Functional screening of cDNA library from a salt tolerant rice genotype Pokkali identifies mannose-1-phosphate guanyl transferase gene (OsMPG1) as a key member of salinity stress response

Genome-Wide Association Study of Early Vigour-Related Traits for a Rice (Oryza sativa L.) japonica Diversity Set Grown in Aerobic Conditions

Aerobic rice production is a relatively new system in which rice is direct-seeded and grown in non-flooded but well-watered conditions to improve water productivity. Early vigour-related traits are likely to be important in aerobic conditions. This study aimed to identify quantitative trait loci (QTL) and candidate genes associated with early vigour-related traits in aerobic conditions using a japonica rice diversity set. Field experiments and glasshouse experiments conducted under aerobic conditions revealed significant genotypic variation in early vigour-related traits. Genome-wide association analysis identified 32 QTL associated with early vigour-related traits. Notably, two QTL, qAEV1.5 and qAEV8, associated with both early vigour score and mesocotyl length, explained up to 22.1% of the phenotypic variance. In total, 23 candidate genes related to plant growth development and abiotic stress response were identified in the two regions. This study provides novel insights into the genetic basis of early vigour under aerobic conditions. Validation of identified QTL and candidate genes in different genetic backgrounds is crucial for future studies. Moreover, testing the effect of QTL on yield under different environments would be valuable. After validation, these QTL and genes can be considered for developing markers in marker-assisted selection for aerobic rice production.

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.

Multi-index fuzzy comprehensive evaluation model with information entropy of alfalfa salt tolerance based on LiDAR data and hyperspectral image data

Rapid, non-destructive and automated salt tolerance evaluation is particularly important for screening salt-tolerant germplasm of alfalfa. Traditional evaluation of salt tolerance is mostly based on phenotypic traits obtained by some broken ways, which is time-consuming and difficult to meet the needs of large-scale breeding screening. Therefore, this paper proposed a non-contact and non-destructive multi-index fuzzy comprehensive evaluation model for evaluating the salt tolerance of alfalfa from Light Detection and Ranging data (LiDAR) and HyperSpectral Image data (HSI). Firstly, the structural traits related to growth status were extracted from the LiDAR data of alfalfa, and the spectral traits representing the physical and chemical characteristics were extracted from HSI data. In this paper, these phenotypic traits obtained automatically by computation were called Computing Phenotypic Traits (CPT). Subsequently, the multi-index fuzzy evaluation system of alfalfa salt tolerance was constructed by CPT, and according to the fuzzy mathematics theory, a multi-index Fuzzy Comprehensive Evaluation model with information Entropy of alfalfa salt tolerance (FCE-E) was proposed, which comprehensively evaluated the salt tolerance of alfalfa from the aspects of growth structure, physiology and biochemistry. Finally, comparative experiments showed that: (1) The multi-index FCE-E model based on the CPT was proposed in this paper, which could find more salt-sensitive information than the evaluation method based on the measured Typical Phenotypic Traits (TPT) such as fresh weight, dry weight, water content and chlorophyll. The two evaluation results had 66.67% consistent results, indicating that the multi-index FCE-E model integrates more information about alfalfa and more comprehensive evaluation. (2) On the basis of the CPT, the results of the multi-index FCE-E method were basically consistent with those of Principal Component Analysis (PCA), indicating that the multi-index FCE-E model could accurately evaluate the salt tolerance of alfalfa. Three highly salt-tolerant alfalfa varieties and two highly salt-susceptible alfalfa varieties were screened by the multi-index FCE-E method. The multi-index FCE-E method provides a new method for non-contact non-destructive evaluation of salt tolerance of alfalfa.

Integrated Transcriptomic and Metabolomic Analyses Uncover the Differential Mechanism in Saline-Alkaline Tolerance between Indica and Japonica Rice at the Seedling Stage

Saline-alkaline stress is one of the major damages that severely affects rice (Oryza sativa L.) growth and grain yield; however, the mechanism of the tolerance remains largely unknown in rice. Herein, we comparatively investigated the transcriptome and metabolome of two contrasting rice subspecies genotypes, Luohui 9 (abbreviation for Chao2R under study, O. sativa ssp. indica, saline-alkaline-sensitive) and RPY geng (O. sativa ssp. japonica, saline-alkaline-tolerant), to identify the main pathways and important factors related to saline-alkaline tolerance. Transcriptome analysis showed that 68 genes involved in fatty acid, amino acid (such as phenylalanine and tryptophan), phenylpropanoid biosynthesis, energy metabolism (such as Glycolysis and TCA cycle), as well as signal transduction (such as hormone and MAPK signaling) were identified to be specifically upregulated in RPY geng under saline-alkaline conditions, implying that a series of cascade changes from these genes promotes saline-alkaline stress tolerance. The transcriptome changes observed in RPY geng were in high accordance with the specifically accumulation of metabolites, consisting mainly of 14 phenolic acids, 8 alkaloids, and 19 lipids based on the combination analysis of transcriptome and metabolome. Moreover, some genes involved in signal transduction as hub genes, such as PR5, FLS2, BRI1, and NAC, may participate in the saline-alkaline stress response of RPY geng by modulating key genes involved in fatty acid, phenylpropanoid biosynthesis, amino acid metabolism, and glycolysis metabolic pathways based on the gene co-expression network analysis. The present research results not only provide important insights for understanding the mechanism underlying of rice saline-alkaline tolerance at the transcriptome and metabolome levels but also provide key candidate target genes for further enhancing rice saline-alkaline stress tolerance.

Salt Tolerance of Rice Is Enhanced by the SS3 Gene, Which Regulates Ascorbic Acid Synthesis and ROS Scavenging

Mining the key genes involved in the balance of rice salt tolerance is extremely important for developing salt-tolerant rice varieties. A library of japonica mutants was screened under salinity conditions to identify putative salt stress-responsive genes. We identified a highly salt-sensitive mutant ss3 and used a map-based cloning approach to isolate the gene SS3, which encodes mannose-1-phosphate guanylyltransferase. Under salt treatment, ss3 mutants have decreased ascorbic acid (AsA) content and increased reactive oxygen species (ROS) levels compared with the wild type (WT). Exogenous AsA restored the salt tolerance of ss3 plants, indicating that inhibition of AsA synthesis was an important factor in the salt sensitivity of the mutant. Functional complementation using the WT allele rescued the mutation, and transcription of SS3 was induced by salt stress. Vector SS3p:SS3 was constructed containing the 1086 bp coding sequence of SS3. Under salinity conditions, transgenic seedlings expressing SS3p:SS3 had improved salt tolerance relative to WT, as demonstrated by better growth status, higher chlorophyll content, a lower level of Na⁺, and a reduced Na⁺/K⁺ ratio. Further investigation revealed that several senescence- and autophagy-related genes were expressed at lower levels in salt-stressed transgenic lines compared to WT. These results demonstrate the positive impact of SS3 on salt tolerance in rice through the regulation of AsA synthesis and ROS accumulation, and indicate that SS3 is a valuable target for genetic manipulation.

How do rice seedlings of landrace Pokkali survive in saline fields after transplantation? Physiology, biochemistry, and photosynthesis

Rice, one of the most important staple food crops in the world, is highly sensitive to soil salinity at the seedling stage. The ultimate yield of this crop is a function of the number of seedlings surviving after transplantation in saline water. Oryza sativa cv. IR64 is a high-yielding salinity-sensitive variety, while Pokkali is a landrace traditionally cultivated by the local farmers in the coastal regions in India. However, the machinery responsible for the seedling-stage tolerance in Pokkali is not understood. To bridge this gap, we subjected young seedlings of these contrasting genotypes to salinity and performed detailed investigations about their growth parameters, ion homeostasis, biochemical composition, and photosynthetic parameters after every 24 h of salinity for three days. Taken together, all the physiological and biochemical indicators, such as proline accumulation, K⁺/Na⁺ ratio, lipid peroxidation, and electrolyte leakage, clearly revealed significant differences between IR64 and Pokkali under salinity, establishing their contrasting nature at this stage. In response to salinity, the F_v/F_m ratio (maximum quantum efficiency of Photosystem II as inferred from Chl a fluorescence) and the energy conserved for the electron transport after the reduction of Q_A (the primary electron acceptor of PSII), to Q_A^-, and reduction of the end electron acceptor molecules towards the PSI (Photosystem I) electron acceptor side was higher in Pokkali than IR64 plants. These observations reflect a direct contribution of photosynthesis towards seedling-stage salinity tolerance in rice. These findings will help to breed high-yielding crops for salinity prone agricultural lands.

Profiling of rice Cd-tolerant genes through yeast-based cDNA library survival screening

The bioaccumulation of cadmium (Cd) in crop and the subsequent food chain has aroused extensive concerns. However, the underlying molecular mechanisms of plant Cd tolerance remain to be clarified from the viewpoint of novel candidate genes. Here we described a highly efficient approach for preliminary identifying rice Cd-tolerant genes through the yeast-based cDNA library survival screening combined with high-throughput sequencing strategy. About 690 gene isoforms were identified as being Cd-tolerant candidates using this shotgun approach. Among the Cd-tolerant genes identified, several categories of genes such as BAX inhibitor (BI), NAC transcription factors and Rapid ALkalinization Factors (RALFs) were of particular interest, and their function of Cd tolerance was further validated via heterologous expression, which suggested that SNAC1, RALF12, OsBI-1 can confer Cd tolerance in yeast and tobacco leaves. Regarding the genes involved in ion transport, the validated Cd-tolerant heavy metal-associated domain (HMAD) isoprenylated protein HIPP42 was particularly noteworthy. Further elucidation of these genes associated with Cd tolerance in rice will benefit agricultural activities.

Harmonizing technological advances in phenomics and genomics for enhanced salt tolerance in rice from a practical perspective

Half of the global human population is dependent on rice as a staple food crop and more than 25% increase in rice productivity is required to feed the global population by 2030. With increase in irrigation, global warming and rising sea level, rising salinity has become one of the major challenges to enhance the rice productivity. Since the loss on this account is to the tune of US$12 billion per annum, it necessitates the global attention. In the era of technological advancement, substantial progress has been made on phenomics and genomics data generation but reaping benefit of this in rice salinity variety development in terms of cost, time and precision requires their harmonization. There is hardly any comprehensive holistic review for such combined approach. Present review describes classical salinity phenotyping approaches having morphological, physiological and biochemical components. It also gives a detailed account of invasive and non-invasive approaches of phenomic data generation and utilization. Classical work of rice salinity QLTs mapping in the form of chromosomal atlas has been updated. This review describes how QTLs can be further dissected into QTN by GWAS and transcriptomic approaches. Opportunities and progress made by transgenic, genome editing, metagenomics approaches in combating rice salinity problems are discussed. Major aim of this review is to provide a comprehensive over-view of hitherto progress made in rice salinity tolerance research which is required to understand bridging of phenotype based breeding with molecular breeding. This review is expected to assist rice breeders in their endeavours by fetching greater harmonization of technological advances in phenomics and genomics for better pragmatic approach having practical perspective.

Genome-wide analyses reveal the role of noncoding variation in complex traits during rice domestication

Genomes carry millions of noncoding variants, and identifying the tiny fraction with functional consequences is a major challenge for genomics. We assessed the role of selection on long noncoding RNAs (lncRNAs) for domestication-related changes in rice grains. Among 3363 lncRNA transcripts identified in early developing panicles, 95% of those with differential expression (329 lncRNAs) between Oryza sativa ssp. japonica and wild rice were significantly down-regulated in the domestication event. Joint genome and transcriptome analyses reveal that directional selection on lncRNAs altered the expression of energy metabolism genes during domestication. Transgenic experiments and population analyses with three focal lncRNAs illustrate that selection on these loci led to increased starch content and grain weight. Together, our findings indicate that genome-wide selection for lncRNA down-regulation was an important mechanism for the emergence of rice domestication traits.

Methylation content sensitive enzyme ddRAD (MCSeEd): a reference-free, whole genome profiling system to address cytosine/adenine methylation changes

Methods for investigating DNA methylation nowadays either require a reference genome and high coverage, or investigate only CG methylation. Moreover, no large-scale analysis can be performed for N⁶-methyladenosine (6 mA) at an affordable price. Here we describe the methylation content sensitive enzyme double-digest restriction-site-associated DNA (ddRAD) technique (MCSeEd), a reduced-representation, reference-free, cost-effective approach for characterizing whole genome methylation patterns across different methylation contexts (e.g., CG, CHG, CHH, 6 mA). MCSeEd can also detect genetic variations among hundreds of samples. MCSeEd is based on parallel restrictions carried out by combinations of methylation insensitive and sensitive endonucleases, followed by next-generation sequencing. Moreover, we present a robust bioinformatic pipeline (available at https://bitbucket.org/capemaster/mcseed/src/master/ ) for differential methylation analysis combined with single nucleotide polymorphism calling without or with a reference genome.

Role of brassinosteroids in rice spikelet differentiation and degeneration under soil-drying during panicle development

BACKGROUND

Brassinosteroids (BRs) are a new group of plant hormones and play important roles in plant growth and development. However, little information is available if BRs could regulate spikelet development in rice (Oryza sativa L.) especially under soil-drying conditions. This study investigated whether and how BRs mediate the effect of soil-drying on spikelet differentiation and degeneration in rice. A rice cultivar was field-grown and exposed to three soil moisture treatments during panicle development, that is, well-watered (WW), moderate soil-drying (MD) and severe soil-drying (SD).

RESULTS

Compared with the WW treatment, the MD treatment enhanced BRs biosynthesis in young panicles, increased spikelet differentiation and reduced spikelet degeneration. The SD treatment had the opposite effects. Changes in expression levels of key rice inflorescence development genes (OsAPO2 and OsTAW1), ascorbic acid (AsA) content, and activities of enzymes involved AsA synthesis and recycle, and amount of nonstructural carbohydrates (NSC) in young panicles were consistent with those in BRs levels, whereas hydrogen peroxide (H₂O₂) content showed opposite trend. Knockdown of the BRs synthesis gene OsD11 or application of a BRs biosynthesis inhibitor to young panicles markedly decreased OsAPO2 and OsTAW1 expression levels, BRs and AsA contents, activities of enzymes involved AsA synthesis and recycle, NSC amount in rice panicles and spikelet differentiation but increased the H₂O₂ content and spikelet degeneration compared to the control (the wide type or application of water). The opposite effects were observed when exogenous BRs were applied.

CONCLUSIONS

The results suggest that BRs mediate the effect of soil-drying on spikelet differentiation and degeneration, and elevated BRs levels in rice panicles promote spikelet development under MD by enhancing inflorescence meristem activity, AsA recycle and NSC partitioning to the growing panicles.

Saccharomyces cerevisiae as a Tool to Investigate Plant Potassium and Sodium Transporters

Sodium and potassium are two alkali cations abundant in the biosphere. Potassium is essential for plants and its concentration must be maintained at approximately 150 mM in the plant cell cytoplasm including under circumstances where its concentration is much lower in soil. On the other hand, sodium must be extruded from the plant or accumulated either in the vacuole or in specific plant structures. Maintaining a high intracellular K+/Na+ ratio under adverse environmental conditions or in the presence of salt is essential to maintain cellular homeostasis and to avoid toxicity. The baker's yeast, Saccharomyces cerevisiae, has been used to identify and characterize participants in potassium and sodium homeostasis in plants for many years. Its utility resides in the fact that the electric gradient across the membrane and the vacuoles is similar to plants. Most plant proteins can be expressed in yeast and are functional in this unicellular model system, which allows for productive structure-function studies for ion transporting proteins. Moreover, yeast can also be used as a high-throughput platform for the identification of genes that confer stress tolerance and for the study of protein-protein interactions. In this review, we summarize advances regarding potassium and sodium transport that have been discovered using the yeast model system, the state-of-the-art of the available techniques and the future directions and opportunities in this field.

Advances in understanding salt tolerance in rice

This review presents a comprehensive overview of the recent research on rice salt tolerance in the areas of genomics, proteomics, metabolomics and chemical genomics. Salinity is one of the major constraints in rice cultivation globally. Traditionally, rice is a glycophyte except for a few genotypes that have been widely used in salinity tolerance breeding of rice. Both seedling and reproductive stages of rice are considered to be the salt-susceptible stages; however, research efforts have been biased towards improving the understanding of seedling-stage salt tolerance. An extensive literature survey indicated that there have been very few attempts to develop reproductive stage-specific salt tolerance in rice probably due to the lack of salt-tolerant phenotypes at the reproductive stage. Recently, the role of DNA methylation, genome duplication and codon usage bias in salinity tolerance of rice have been studied. Furthermore, the study of exogenous salt stress alleviants in rice has opened up another potential avenue for understanding and improving its salt tolerance. There is a need to not only generate additional genomic resources in the form of salt-responsive QTLs and molecular markers and to characterize the genes and their upstream regulatory regions, but also to use them to gain deep insights into the mechanisms useful for developing tolerant varieties. We analysed the genomic locations of diverse salt-responsive genomic resources and found that rice chromosomes 1-6 possess the majority of these salinity-responsive genomic resources. The review presents a comprehensive overview of the recent research on rice salt tolerance in the areas of genomics, proteomics, metabolomics and chemical genomics, which should help in understanding the molecular basis of salinity tolerance and its more effective improvement in rice.

Identification of wheat stress-responding genes and TaPR-1-1 function by screening a cDNA yeast library prepared following abiotic stress

Abiotic stress significantly impacts growth and yield of crop plants. It is imperative for crop improvement to discover and utilize stress-tolerant functional genes. In this study, genes responding to abiotic stresses, such as freezing, salt and osmotic stress, were screened from a cDNA yeast library that was constructed from the drought- and heat-tolerant wheat variety Hanxuan 10. After screening for surviving clones we isolated 7,249, 4,313 and 4,469 raw sequences, corresponding to 4,695, 2,641 and 2,771 genes following each treatment. Venn diagrams revealed 377 overlapping genes. GO analysis suggested that these genes were mainly involved in the metabolic and stress signal pathways. KEGG pathway enrichment analysis indicated that the isolated genes predominantly belonged to pathways concerning energy and metabolism. Overlapping gene TaPR-1-1 within the pathogenesis-related (PR) protein family was selected for detailed characterization. Although previous studies had shown that PR genes function during pathogen attack, our results demonstrated that TaPR-1-1 expression was also induced by freezing, salinity, and osmotic stresses. Overexpression in yeast and Arabidopsis showed that TaPR-1-1 conferred tolerance to these stresses. We concluded that screening cDNA yeast libraries following abiotic stress is an efficient way to identify stress-tolerance genes.

Functional screening of salt tolerance genes from a halophyte Sporobolus virginicus and transcriptomic and metabolomic analysis of salt tolerant plants expressing glycine-rich RNA-binding protein

Sporobolus virginicus is a halophytic C₄ grass found worldwide, from tropical to warm temperate regions. One Japanese genotype showed a salinity tolerance up to 1.5 M NaCl, a three-fold higher concentration than the salinity of sea water. To identify the key genes involved in the regulation of salt tolerance in S. virginicus, we produced 3500 independent transgenic Arabidopsis lines expressing random cDNA from S. virginicus and screened 10 lines which showed enhanced salt tolerance compared with the wild type in a medium containing 150 mM NaCl. Among the selected lines, two contained cDNA coding glycine-rich RNA-binding proteins (SvGRP1 and SvGRP2). This is the first reports on the function of GRPs from halophytes in salt tolerance though reports have shown GRPs are involved in diverse biological and biochemical processes including salt tolerance in Arabidopsis and some other glycophytes. Transcriptomic analysis and GO enrichment analysis of SvGRP1-expressing Arabidopsis under salt stress revealed upregulation of polyol and downregulation of glucosinolate and indole acetic acid biosynthesis/metabolic pathways. Metabolomic analysis of the SvGRP1-transformant suggested that the increase in 3-aminoppropanoic acid, citramalic acid, and isocitric acid content was associated with enhanced salt tolerance. These findings could provide novel insight into the roles of GRPs in plant salt tolerance.

Comprehensive Analysis of the Cadmium Tolerance of Abscisic Acid-, Stress- and Ripening-Induced Proteins (ASRs) in Maize

In plants, abscisic acid-, stress-, and ripening-induced (ASR) proteins have been shown to impart tolerance to multiple abiotic stresses such as drought and salinity. However, their roles in metal stress tolerance are poorly understood. To screen plant Cd-tolerance genes, the yeast-based gene hunting method which aimed to screen Cd-tolerance colonies from maize leaf cDNA library hosted in yeast was carried out. Here, maize ZmASR1 was identified to be putative Cd-tolerant through this survival screening strategy. In silico analysis of the functional domain organization, phylogenetic classification and tissue-specific expression patterns revealed that maize ASR1 to ASR5 are typical ASRs with considerable expression in leaves. Further, four of them were cloned for testifying Cd tolerance using yeast complementation assay. The results indicated that they all confer Cd tolerance in Cd-sensitive yeast. Then they were transiently expressed in tobacco leaves for subcellular localization analysis and for Cd-challenged lesion assay, continuously. The results demonstrated that all 4 maize ASRs tested are localized to the cell nucleus and cytoplasm in tobacco leaves. Moreover, they were confirmed to be Cd-tolerance genes in planta through lesion analysis in Cd-infiltrated leaves transiently expressing them. Taken together, our results demonstrate that maize ASRs play important roles in Cd tolerance, and they could be used as promising candidate genes for further functional studies toward improving the Cd tolerance in plants.

Molecular cloning and functional analysis of the phosphomannomutase (PMM) gene from Dendrobium officinale and evidence for the involvement of an abiotic stress response during germination

Phosphomannomutase (PMM, EC 5.4.2.8) catalyzes the interconversion of mannose-6-phosphate to mannose-1-phosphate, the precursor for the synthesis of GDP-mannose. In this study, the complementary DNA (cDNA) of the Phosphomannomutase (PMM) gene was initially cloned from Dendrobium officinale by RACE method. Transient transform result showed that the DoPMM protein was localized in the cytoplasm. The DoPMM gene was highly expressed in the stems of D. officinale both in vegetative and reproductive developmental stages. The putative promoter was cloned by TAIL-PCR and used for searched cis-elements. Stress-related cis-elements like ABRE, TCA-element, and MBS were found in the promoter regions. The DoPMM gene was up-regulated after treatment with abscisic acid, salicylic acid, cold, polyethylene glycol, and NaCl. The total ascorbic acid (AsA) and polysaccharide content in all of the 35S::DoPMM Arabidopsis thaliana transgenic lines #1, #2, and #5 showed a 40, 39, and 31% increase in AsA and a 77, 22, and 39% increase in polysaccharides, respectively more than wild-type (WT) levels. All three 35S::DoPMM transgenic lines exhibited a higher germination percentage than WT plants when seeded on half-strength MS medium supplemented with 150 mM NaCl or 300 mM mannitol. These results provide genetic evidence for the involvement of PMM genes in the biosynthesis of AsA and polysaccharides and the mediation of PMM genes in abiotic stress tolerance during seed germination in A. thaliana.

Comparative miRomics of Salt-Tolerant and Salt-Sensitive Rice

Increase in soil salt causes osmotic and ionic stress to plants, which inhibits their growth and productivity. Rice production is also hampered by salinity and the effect of salt is most severe at the seedling and reproductive stages. Salainity tolerance is a quantitative property controlled by multiple genes coding for signaling molecules, ion transporters, metabolic enzymes and transcription regulators. MicroRNAs are key modulators of gene-expression that act at the post-transcriptional level by translation repression or transcript cleavage. They also play an important role in regulating plant's response to salt-stress. In this work we adopted the approach of comparative and integrated data-mining to understand the miRNA-mediated regulation of salt-stress in rice. We profiled and compared the miRNA regulations using natural varieties and transgenic lines with contrasting behaviors in response to salt-stress. The information obtained from sRNAseq, RNAseq and degradome datasets was integrated to identify the salt-deregulated miRNAs, their targets and the associated metabolic pathways. The analysis revealed the modulation of many biological pathways, which are involved in salt-tolerance and play an important role in plant phenotype and physiology. The end modifications of the miRNAs were also studied in our analysis and isomiRs having a dynamic role in salt-tolerance mechanism were identified.

DoGMP1 from Dendrobium officinale contributes to mannose content of water-soluble polysaccharides and plays a role in salt stress response

GDP-mannose pyrophosphorylase (GMP) catalyzed the formation of GDP-mannose, which serves as a donor for the biosynthesis of mannose-containing polysaccharides. In this study, three GMP genes from Dendrobium officinale (i.e., DoGMPs) were cloned and analyzed. The putative 1000 bp upstream regulatory region of these DoGMPs was isolated and cis-elements were identified, which indicates their possible role in responses to abiotic stresses. The DoGMP1 protein was shown to be localized in the cytoplasm. To further study the function of the DoGMP1 gene, 35S:DoGMP1 transgenic A. thaliana plants with an enhanced expression level of DoGMP1 were generated. Transgenic plants were indistinguishable from wild-type (WT) plants in tissue culture or in soil. However, the mannose content of the extracted water-soluble polysaccharides increased 67%, 96% and 92% in transgenic lines #1, #2 and #3, respectively more than WT levels. Germination percentage of seeds from transgenic lines was higher than WT seeds and the growth of seedlings from transgenic lines was better than WT seedlings under salinity stress (150 mM NaCl). Our results provide genetic evidence for the involvement of GMP genes in the biosynthesis of mannose-containing polysaccharides and the mediation of GMP genes in the response to salt stress during seed germination and seedling growth.

Knocking Down the Expression of GMPase Gene OsVTC1-1 Decreases Salt Tolerance of Rice at Seedling and Reproductive Stages

Salinity is a severe environmental stress that greatly impairs production of crops worldwide. Previous studies have shown that GMPase plays an important role in tolerance of plants to salt stress at vegetative stage. However, the function of GMPase in plant responses to salt stress at reproductive stage remains unclear. Studies have shown that heterologous expression of rice GMPase OsVTC1-1 enhanced salt tolerance of tobacco seedlings, but the native role of OsVTC1-1 in salt stress tolerance of rice is unknown. To illustrate the native function of GMPase in response of rice to salt stress, OsVTC1-1 expression was suppressed using RNAi-mediated gene silencing. Suppressing OsVTC1-1 expression obviously decreased salt tolerance of rice varieties at vegetative stage. Intriguingly, grain yield of OsVTC1-1 RNAi rice was also significantly reduced under salt stress, indicating that OsVTC1-1 plays an important role in salt tolerance of rice at both seedling and reproductive stages. OsVTC1-1 RNAi rice accumulated more ROS under salt stress, and supplying exogenous ascorbic acid restored salt tolerance of OsVTC1-1 RNAi lines, suggesting that OsVTC1-1 is involved in salt tolerance of rice through the biosynthesis regulation of ascorbic acid. Altogether, results of present study showed that rice GMPase gene OsVTC1-1 plays a critical role in salt tolerance of rice at both vegetative and reproductive stages through AsA scavenging of excess ROS.

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.

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

Soil salinity is being perceived as a major threat to agriculture. Plant breeders and molecular biologist are putting their best efforts to raise salt-tolerant crops. The discovery of the Saltol QTL, a major QTL localized on chromosome I, responsible for salt tolerance at seedling stage in rice has given new hopes for raising salinity tolerant rice genotypes. In the present study, we have functionally characterized a Saltol QTL localized cytoskeletal protein, intermediate filament like protein (OsIFL), of rice. Studies related to intermediate filaments are emerging in plants, especially with respect to their involvement in abiotic stress response. Our investigations clearly establish that the heterologous expression of OsIFL in three diverse organisms (bacteria, yeast and tobacco) provides survival advantage towards diverse abiotic stresses. Screening of rice cDNA library revealed OsIFL to be strongly interacting with metallothionein protein. Bimolecular fluorescence complementation assay further confirmed this interaction to be occurring inside the nucleus. Overexpression of OsIFL in transgenic tobacco plants conferred salinity stress tolerance by maintaining favourable K⁺/Na⁺ ratio and thus showed protection from salinity stress induced ion toxicity. This study provides the first evidence for the involvement of a cytoskeletal protein in salinity stress tolerance in diverse organisms.

Transcriptome analysis in different rice cultivars provides novel insights into desiccation and salinity stress responses

Drought and salinity are the major environmental factors that affect rice productivity. Comparative transcriptome analysis between tolerant and sensitive rice cultivars can provide insights into the regulatory mechanisms involved in these stress responses. In this study, the comparison of transcriptomes of a drought-tolerant [Nagina 22 (N22)] and a salinity-tolerant (Pokkali) rice cultivar with IR64 (susceptible cultivar) revealed variable transcriptional responses under control and stress conditions. A total of 801 and 507 transcripts were exclusively differentially expressed in N22 and Pokkali rice cultivars, respectively, under stress conditions. Gene ontology analysis suggested the enrichment of transcripts involved in response to abiotic stress and regulation of gene expression in stress-tolerant rice cultivars. A larger number of transcripts encoding for members of NAC and DBP transcription factor (TF) families in N22 and members of bHLH and C₂H₂ TF families in Pokkali exhibited differential regulation under desiccation and salinity stresses, respectively. Transcripts encoding for thioredoxin and involved in phenylpropanoid metabolism were up-regulated in N22, whereas transcripts involved in wax and terpenoid metabolism were up-regulated in Pokkali. Overall, common and cultivar-specific stress-responsive transcripts identified in this study can serve as a helpful resource to explore novel candidate genes for abiotic stress tolerance in rice.

Functional Identification and Characterization of Genes Cloned from Halophyte Seashore Paspalum Conferring Salinity and Cadmium Tolerance

Salinity-affected and heavy metal-contaminated soils limit the growth of glycophytic plants. Identifying genes responsible for superior tolerance to salinity and heavy metals in halophytes has great potential for use in developing salinity- and Cd-tolerant glycophytes. The objective of this study was to identify salinity- and Cd-tolerance related genes in seashore paspalum (Paspalum vaginatum), a halophytic perennial grass species, using yeast cDNA expression library screening method. Based on the Gateway-compatible vector system, a high-quality entry library was constructed, which contained 9.9 × 10(6) clones with an average inserted fragment length of 1.48 kb representing a 100% full-length rate. The yeast expression libraries were screened in a salinity-sensitive and a Cd-sensitive yeast mutant. The screening yielded 32 salinity-tolerant clones harboring 18 salinity-tolerance genes and 20 Cd-tolerant clones, including five Cd-tolerance genes. qPCR analysis confirmed that most of the 18 salinity-tolerance and five Cd-tolerance genes were up-regulated at the transcript level in response to salinity or Cd stress in seashore paspalum. Functional analysis indicated that salinity-tolerance genes from seashore paspalum could be involved mainly in photosynthetic metabolism, antioxidant systems, protein modification, iron transport, vesicle traffic, and phospholipid biosynthesis. Cd-tolerance genes could be associated with regulating pathways that are involved in phytochelatin synthesis, HSFA4-related stress protection, CYP450 complex, and sugar metabolism. The 18 salinity-tolerance genes and five Cd-tolerance genes could be potentially used as candidate genes for genetic modification of glycophytic grass species to improve salinity and Cd tolerance and for further analysis of molecular mechanisms regulating salinity and Cd tolerance.

OsSRO1a Interacts with RNA Binding Domain-Containing Protein (OsRBD1) and Functions in Abiotic Stress Tolerance in Yeast

SRO1 is an important regulator of stress and hormonal response in plants and functions by interacting with transcription factors and several other proteins involved in abiotic stress response. In the present study, we report OsRBD1, an RNA binding domain 1- containing protein as a novel interacting partner of OsSRO1a from rice. The interaction of OsSRO1a with OsRBD1 was shown in yeast as well as in planta. Domain-domain interaction study revealed that C-terminal RST domain of OsSRO1a interacts with the N-terminal RRM1 domain of OsRBD1 protein. Both the proteins were found to co-localize in nucleus. Transcript profiling under different stress conditions revealed co-regulation of OsSRO1a and OsRBD1 expression under some abiotic stress conditions. Further, co-transformation of both OsSRO1a and OsRBD1 in yeast conferred enhanced tolerance toward salinity, osmotic, and methylglyoxal treatments. Our study suggests that the interaction of OsSRO1a with OsRBD1 confers enhanced stress tolerance in yeast and may play an important role under abiotic stress responses in plants.

Systematic mining of salt-tolerant genes in halophyte-Zoysia matrella through cDNA expression library screening

Though a large number of salt-tolerant genes were identified from Glycophyte in previous study, genes involved in salt-tolerance of halophyte were scarcely studied. In this report, an important halophyte turfgrass, Zoysia matrella, was used for systematic excavation of salt-tolerant genes using full-length cDNA expression library in yeast. Adopting the Gateway-compatible vector system, a high quality entry library was constructed, containing 3 × 10(6) clones with an average inserted fragments length of 1.64 kb representing a 100% full-length rate. The yeast expression library was screened in a salt-sensitive yeast mutant. The screening yielded dozens of salt-tolerant clones harboring 16 candidate salt-tolerant genes. Under salt-stress condition, these 16 genes exhibited different transcription levels. According to the results, we concluded that the salt-tolerance of Z. matrella might result from known genes involved in ion regulation, osmotic adjustment, as well as unknown pathway associated with protein folding and modification, RNA metabolism, and mitochondrial membrane translocase, etc. In addition, these results shall provide new insight for the future researches with respect to salt-tolerance.

Use of MSAP markers to analyse the effects of salt stress on DNA methylation in rapeseed (Brassica napus var. oleifera)

Excessive soil salinity is a major ecological and agronomical problem, the adverse effects of which are becoming a serious issue in regions where saline water is used for irrigation. Plants can employ regulatory strategies, such as DNA methylation, to enable relatively rapid adaptation to new conditions. In this regard, cytosine methylation might play an integral role in the regulation of gene expression at both the transcriptional and post-transcriptional levels. Rapeseed, which is the most important oilseed crop in Europe, is classified as being tolerant of salinity, although cultivars can vary substantially in their levels of tolerance. In this study, the Methylation Sensitive Amplified Polymorphism (MSAP) approach was used to assess the extent of cytosine methylation under salinity stress in salinity-tolerant (Exagone) and salinity-sensitive (Toccata) rapeseed cultivars. Our data show that salinity affected the level of DNA methylation. In particular methylation decreased in Exagone and increased in Toccata. Nineteen DNA fragments showing polymorphisms related to differences in methylation were sequenced. In particular, two of these were highly similar to genes involved in stress responses (Lacerata and trehalose-6-phosphatase synthase S4) and were chosen to further characterization. Bisulfite sequencing and quantitative RT-PCR analysis of selected MSAP loci showed that cytosine methylation changes under salinity as well as gene expression varied. In particular, our data show that salinity stress influences the expression of the two stress-related genes. Moreover, we quantified the level of trehalose in Exagone shoots and found that it was correlated to TPS4 expression and, therefore, to DNA methylation. In conclusion, we found that salinity could induce genome-wide changes in DNA methylation status, and that these changes, when averaged across different genotypes and developmental stages, accounted for 16.8% of the total site-specific methylation differences in the rapeseed genome, as detected by MSAP analysis.

A suite of new genes defining salinity stress tolerance in seedlings of contrasting rice genotypes

Salinity is one of the major constraints adversely influencing crop productivity. Saltol QTL is a major QTL associated with Na⁺-K⁺ ratio and seedling stage salinity tolerance in rice. With an aim to understand the contribution of individual genes localized within saltol towards salinity tolerance, we analysed the transcript abundance of a set of these genes in seedlings of contrasting genotypes of rice. We hypothesize that this approach may be helpful in identifying new 'candidate genes' for improving salinity tolerance in crops. For this purpose, seedlings of Oryza sativa cv. IR64 (sensitive) and the landrace Pokkali (tolerant) were subjected to short/long durations of salinity. qRT-PCR analysis clearly exhibited differential regulation of genes encoding signaling related protein (SRPs), where higher transcript abundance for most of them was observed in Pokkali than IR64 under non-stress conditions, thereby indicating towards well preparedness of the former to handle stress, in anticipation. Genes encoding proteins of unknown function (PUFs), though, constitute a considerable portion of plant genome, have so far been neglected in most studies. Time course analysis of these genes showed a continuous increase in their abundance in Pokkali, while in IR64, their abundance increased till 24 h followed by a clear decrease, thereby justifying their nomenclature as 'salinity induced factors' (SIFs). This is the first report showing possible involvement of SIFs localized within salinity related QTL towards salinity stress response. Based on the phenotypes of insertional mutants, it is proposed that these SIFs may have a putative function in vegetative growth (SIFVG), fertility (SIFF), viability (SIFV) or early flowering (SIFEF).

Genomics approaches for crop improvement against abiotic stress

As sessile organisms, plants are inevitably exposed to one or a combination of stress factors every now and then throughout their growth and development. Stress responses vary considerably even in the same plant species; stress-susceptible genotypes are at one extreme, and stress-tolerant ones are at the other. Elucidation of the stress responses of crop plants is of extreme relevance, considering the central role of crops in food and biofuel production. Crop improvement has been a traditional issue to increase yields and enhance stress tolerance; however, crop improvement against abiotic stresses has been particularly compelling, given the complex nature of these stresses. As traditional strategies for crop improvement approach their limits, the era of genomics research has arisen with new and promising perspectives in breeding improved varieties against abiotic stresses.

Narrowing down the targets for yield improvement in rice under normal and abiotic stress conditions via expression profiling of yield-related genes

BACKGROUND

Crop improvement targeting high yield and tolerance to environmental stresses has become the need of the hour. Yield improvement via breeding or gene pyramiding aiming comprehensive incorporation of the agronomically favored traits requires an in-depth understanding of the molecular basis of these traits. The present study describes expression profiling of yield-related genes in rice with respect to different developmental stages and various abiotic stress conditions.

RESULTS

Our analysis indicates developmental regulation of the yield-related genes pertaining to the genetic reprogramming involved at the corresponding developmental stage. The gene expression data can be utilized to specifically select particular genes which can potentially function synergistically for enhancing the yield while maintaining the source-sink balance. Furthermore, to gain some insights into the molecular basis of yield penalty during various abiotic stresses, the expression of selected yield-related genes has also been analyzed by qRT-PCR under such stress conditions. Our analysis clearly showed a tight transcriptional regulation of a few of these yield-related genes by abiotic stresses. The stress-responsive expression patterns of these genes could explain some of the most important stress-related physiological manifestations such as reduced tillering, smaller panicles and early completion of the life cycle owing to reduced duration of vegetative and reproductive phases.

CONCLUSIONS

Development of high yielding rice varieties which maintain their yield even under stress conditions may be achieved by simultaneous genetic manipulation of certain combination of genes such as LRK1 and LOG, based on their function and expression profile obtained in the present study. Our study would aid in investigating in future, whether over-expressing or knocking down such yield-related genes can improve the grain yield potential in rice.