Publications of NIPGR Scientists
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Item Genome-wide DNA methylation dynamics at "heading" stage of panicle and flag leaf in contrasting rice cultivars under field drought conditions(Frontiers Media S.A., 2025) Jajo, Ringyao; Kansal, Shivani; Mathur, Saloni; Raghuvanshi, SaurabhAbstract Introduction: Drought stress induces widespread genome-wide alterations in DNA methylation of rice. These changes work to alter gene expression and are relatively unexplored in reproductive tissues like flag leaf and panicle under field drought conditions. This study aims to explore the same in the panicle and flag leaf tissue of IR64 (drought-sensitive) and N22 (drought-tolerant) rice cultivars under field-drought conditions during the 'heading' stage of development. Methods: For the same, we generated whole-genome bisulfite sequencing libraries from the corresponding tissues and analysed them in detail. Results and discussion: The DNA methylation dynamics in adult tissue (flowering stage) was found to be clearly distinct from that of the seedling stage. Further, the contrasting rice genotypes also exhibited cultivar-specific and drought-induced dynamism in the methylation signatures. Notably, the two cultivars demonstrate inherent distinctions in sequence preferences of hyper- and hypo-methylation even prior to experiencing drought stress, and these preferences persist under the influence of the stress. Approximately 90% of the drought-induced differentially methylated region (DMR) are cultivar-specific, and about 70% of the cultivar differences (cultivar-DMR) under stress are unique compared to control condition. There is higher prevalence of hyper-methylated DMR that co-localized with differentially expressed genes in panicle. DMR of CHH sequence exhibit stronger negative correlation with expression compared to CpG and CHG sequence. Examination of differentially expressed genes with DMR highlights their functional relevance under drought stress, especially with DMR found in gene bodies and promoter regions. Notably, in panicle, methylation divergence of the two cultivars influences flowering regulation genes. Additionally, the findings also suggest a regulatory role for DNA methylation in drought induced response of miRNA genes, particularly in the panicle of N22 cultivars.Item When two negatives make a positive: The favorable impact of the combination of abiotic stress and pathogen infection on plants(Oxford University Press, 2024) Pandey, Prachi; Patil, Mahesh; Priya, Piyush; Senthil-Kumar, MuthappaCombined abiotic and biotic stresses modify plant defense signaling, leading to either the activation or suppression of defense responses. Although the majority of combined abiotic and biotic stresses reduce plant fitness, certain abiotic stresses reduce the severity of pathogen infection in plants. Remarkably, certain pathogens also improve the tolerance of some plants to a few abiotic stresses. While considerable research focuses on the detrimental impact of combined stresses on plants, the upside of combined stress remains hidden. This review succinctly discusses the interactions between abiotic stresses and pathogen infection that benefit plant fitness. Here, we discuss various factors that govern the positive influence of combined abiotic stress and pathogen infection on plant performance. We also provide a brief overview of the role of pathogens, mainly viruses, in improving plant responses to abiotic stresses. We further highlight the critical nodes in defense signaling that guide plant responses during abiotic stress towards enhanced resistance to pathogens. Studies on antagonistic interactions between abiotic and biotic stressors can uncover candidates in host plant defense that may shield plants from combined stresses.Item MicroRNA397 regulates tolerance to drought and fungal infection by regulating lignin deposition in chickpea root(John Wiley & Sons, 2023) Sharma, Nilesh Kumar; Yadav, Shalini; Gupta, Santosh Kumar; Irulappan, Vadivelmurugan; Francis, Aleena; Senthil-Kumar, Muthappa; Chattopadhyay, DebasisPlants deposit lignin in the secondary cell wall as a common response to drought and pathogen attacks. Cell wall localised multicopper oxidase family enzymes LACCASES (LACs) catalyse the formation of monolignol radicals and facilitate lignin formation. We show an upregulation of the expression of several LAC genes and a downregulation of microRNA397 (CamiR397) in response to natural drought in chickpea roots. CamiR397 was found to target LAC4 and LAC17L out of twenty annotated LACs in chickpea. CamiR397 and its target genes are expressed in the root. Overexpression of CamiR397 reduced expression of LAC4 and LAC17L and lignin deposition in chickpea root xylem causing reduction in xylem wall thickness. Downregulation of CamiR397 activity by expressing a short tandem target mimic (STTM397) construct increased root lignin deposition in chickpea. CamiR397-overexpressing and STTM397 chickpea lines showed sensitivity and tolerance, respectively, towards natural drought. Infection with a fungal pathogen Macrophomina phaseolina, responsible for dry root rot (DRR) disease in chickpea, induced local lignin deposition and LAC gene expression. CamiR397-overexpressing and STTM397 chickpea lines showed more sensitivity and tolerance, respectively, to DRR. Our results demonstrated the regulatory role of CamiR397 in root lignification during drought and DRR in an agriculturally important crop chickpea.Item A superior gene allele involved in abscisic acid signaling enhances drought tolerance and yield in chickpea(Oxford University Press, 2023) Thakro, Virevol; Malik, Naveen; Basu, Udita; Srivastava, Rishi; Narnoliya, Laxmi; Daware, Anurag; Varshney, Nidhi; Mohanty, Jitendra K; Bajaj, Deepak; Dwivedi, Vikas; Tripathi, Shailesh; Jha, Uday Chand; Dixit, Girish Prasad; Singh, Ashok K; Tyagi, Akhilesh K.; Upadhyaya, Hari D; Parida, Swarup K.Identifying potential molecular tags for drought tolerance is essential for achieving higher crop productivity under drought stress. We employed an integrated genomics-assisted breeding and functional genomics strategy involving association mapping, fine mapping, map-based cloning, molecular haplotyping and transcript profiling in the introgression lines (ILs)- and near isogenic lines (NILs)-based association panel and mapping population of chickpea (Cicer arietinum). This combinatorial approach delineated a bHLH (basic helix-loop-helix) transcription factor, CabHLH10 (Cicer arietinum bHLH10) underlying a major QTL, along with its derived natural alleles/haplotypes governing yield traits under drought stress in chickpea. CabHLH10 binds to a cis-regulatory G-box promoter element to modulate the expression of RD22 (responsive to desiccation 22), a drought/ABA-responsive gene (via a trans-expression QTL), and two strong yield-enhancement photosynthetic efficiency (PE) genes. This, in turn, upregulates other downstream drought-responsive and abscisic acid signaling genes, as well as yield-enhancing PE genes, thus increasing plant adaptation to drought with reduced yield penalty. We showed that a superior allele of CabHLH10 introgressed into the NILs improved root and shoot biomass and PE, thereby enhancing yield and productivity during drought without compromising agronomic performance. Furthermore, overexpression of CabHLH10 in chickpea and Arabidopsis (Arabidopsis thaliana) conferred enhanced drought tolerance by improving root and shoot agro-morphological traits. These findings facilitate translational genomics for crop improvement and the development of genetically-tailored, climate-resilient, high-yielding chickpea cultivars.Item AtSWEET11 and AtSWEET12: the twin traders of sucrose(Elsevier B.V., 2022) Fatima, Urooj; Anjali, Anjali; Senthil-Kumar, MuthappaAtSWEET11 and AtSWEET12 are central players in phloem loading and long-distance sucrose translocation. During drought stress, these transporters enhance sucrose transport from shoot to root, increasing root proliferation. Chen et al. have now unravelled novel aspects of sucrose transport regulation, occurring via AtSWEET11 and AtSWEET12 phosphorylation and oligomerisation.Item Combined drought and heat stress influences the root water relation and determine the dry root rot disease development under field conditions: A study using contrasting chickpea genotypes(Frontiers Media S.A., 2022) Chilakala, Aswin Reddy; Mali, Komal Vitthalrao; Irulappan, Vadivelmurugan; Patil, Basavanagouda S.; Pandey, Prachi; Rangappa, Krishnappa; Ramegowda, Venkategowda; Kumar, M. Nagaraj; Puli, Chandra Obul Reddy; Mohan-Raju, Basavaiah; Senthil-Kumar, MuthappaAbiotic stressors such as drought and heat predispose chickpea plants to pathogens of key importance leading to significant crop loss under field conditions. In this study, we have investigated the influence of drought and high temperature on the incidence and severity of dry root rot disease (caused by Macrophomina phaseolina) in chickpea, under extensive on- and off-season field trials and greenhouse conditions. We explored the association between drought tolerance and dry root rot resistance in two chickpea genotypes, ICC 4958 and JG 62, with contrasting resistance to dry root rot. In addition, we extensively analyzed various patho-morphological and root architecture traits altered by combined stresses under field and greenhouse conditions in these genotypes. We further observed the role of edaphic factors in dry root rot incidence under field conditions. Altogether, our results suggest a strong negative correlation between the plant water relations and dry root rot severity in chickpeas, indicating an association between drought tolerance and dry root rot resistance. Additionally, the significant role of heat stress in altering the dynamics of dry root rot and the importance of combinatorial screening of chickpea germplasm for dry root rot resistance, drought, and heat stress have been revealed.Item Drought stress exacerbates fungal colonization and endodermal invasion and dampens defense responses to increase dry root rot in chickpea(American Phytopathological Society, 2022) Irulappan, Vadivelmurugan; Kandpal, Manu; Saini, Kumud; Rai, Avanish; Ranjan, Aashish; Sinharoy, Senjuti; Senthil-Kumar, MuthappaDrought plays a central role in increasing the incidence and severity of dry root rot (DRR) disease in chickpea. This is an economically devastating disease, compromising chickpea yields particularly severely in recent years due to erratic rainfall patterns. Macrophomina phaseolina (formerly Rhizoctonia bataticola) is the causal agent of DRR disease in the chickpea plant. The infection pattern in chickpea roots under well-watered conditions and drought stress are poorly understood at present. This study provides detailed disease symptomatology and the characteristics of DRR fungus at morphological and molecular levels. Using microscopy techniques, the infection pattern of DRR fungus in susceptible chickpea roots was investigated under well-watered and drought stress conditions. Our observations suggested that drought stress intensifies the progression of already ongoing infection by weakening the endodermal barrier and overall defense. Transcriptomic analysis suggested that the plant’s innate immune defense program is downregulated in infected roots when subjected to drought stress. Further, genes involved in hormonal regulation are differentially expressed under drought stress. These findings provide hints in terms of potential chickpea genes to target in crop improvement programs to develop climate change-resilient cultivars.Item Drought attenuates plant defence against bacterial pathogens by suppressing the expression of CBP60g/SARD1 during combined stress(John Wiley & Sons, 2022) Choudhary, Aanchal; Senthil-Kumar, MuthappaIn nature, plants are frequently exposed to drought and bacterial pathogens simultaneously. However, information on how the drought and defence pathways interact and orchestrate global transcriptional regulation is limited. Here, we show that moderate drought stress enhances the susceptibility of Arabidopsis thaliana to Pseudomonas syringae pv. tomato DC3000. Using transcriptome meta-analysis, we found that drought and bacterial stress antagonistically modulate a large set of genes predominantly involved in salicylic acid (SA) and abscisic acid (ABA) signalling networks. We identified that the levels of SA and ABA are dynamically regulated during the course of stress. Importantly, under combined stress, drought through the ABA pathway downregulates the induction of CALMODULIN-BINDING PROTEIN 60g (CBP60g) and SYSTEMIC ACQUIRED RESISTANCE DEFICIENT 1 (SARD1), two transcription factors crucial for SA production upon bacterial infection. We also identified an important role of NPR1-LIKE PROTEIN 3 and 4 (NPR3/4) transcriptional repressors in the drought-mediated negative regulation of CBP60g/SARD1 expression. Using a genetic approach, we show that CBP60g/SARD1 expression is the key determinant of plant defence against bacterial pathogens under combined stress. Thus, these transcription factors act as critical nodes for the crosstalk between drought and bacterial stress signalling under combined stress in plants.Item Progress and prospects of concurrent or combined stress studies in plants(John Wiley & Sons, 2021) Mahalingam, Ramamurthy; Pandey, Prachi; Senthil-Kumar, MuthappaPlants growing under field conditions are often exposed to multiple abiotic and biotic stresses occurring simultaneously or sequentially. Biotic stressors often interact with abiotic stressors at the plant interphase, which makes the impact of their combination on plants remarkably variable, though differing with order and intensity of stresses, as well as plant species and pathotypes. In this article, we examine the major abiotic stress combinations, as well as abiotic-biotic stress combinations, and physiological and molecular responses of plants to these combined stresses. Utilizing the available literature, information on the phenomic and transcriptomic response of plants to the combined abiotic and biotic stresses, and the cross-talk during signalling is reviewed. A succinct discussion on the scope and application of combined abiotic and biotic stress studies highlighting major gaps and novel avenues for further research is articulated.Item Delineating the epigenetic regulation of heat and drought response in plants(Taylor & Francis Group, 2022) Singh, Roshan Kumar; Prasad, ManojBeing sessile in nature, plants cannot overlook the incursion of unfavorable environmental conditions, including heat and drought. Heat and drought severely affect plant growth, development, reproduction and therefore productivity which poses a severe threat to global food security. Plants respond to these hostile environmental circumstances by rearranging their genomic and molecular architecture. One such modification commonly known as epigenetic changes involves the perishable to inheritable changes in DNA or DNA-binding histone proteins leading to modified chromatin organization. Reversible epigenetic modifications include DNA methylation, exchange of histone variants, histone methylation, histone acetylation, ATP-dependent nucleosome remodeling, and others. These modifications are employed to regulate the spatial and temporal expression of genes in response to external stimuli or specific developmental requirements. Understanding the epigenetic regulation of stress-related gene expression in response to heat and drought would commence manifold avenues for crop improvement through molecular breeding or biotechnological approaches.