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Item Dynamics of miRNA mediated regulation of legume symbiosis(John Wiley & Sons, 2021) Tiwari, Manish; Pandey, Vimal; Singh, Baljinder; Bhatia, SabhyataSymbiotic nitrogen fixation in legume nodules is important in soils with low nitrogen availability. The initiation and sustainability of symbiosis requires cellular reprogramming that involves the miRNA‐mediated inhibition or activation of specific nodulation genes. The high‐throughput sequencing of small RNA libraries has identified miRNAs and their targets, which are the major players in the post‐transcriptional gene regulation (PTGS) of the different stages of legume‐rhizobia symbiosis ranging from bacterial colonization and organogenesis to symbiotic nitrogen fixation. Here we present an overview of information obtained from the miRNA libraries from nodulating tissues that have been sequenced to date. The functional analysis of miRNAs has revealed roles in phytohormone homeostasis and spatio‐temporal regulation, as well as the mobility of miRNAs and their functions in shoot to root signalling that affects diverse functions, including bacterial entry, meristem division and differentiation, nitrogen fixation and senescence. Furthermore, small RNA fragments of rhizobial origin repress complementary plant mRNAs. We also consider the roles of miRNAs in determinate or indeterminate nodules. Taken together, this overview confirms that miRNAs are master regulators of the legume‐rhizobia symbiosis.Item AtGBF3 confers tolerance to Arabidopsis thaliana against combined drought and Pseudomonas syringae stress(Elsevier B.V., 2019) Dixit, Sandeep Kumar; Gupta, Aarti; Fatima, Urooj; Senthil-Kumar, MuthappaIn field conditions, plants are often exposed to a combination of abiotic and biotic stresses, for instance, drought and pathogen infection. Transcriptome studies on Arabidopsis thaliana and other plants under individual and combined drought and pathogen stresses have unveiled the activation of shared molecular defense mechanisms. These shared plant responses are characterized by commonly regulated genes under both individual as well as combined stresses. Therefore, the identification of commonly regulated genes during individual and combined stress conditions can reveal plant responses towards combined stress. Available transcriptome studies on combined-stressed plants have hinted at G-Box Binding Factor 3 (GBF3) as one of the regulatory components of the shared response. However, the mechanistic understanding of the role of AtGBF3 under combined drought and pathogen stress is not yet decoded. In the current study, we used genetic approaches to identify the role of AtGBF3 in conferring tolerance to individual and combined drought and pathogen stress. Atgbf3 mutant plants showed increased susceptibility, while AtGBF3-overexpressing plants were tolerant under individual and combined drought and Pseudomonas syringae pv. tomato infection stresses as compared to wild-type plants. We further analyzed the global transcriptome of Atgbf3 mutant plants under combined stress to identify its downstream targets. We also established a high-throughput method to apply combined polyethylene glycol and pathogen stress on Murashige and Skoog medium-grown plants to further validate the role of AtGBF3 in combined stress.Item Over-expression of OsHOX24 confers enhanced susceptibility to abiotic stresses in transgenic rice via modulating stress-responsive gene expression(Frontiers Media S.A., 2017) Bhattacharjee, Annapurna; Sharma, Raghvendra; Jain, MukeshHomeobox transcription factors play critical roles in plant development and abiotic stress responses. In the present study, we raised rice transgenics over-expressing stress-responsive OsHOX24 gene (rice homeodomain-leucine zipper I sub-family member) and analyzed their response to various abiotic stresses at different stages of development. At the seed germination stage, rice transgenics over-expressing OsHOX24 exhibited enhanced sensitivity to abiotic stress conditions and abscisic acid as compared to wild-type (WT). OsHOX24 over-expression rice seedlings showed reduced root and shoot growth under salinity and desiccation stress (DS) conditions. Various physiological and phenotypic assays confirmed higher susceptibility of rice transgenics toward abiotic stresses as compared to WT at mature and reproductive stages of rice development too. Global gene expression profiling revealed differential regulation of several genes in the transgenic plants under control and DS conditions. Many of these differentially expressed genes were found to be involved in transcriptional regulatory activities, besides carbohydrate, nucleic acid and lipid metabolic processes and response to abiotic stress and hormones. Taken together, our findings highlighted the role of OsHOX24 in regulation of abiotic stress responses via modulating the expression of stress-responsive genes in rice.Item Concurrent drought stress and vascular pathogen infection induce common and distinct transcriptomic responses in chickpea(Frontiers Media S.A., 2017) Sinha, Ranjita; Gupta, Aarti; Senthil-Kumar, MuthappaChickpea (Cicer arietinum); the second largest legume grown worldwide is prone to drought and various pathogen infections. These drought and pathogen stresses often occur concurrently in the field conditions. However, the molecular events in response to that are largely unknown. The present study examines the transcriptome dynamics in chickpea plants exposed to a combination of water-deficit stress and Ralstonia solanacearum infection. R. solanacearum is a potential wilt disease causing pathogen in chickpea. Drought stressed chickpea plants were infected with this pathogen and the plants were allowed to experience progressive drought with 2 and 4 days of R. solanacearum infection called short duration stress (SD stresses) and long duration stress (LD stresses), respectively. Our study showed that R. solanacearum multiplication decreased under SD-combined stress compared to SD-pathogen but there was no significant change in LD-combined stress compared to LD-pathogen. The microarray analysis during these conditions showed that 821 and 1039 differentially expressed genes (DEGs) were unique to SD- and LD-combined stresses, respectively, when compared with individual stress conditions. Three and fifteen genes were common among all the SD-stress treatments and LD-stress treatments, respectively. Genes involved in secondary cell wall biosynthesis, alkaloid biosynthesis, defense related proteins, and osmo-protectants were up-regulated during combined stress. The expression of genes involved in lignin and cellulose biosynthesis were specifically up-regulated in SD-combined, LD-combined, and LD-pathogen stress. A close transcriptomic association of LD-pathogen stress with SD-combined stress was observed in this study which indicates that R. solanacearum infection also exerts drought stress along with pathogen stress thus mimics combined stress effect. Furthermore the expression profiling of candidate genes using real-time quantitative PCR validated the microarray data. The study showed that down-regulation of defense-related genes during LD-combined stress resulted in an increased bacterial multiplication as compared to SD-combined stress. Overall, our study highlights a sub-set of DEGs uniquely expressed in response to combined stress, which serve as potential candidates for further functional characterization to delineate the molecular response of the plant to concurrent drought-pathogen stress.Item Comparative morphophysiological analyses and molecular profiling reveal Pi-efficient strategies of a traditional rice genotype(Frontiers Media S.A., 2016) Mehra, Poonam; Pandey, Bipin K.; Giri, JitenderPhosphate (Pi) deficiency severely affects crop yield. Modern high yielding rice genotypes are sensitive to Pi deficiency whereas traditional rice genotypes are naturally compatible with low Pi ecosystems. However, the underlying molecular mechanisms for low Pi tolerance in traditional genotypes remain largely elusive. To delineate the molecular mechanisms for low Pi tolerance, two contrasting rice genotypes, Dular (low Pi tolerant), and PB1 (low Pi sensitive), have been selected. Comparative morphophysiological, global transcriptome and lipidome analyses of root and shoot tissues of both genotypes grown under Pi deficient and sufficient conditions revealed potential low Pi tolerance mechanisms of the traditional genotype. Most of the genes associated with enhanced internal Pi utilization (phospholipid remobilization) and modulation of root system architecture (RSA) were highly induced in the traditional rice genotype, Dular. Higher reserves of phospholipids and greater accumulation of galactolipids under low Pi in Dular indicated it has more efficient Pi utilization. Furthermore, Dular also maintained greater root growth than PB1 under low Pi, resulting in larger root surface area due to increased lateral root density and root hair length. Genes involved in enhanced low Pi tolerance of the traditional genotype can be exploited to improve the low Pi tolerance of modern high yielding rice cultivars.Item The interaction between glucose and cytokinin signal transduction pathway in Arabidopsis thaliana(John Wiley & Sons, 2013) Kushwah, Sunita; Laxmi, AshveryaCytokinins (CKs) and glucose (GLC) control a number of common responses in plants. We hypothesize that there may be an extensive overlap between CK- and GLC-signalling pathways. Microarray along with physiological analysis has been performed to find out the interdependence/overlap between CK and GLC signal transduction pathways in Arabidopsis seedlings. GLC could transcriptionally affect 76% of CK-regulated genes at whole genome level, 89% of which are agonistically regulated. GLC may also affect CK-regulated gene expression via non-transcriptional pathways. GLC can regulate several genes involved in CK metabolism and signalling. A number of gene families involved in development and stress are commonly regulated by CK and GLC. Physiologically, both GLC and CK could regulate hypocotyl length in dark. GLC and CK signalling may integrate at the level of type A Arabidopsis response regulators (ARRs) in controlling hypocotyl length. Both GLC and CK signalling cannot alter hypocotyl length in dark in auxin-signalling mutants auxin response2/indole-3-acetic acid7 (AXR2/IAA7) and AXR3/IAA17 suggesting that they may involve auxin-signalling component as a nodal point. Here, we demonstrate that there is an extensive overlap between CK- and GLC-regulated gene expression and physiological responses.Item Microarray analysis reveals overlapping and specific transcriptional responses to different plant hormones in rice(Landes Bioscience, 2012) Garg, Rohini; Tyagi, Akhilesh K.; Jain, MukeshHormones exert pleiotropic effects on plant growth and development throughout the life cycle. Many of these effects are mediated at molecular level via altering gene expression. In this study, we investigated the exogenous effect of plant hormones, including auxin, cytokinin, abscisic acid, ethylene, salicylic acid and jasmonic acid, on the transcription of rice genes at whole genome level using microarray. Our analysis identified a total of 4171 genes involved in several biological processes, whose expression was altered significantly in the presence of different hormones. Further, 28% of these genes exhibited overlapping transcriptional responses in the presence of any two hormones, indicating crosstalk among plant hormones. In addition, we identified genes showing only a particular hormone-specific response, which can be used as hormone-specific markers. The results of this study will facilitate further studies in hormone biology in rice.Item PlantRGS: a web server for the identification of most suitable candidate reference genes for quantitative gene expression studies in plants(Oxford University Press, 2011) Patel, Ravi K.; Jain, MukeshNormalization of quantitative gene expression data with a suitable reference gene is essential for accurate and reliable results. However, the availability and choice of most suitable reference gene(s) showing uniform expression across all the experimental conditions remain a drawback. We have developed a web server, PlantRGS (http://www.nipgr.res.in/PlantRGS), for the identification of most suitable candidate reference gene(s) at the whole-genome level using microarray data for quantitative gene expression studies in plants. Microarray data from more than 11 000 tissue samples for nine plant species have been included in the PlantRGS for meta-analysis. The web server provides a user-friendly graphical user interface-based analysis tool for the identification of most suitable reference genes in the selected plant species under user-defined experimental conditions. Various parameter options and output formats will help users to investigate desired number of most suitable reference genes with wide range of expression levels. Validation of results revealed that novel reference genes identified by the PlantRGS outperforms the traditionally used reference genes in terms of expression stability. We anticipate that the PlantRGS will provide a platform for the identification of most suitable reference gene(s) under given experimental conditions and facilitate quantitative gene expression studies in plants.Item Comparative transcript profiling of TCP family genes provide insight into gene functions and diversification in rice and Arabidopsis(Academy Journals, 2010) Sharma, Rita; Kapoor, Meenu; Tyagi, Akhilesh K.; Kapoor, SanjayPlant-specific TCP transcription factor family has been implicated in diverse aspects of growth and development. Rice and Arabidopsis genomes encode 26 and 24 TCP family genes, respectively. In this study, we have performed an inclusive analysis of their expression during 21 and 18 stages of development in rice and Arabidopsis, respectively. The assorted patterns of expression, exhibited by TCP family genes, provide an evidence for spatiotemporal regulation of their relative abundance throughout plant development. Further profiling of rice genes in three sub-stages of early panicle development revealed differential accumulation of nine genes during panicle initiation and organ development. QPCR-based expression profiling of selected rice genes, during four stages of anther, suggested their involvement in early anther development as well. Eleven genes of rice and seven of Arabidopsis were differentially expressed in response to three abiotic stress treatments viz., cold, dehydration and salt. In silico analysis of 5' regulatory regions of differentially expressed genes revealed the presence of previously characterized cis-regulatory elements. Duplications seem to have played major role in diversification of TCP family genes with 14 genes of rice and 10 of Arabidopsis lying on duplicated segments of the respective genomes. Most of the duplicated genes exhibited varied expression patterns. The knowledge obtained in this study will be useful for selection and assessment of the functions of individual genes using reverse genetics approaches.Item Glycinebetine-induced water-stress tolerance in Cod A-expressing transgenic India rice is associated with up-regulation of several stress responsive genes(Wiley-Blackwell, 2009) Kathuria, Hitesh; Giri, Jitender; Nataraja, Karaba N.; Murata, Norio; Udayakumar, Makarla; Tyagi, Akhilesh K.Rice (Oryza sativa L.), a non-accumulator of glycinebetaine (GB), is highly susceptible to abiotic stress. Transgenic rice with chloroplast-targeted choline oxidase encoded by the codA gene from Arthrobacter globiformis has been evaluated for inheritance of transgene up to R5 generation and water-stress tolerance. During seedling, vegetative and reproductive stages, transgenic plants could maintain higher activity of photosystem II and they show better physiological performance, for example, enhanced detoxification of reactive oxygen species compared to wild-type plants under water-stress. Survival rate and agronomic performance of transgenic plants is also better than wild-type following prolonged water-stress. Choline oxidase converts choline into GB and H2O2 in a single step. It is possible that H2O2/GB might activate stress response pathways and prepare transgenic plants to mitigate stress. To check this possibility, microarray-based transcriptome analysis of transgenic rice has been done. It unravelled altered expression of many genes involved in stress responses, signal transduction, gene regulation, hormone signalling and cellular metabolism. Overall, 165 genes show more than two-fold up-regulation at P-value < 0.01 in transgenic rice. Out of these, at least 50 genes are known to be involved in plant stress response. Exogenous application of H2O2 or GB to wild-type plants also induces such genes. Our data show that metabolic engineering for GB is a promising strategy for introducing stress tolerance in crop plants and which could be imparted, in part, by H2O2- and/or GB-induced stress response genes.