Publications of NIPGR Scientists
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Item Genome wide investigation and transcriptional profiling of SWEET genes in two contrasting cultivars of foxtail millet under abiotic stresses(Elsevier B.V., 2025) Singh, Jitender; Singh, Kajol BM.; Sutar, Rashmi Ranjan; Kumar, Angad; Prasad, Manoj; Thakur, Jitendra K.The SWEET (Sugars will eventually be exported transporter) gene family is an important class of sugar transporters that regulates diverse aspects of plant physiology such as apoplastic phloem loading, plant-pathogen interactions and plant responses to abiotic stresses. While majority of the studies on SWEET family in plants have been performed in C3 species, there are limited reports on C4 plants. In this study we conducted genome wide investigation of the SWEET gene family in foxtail millet, a naturally stress tolerant C4 crop. In-silico analysis identified 24 SWEET genes in foxtail millet genome that were classified into 4 distinct clades. Domain analysis revealed the presence of conserved MtN3_slv/PQ-loop domains in all identified SWEET proteins. Interestingly, many SWEET proteins also harboured the prokaryotic SemiSWEET/PQ-loop domain suggesting an evolutionary link to their prokaryotic Semi-SWEET ancestors. In-silico analysis predicted the presence of abscisic acid and drought responsive cis-elements in the promoter region of SWEET genes. Transcriptional analysis under control, drought, and salinity stress revealed differential expression patterns of SWEET genes in stress resistant and stress susceptible foxtail millet cultivars. Moreover, the differential expression of SWEET genes altered the soluble sugar content in leaves and roots under stress conditions suggesting altered carbon re-allocation between source and sink tissues. This study significantly advances our understanding of the SWEET gene family in C4 plants, particularly in foxtail millet, and provides insights into its role in stress tolerance mechanisms and carbohydrate re-allocation under stress conditions.Item Heterologous overexpression of PDH45 gene of pea provides tolerance against sheath blight disease and drought stress in rice(Elsevier B.V., 2022) Sahoo, Ranjan Kumar; Chandan, Ravindra Kumar; Swain, Durga Madhab; Tuteja, Narendra; Jha, GopaljeeBiotic and abiotic stress tolerant crops are required for sustainable agriculture as well as ensuring global food security. In a previous study, we have reported that heterologous overexpression of pea DNA helicase (PDH45), a DEAD-box family member protein, provides salinity stress tolerance in rice. The improved management of photosynthetic machinery and scavenging of reactive oxygen species (ROS) are associated with PDH45 mediated salinity stress tolerance. However, the role of PDH45 in biotic and other abiotic stress (drought) tolerance remains unexplored. In the present study, we have generated marker-free transgenic IR64 rice lines that overexpress PDH45 under the CaMV35S promoter. The transgenic rice lines exhibited a significant level of tolerance against sheath blight disease, caused by Rhizoctonia solani, a polyphagous necrotrophic fungal pathogen. The defense as well as antioxidant responsive marker genes were significantly upregulated in the PDH45 overexpressing (OE) rice lines, upon pathogen infection. Moreover, the OE lines exhibited tolerance to drought stress and various antioxidant as well as drought responsive marker genes were significantly upregulated in them, upon drought stress. Overall, the current study emphasizes that heterologous overexpression of PDH45 provides abiotic as well as biotic stress tolerance in rice. Tolerance against drought as well as sheath blight disease by overexpression of a single gene (PDH45) signifies the practical implication of the present study. Moreover, considering the conserved nature of the gene in different plant species, we anticipate that PDH45 can be gainfully deployed to impart tolerance against multiple stresses in agriculturally important crops.Item Recent insights into plant circadian clock response against abiotic stress(Springer Nature Publishing AG, 2022) Sharma, Megha; Irfan, Mohammad; Kumar, Arun; Kumar, Pankaj; Datta, AsisThe circadian clock is a cell autonomously and endogenously regulated biological timekeeper that detects changes in environmental stimuli and generates 24-h rhythms that are synched with day to day and periodic oscillations to govern many biological functions. Plant's circadian clocks enable them to anticipate environmental changes by modifying their physiological and biological traits to improve plant fitness. The internal circadian clock not only aids fitness but also allows the plant to time-gate the response to environmental stimuli. The latest evidence on the circadian clock suggests that the clock regulates/modulates the expression of abiotic stress-responsive pathways to improve tolerance to stresses without hampering plant growth. In turn, stress signaling also influences the activity of several clock components. This review emphasizes the interplay of the biological circadian clock with abiotic stress-responsive pathways (drought, heat, cold, and salt) for plant growth and survival as well as for stress resilience. A better comprehension of these mechanisms could aid in the development of genetic tools to improve breeding procedures and plant stress tolerance, thereby increasing crop yield and quality under changing ecological conditions.Item OsJAZ9 is involved in water-deficit stress tolerance by regulating leaf width and stomatal density in rice(Elsevier B.V., 2021) Singh, Ajit Pal; Mani, Balaji; Giri, JitenderDrought stress poses a severe threat to grain yield in rice. Our previous report demonstrated the role of OsJAZ9 in potassium homeostasis by modulating Jasmonic Acid (JA) signalling. While both potassium (K) and JA are known to have an important role in drought stress response, JA's repressor, i.e., JAZs' role in drought stress, remains elusive. Here we report that OsJAZ9 plays a critical role in rice water-deficit stress tolerance via influencing JA and ABA signalling. Overexpression of OsJAZ9 led to the enhanced ABA and JA levels. Our data further revealed that exogenous JA application antagonises the ABA-mediated inhibition of seed germination. Further, OsJAZ9 overexpression reduces leaf width and stomata density, leading to lower leaf transpiration rates than WT. This reduced transpiration and higher K content as osmoticum improved the water-deficit stress tolerance in OsJAZ9 overexpression lines. On the contrary, OsJAZ9 RNAi lines displayed enhanced sensitivity towards water-deficit stress. Our data provide new insights on the role of JA signalling repressors in rice response to water-deficit stress.Item Concurrent overexpression of rice G-protein β and γ subunits provide enhanced tolerance to sheath blight disease and abiotic stress in rice(Springer Nature Publishing AG, 2019) Swain, Durga Madhab; Sahoo, Ranjan Kumar; Chandan, Ravindra Kumar; Ghosh, Srayan; Kumar, Rahul; Jha, Gopaljee; Tuteja, NarendraThe heterotrimeric G-proteins act as signalling molecules and modulate various cellular responses including stress tolerance in eukaryotes. The gamma (γ) subunit of rice G-protein (RGG1) was earlier reported to promote salinity stress tolerance in rice. In the present study, we report that a rice gene-encoding beta (β) subunit of G-protein (RGB1) gets upregulated during both biotic (upon a necrotrophic fungal pathogen, Rhizoctonia solani infection) and drought stresses. Markerfree transgenic IR64 rice lines that simultaneously overexpress both RGB1 and RGG1 genes under CaMV35S promoter were raised. The overexpressing (OE) lines showed enhanced tolerance to R. solani infection and salinity/drought stresses. Several defense marker genes including OsMPK3 were signifcantly upregulated in the R. solani-infected OE lines. We also found the antioxidant machineries to be upregulated during salinity as well as drought stress in the OE lines. Overall, the present study provides evidence that concurrent overexpression of G-protein subunits (RGG1 and RGB1) impart multiple (both biotic and abiotic) stress tolerance in rice which could be due to the enhanced expression of stress-marker genes and better management of reactive oxygen species (ROS)-scavenging/photosynthetic machinery. The current study suggests an improved approach for simultaneous improvement of biotic and abiotic stress tolerance in rice which remains a major challenge for its sustainable cultivation.Item Genetic determinants of drought stress tolerance in Setaria(Springer, 2017) Muthamilarasan, Mehanathan; Prasad, ManojCultivated foxtail millet (Setaria italica) and its wild progenitor (S. viridis) have collectively been considered as tractable model species for studying C4 photosynthesis, stress biology, and biofuel traits. Being cultivated in arid and semiarid tropics of the world, these species are well adapted to harsh environments such as drought, heat, and salinity. This adaptation or acclimation potential of Setaria spp. has drawn research interest, and attempts have been made to dissect the molecular mechanisms of stress tolerance. Compared to other stresses, drought response has been studied extensively in S. italica and many drought-responsive genes encoding for transcription factors, signaling molecules, and enzymes have been identified and characterized. Several genome-wide studies have reported on identification of stress-responsive gene family members, and speculated on the potential for expansion and neofunctionalization of paralogs in these gene families. In this context, this chapter discusses the key genetic determinants identified for stress tolerance in S. italica and demonstrates their use in improving drought tolerance. In addition, strategies for identification of genes underlying stress tolerance are also described. Little effort has so far been made towards understanding the stress-tolerance characteristics of Setaria as compared to studies reported in other crops. Comprehensive functional studies along with the use of integrated -omics approaches are required to elucidate the genetics and genomics of stress tolerance in Setaria, as it is important to develop climate change resilient crops to meet the growing demand for food and feed.Item Dehydration-responsive miRNAs in foxtail millet: genome-wide identification, characterization and expression profiling(Springer, 2016) Yadav, Amita; Khan, Yusuf; Prasad, ManojMAIN CONCLUSION: A set of novel and known dehydration-responsive miRNAs have been identified in foxtail millet. These findings provide new insights into understanding the functional role of miRNAs and their respective targets in regulating plant response to dehydration stress. MicroRNAs perform significant regulatory roles in growth, development and stress response of plants. Though the miRNA-mediated gene regulatory networks under dehydration stress remain largely unexplored in plant including foxtail millet (Setaria italica), which is a natural abiotic stress tolerant crop. To find out the dehydration-responsive miRNAs at the global level, four small RNA libraries were constructed from control and dehydration stress treated seedlings of two foxtail millet cultivars showing contrasting tolerance behavior towards dehydration stress. Using Illumina sequencing technology, 55 known and 136 novel miRNAs were identified, representing 22 and 48 miRNA families, respectively. Eighteen known and 33 novel miRNAs were differentially expressed during dehydration stress. After the stress treatment, 32 dehydration-responsive miRNAs were up-regulated in tolerant cultivar and 22 miRNAs were down-regulated in sensitive cultivar, suggesting that miRNA-mediated molecular regulation might play important roles in providing contrasting characteristics to these cultivars. Predicted targets of identified miRNAs were found to encode various transcription factors and functional enzymes, indicating their involvement in broad spectrum regulatory functions and biological processes. Further, differential expression patterns of seven known miRNAs were validated by northern blot and expression of ten novel dehydration-responsive miRNAs were confirmed by SL-qRT PCR. Differential expression behavior of five miRNA-target genes was verified under dehydration stress treatment and two of them also validated by RLM RACE. Overall, the present study highlights the importance of dehydration stress-associated post-transcriptional regulation governed by miRNAs and their targets in a naturally stress-tolerant model crop.Item Impact of concurrent drought stress and pathogen infection on plants(Springer, 2015) Pandey, Prachi; Sinha, Ranjita; Mysore, Kirankumar S.; Senthil-Kumar, MuthappaConcurrent abiotic and biotic stress situations greatly limit the crop productivity. The global climate change is predicted to bring forth the frequent incidences of concurrent stresses, predominantly drought and pathogen infections. Thus, understanding the impact of drought on plant–pathogen interaction is important. In this chapter, we review the recent studies that focus on the effect of concurrent drought and pathogen infection on plants. These studies indicate that concurrent stress conditions lead to the activation of unique combat pathways that are otherwise not elicited under independent stresses. Plant responses, thus, seem to be adaptively tailored for combating the combined stresses. Here, we focus on the impact of drought stress on plant–pathogen relations and highlight the different ways by which plant–pathogen interactions are modulated at physiological and molecular level. Various studies reviewed in this chapter show that the stress combinations should be considered as a “unique stress” and a better understanding of plant responses to these conditions is needed. Therefore, we propose that further efforts should be directed to identify the potential pathways conferring concurrent stress tolerance.Item Role of mitogen activated protein kinase cascade in combating abiotic stress in plants(Springer, 2015) Ara, Hussain; Sinha, Alok KrishnaPlants being sessile have to counter a plethora of stresses, both biotic and abiotic in order to grow and survive. The ability of plants to perceive these stresses at the cell surface and transduce them to the nucleus for appropriate cellular readjustment is one of the most sophisticated mechanisms they have developed during the process of evolution. Among several cascades helping in signal transduction, mitogen-activated protein kinase (MAPK) cascade is one of the most important cascades that is ubiquitously present in all eukaryotes. This unique protein cascade is also involved in several developmental and vital processes in plants. This is essentially a phosphorelay cascade consisting of three components, a MAPK kinase kinase (MAPKKK/MAP3K/MEKK/MKKK), a MAPK kinase (MAPKK/MAP2K/MEK/MKK), and a MAPK (MPK) connected to each other by the event of phosphorylation. All these components of MAPK cascade are multigene family and are involved in efficient transmission of specific stimuli in response to stress signaling. In the present chapter, we will highlight the involvement of different members of this phosphorelay cascade during abiotic stress in plants.Item Cloning, expression and functional validation of drought inducible ascorbate peroxidase (Ec-apx1) from Eleusine coracana(Springer, 2013) Bhatt, Deepesh; Saxena, Saurabh C.; Jain, Sourabh; Dobriyal, Anoop K.; Majee, Manoj; Arora, SandeepEleusine coracana (finger millet) is a stress-hardy but under-utilized cereal crop that possesses an efficient antioxidant defense system. The plant is capable of enduring long durations of water deficit stress. Experiments were conducted to clone a potent stress responsive isoform of ascorbate peroxidase and validate its role under drought stress. Reverse transcriptase PCR was used to obtain the partial cDNA of apx1 gene, from a meticulously screened drought tolerant genotype of E. coracana (PR202). Using RACE strategy, the full length apx1 cDNA was cloned and sequenced. The cDNA length of the E. coracana apx1 (Ec-apx1) gene is 1,047 bp with a 750 bp ORF, encoding a 250 amino acid protein having a molecular weight of 28.5 kDa. The identity of the amino acid sequence, deduced from the cDNA, with the APX family homologs was about 74-97 %. The full-length apx1 ORF was sub-cloned in a prokaryotic expression vector pET23b. The recombinant fusion protein, Ec-apx1, had high expression level in BL21 strain of E. coli and exhibited APX enzyme activity. The structure-function relationship of the protein was deduced by modelling a three-dimensional structure of Ec-apx1, on the basis of comparative homology using SWISS-MODEL. Real time PCR analysis of Ec-apx1 expression at mRNA level showed that the transcript increased under drought stress, with maximum levels attained 5-days after imposition of stress. Our results suggest that Ec-apx1 has a distinct pattern of expression and plays a pivotal role in drought stress tolerance. Therefore, the cloned isoform of ascorbate peroxidase can be used for developing stress tolerant genotypes of important crops, through transgenic approach.