to understand the different components of salt-tolerant network in plants in order to produce the salt-tolerant cultivars. High-affinity potassium transporter- and myelocytomatosis proteins have been shown to play a critical role for salinity tolerance through exclusion of sodium (Na⁺) ions from sensitive shoot tissues in plants. Numerous genes, that limit the uptake of salts from soil and their transport throughout the plant body, adjust the ionic and osmotic balance of cells in roots and shoots. In the present review, we have tried to provide a comprehensive report of major research advances on different mechanisms regulating plant tolerance to salinity stress at proteomics, metabolomics, genomics and transcriptomics levels. Along with the role of ionic homeostasis, a major focus was given on other salinity tolerance mechanisms in plants including osmoregulation and osmo-protection, cell wall remodeling and integrity, and plant antioxidative defense. Major proteins and genes expressed under salt-stressed conditions and their role in enhancing salinity tolerance in plants are discussed as well. Moreover, this manuscript identifies and highlights the key questions on plant salinity tolerance that remain to be discussed in the future.

Cell cycle-dependent dynamics of a plant intermediate filament motif protein with intracellular localization related to microtubules

Although intermediate filaments (IFs) are biochemically and immunologically suggested to exist in plant cells, there are few molecular genetic studies related to the proteins that form these structures. In this study, Arabidopsis AT3G05270 was selected as a candidate gene for a protein constituting IF in plant cells. The protein encoded by AT3G05270 has a large α-helix as well as the IF protein motif indispensable for maintaining the structures of IF. Moreover, fluorescence signals of this protein fused with GFP exhibited cytoskeleton-like filamentous structures in plant cells. Thus, we named the protein encoded by AT3G05270 as Intermediate Filament Motif Protein 1 (IFMoP1). The structures composed of IFMoP1 and their localizations were examined in IFMoP1-GFP-expressing tobacco BY-2 cells whose cell cycle was synchronized using aphidicolin, a DNA synthesis inhibitor, and propyzamide, a microtubule-disrupting agent. The IFMoP1-GFP signals were present at the spindles and phragmoplasts in the mitotic phase. In addition, the frequency of cells with cytoskeleton-like filamentous structures composed of IFMoP1-GFP increased with the increase in cells that completed cell division, and then decreased after several hours. In terms of the relationship in intracellular localization between IFMoP1 and microtubules, the filamentous structures composed of IFMoP1 were present independently of microtubules during interphase. In living cells, these filamentous structures moved along with the nucleus. IFMoP1 co-localized with spindle and phragmoplast microtubules during mitosis, as well as with a part of the cortical microtubules in interphase.

The Saltol QTL-localized transcription factor OsGATA8 plays an important role in stress tolerance and seed development in Arabidopsis and rice

GATA represents a highly conserved family of transcription factors reported in organisms ranging from fungi to angiosperms. A member of this family, OsGATA8, localized within the Saltol QTL in rice, has been reported to be induced by salinity, drought, and ABA. However, its precise role in stress tolerance has not yet been elucidated. Using genetic, molecular, and physiological analyses, in this study we show that OsGATA8 increases seed size and tolerance to abiotic stresses in both Arabidopsis and rice. Transgenic lines of rice were generated with 3-fold overexpression of OsGATA8 compared to the wild-type together with knockdown lines with 2-fold lower expression. The overexpressing lines showed higher biomass accumulation and higher photosynthetic efficiency in seedlings compared to the wild-type and knockdown lines under both normal and salinity-stress conditions. OsGATA8 appeared to be an integrator of diverse cellular processes, including K+/Na+ content, photosynthetic efficiency, relative water content, Fv/Fm ratio, and the stability to sub-cellular organelles. It also contributed to maintaining yield under stress, which was ~46% higher in overexpression plants compared with the wild-type. OsGATA8 produced these effects by regulating the expression of critical genes involved in stress tolerance, scavenging of reactive oxygen species, and chlorophyll biosynthesis.

Tamarix microRNA Profiling Reveals New Insight into Salt Tolerance

The halophyte tamarisk (Tamarix) is extremely salt tolerant, making it an ideal material for salt tolerance-related studies. Although many salt-responsive genes of Tamarix were identified in previous studies, there are no reports on the role of post-transcriptional regulation in its salt tolerance. We constructed six small RNA libraries of Tamarix chinensis roots with NaCl treatments. High-throughput sequencing of the six libraries was performed and microRNA expression profiles were constructed. We investigated salt-responsive microRNAs to uncover the microRNA-mediated genes regulation. From these analyses, 251 conserved and 18 novel microRNA were identified from all small RNAs. From 191 differentially expressed microRNAs, 74 co-expressed microRNAs were identified as salt-responsive candidate microRNAs. The most enriched GO (gene ontology) terms for the 157 genes targeted by differentially expressed microRNAs suggested that transcriptions factors were highly active. Two hub microRNAs (miR414, miR5658), which connected by several target genes into an organic microRNA regulatory network, appeared to be the key regulators of post-transcriptional salt-stress responses. As the first survey on the tamarisk small RNAome, this study improves the understanding of tamarisk salt-tolerance mechanisms and will contribute to the molecular-assisted resistance breeding.

Rice intermediate filament, OsIF, stabilizes photosynthetic machinery and yield under salinity and heat stress

Cytoskeleton plays a vital role in stress tolerance; however, involvement of intermediate filaments (IFs) in such a response remains elusive in crop plants. This study provides clear evidence about the unique involvement of IFs in cellular protection against abiotic stress in rice. Transcript abundance of Oryza sativa intermediate filament (OsIF) encoding gene showed 2-10 fold up-regulation under different abiotic stress. Overexpression of OsIF in transgenic rice enhanced tolerance to salinity and heat stress, while its knock-down (KD) rendered plants more sensitive thereby indicating the role of IFs in promoting survival under stress. Seeds of OsIF overexpression rice germinated normally in the presence of high salt, showed better growth, maintained chloroplast ultrastructure and favourable K+/Na+ ratio than the wild type (WT) and KD plants. Analysis of photosynthesis and chlorophyll a fluorescence data suggested better performance of both photosystem I and II in the OsIF overexpression rice under salinity stress as compared to the WT and KD. Under salinity and high temperature stress, OsIF overexpressing plants could maintain significantly high yield, while the WT and KD plants could not. Further, metabolite profiling revealed a 2-4 fold higher accumulation of proline and trehalose in OsIF overexpressing rice than WT, under salinity stress.

Functional characterization of a type 2 metallothionein gene, SsMT2, from alkaline-tolerant Suaeda salsa

A type 2 metallothionein gene, SsMT2, was cloned from Suaeda salsa, a salt- and alkali-tolerant plant, which is dominant species on the saline/alkali soil of northeast China. The SsMT2 gene was expressed in all organs except the flower and its expression was induced by various stresses such as CdCl₂, NaCl, NaHCO₃, and H₂O₂ treatments. SsMT2-transgenic yeast (Saccharomyces cerevisiae) and plants (Arabidopsis thaliana) showed significantly increased resistance to metal, salt and oxidant stresses. These transgenics accumulated more Cd²⁺, but less Na⁺ than their wild type counterparts. SsMT2 transgenic Arabidopsis maintained lower level of H₂O₂ than wild type plants did in response to the stress treatments. These results demonstrated that the SsMT2 gene plays an important role in reactive oxygen species scavenging and confers enhanced metal and oxidant tolerance to plants.

Mapping the 'Two-component system' network in rice

Two-component system (TCS) in plants is a histidine to aspartate phosphorelay based signaling system. Rice genome has multifarious TCS signaling machinery comprising of 11 histidine kinases (OsHKs), 5 histidine phosphotransferases (OsHPTs) and 36 response regulators (OsRRs). However, how these TCS members interact with each other and comprehend diverse signaling cascades remains unmapped. Using a highly stringent yeast two-hybrid (Y2H) platform and extensive in planta bimolecular fluorescence complementation (BiFC) assays, distinct arrays of interaction between various TCS proteins have been identified in the present study. Based on these results, an interactome map of TCS proteins has been assembled. This map clearly shows a cross talk in signaling, mediated by different sensory OsHKs. It also highlights OsHPTs as the interaction hubs, which interact with OsRRs, mostly in a redundant fashion. Remarkably, interactions between type-A and type-B OsRRs have also been revealed for the first time. These observations suggest that feedback regulation by type-A OsRRs may also be mediated by interference in signaling at the level of type-B OsRRs, in addition to OsHPTs, as known previously. The interactome map presented here provides a starting point for in-depth molecular investigations for signal(s) transmitted by various TCS modules into diverse biological processes.

Overview of Methods for Assessing Salinity and Drought Tolerance of Transgenic Wheat Lines

Salinity and drought are interconnected, causing phenotypic, physiological, biochemical, and molecular changes in a cell. These stresses are the major factors adversely affecting growth and productivity in cereals. Genetic engineering methods have advanced to enable development of genotypes with improved salinity and drought tolerance. The resulting transgenic plant produces a group of progenies which includes moderate to high-stress tolerant transgenic lines. Development of reproducible screening methods to identify high-stress tolerant germplasm under laboratory, greenhouse, or field conditions is must. Further, field level demonstration of improved phenotypes and yield under salinity and drought stress conditions is both challenging and expensive. Fast and efficient screening techniques that could be used to screen transgenic lines under greenhouse conditions, for salt and drought stress tolerance, may contribute toward the identification of promising lines for field conditions. This chapter provides information on various approaches which can be developed during different stages of plant development for selecting salinity and drought tolerant plants in cereals, especially wheat.

Transcription dynamics of Saltol QTL localized genes encoding transcription factors, reveals their differential regulation in contrasting genotypes of rice

Salinity is one of the major environmental factors affecting the growth and yield of rice crop. Salinity stress response is a multigenic trait and numerous approaches have been used to dissect out the key determinants of complex salt tolerance trait and their regulation in plant. In the current study, we have investigated expression dynamics of the genes encoding transcription factors (SalTFs) localized within a major salinity tolerance related QTL-'Saltol' in the contrasting cultivars of rice. SalTFs were found to be differentially regulated between the contrasting genotypes of rice, with higher constitutive expression in the salt tolerant landrace, Pokkali than the cultivar IR64. Moreover, SalTFs were found to exhibit inducibility in the salt sensitive cultivar at late duration (after 24 h) of salinity stress. Further, the transcript abundance analysis of these SalTFs at various developmental stages of rice revealed that low expressing genes may be involved in developmental responses, while high expressing genes can be linked with the salt stress response. Grouping of these genes was well supported by in silico protein-protein interaction studies and distribution of single-nucleotide polymorphisms (SNPs) and insertions/deletions (InDels) in the promoter and genic regions of these genes. Taken together, we propose that out of 14 SalTFs, eight members are strongly correlated with the salinity stress tolerance in rice and six are involved in plant growth and development.