Publications of NIPGR Scientists
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Item Molecular intricacies of modulating seed dormancy through CRISPR/Cas9 technology(Oxford University Press, 2026) Gautam, Shikha; Kamble, Nitin Uttam; Majee, ManojThe processes of seed development, maturation, and dormancy acquisition are complex and tightly regulated, and play a critical role in plant survival and propagation. Over the past decades, significant advances have been made in elucidating the molecular mechanisms that govern these intricate processes. The interplay among hormone signaling, epigenetic regulation, reactive oxygen species (ROS), and environmental cues has been recognized as central to determining seed fate. Despite these advancements, many molecular components remain to be fully discovered. Recent developments in CRISPR-based gene-editing technologies have provided promising tools for the precise regulation of seed dormancy without compromising other seed traits. Although CRISPR has been effectively utilized to modify genes controlling physiological characteristics in a wide range of crops, its application in regulating dormancy remains at an early stage. This review synthesizes current knowledge on the molecular and genetic mechanisms controlling seed maturation, dormancy acquisition and germination, with particular emphasis on emerging CRISPR-based strategies. Realizing this potential, however, requires a deeper understanding of the complex regulatory networks orchestrating seed dormancy acquisition and germination. Identifying optimal gene targets and refining editing strategies will be crucial for developing reliable and sustainable dormancy-control systems. Therefore, we highlight key gene targets, summarize their functional relevance, and discuss how genome editing could be leveraged to fine-tune dormancy and germination behaviour. The studies discussed herein underscore the transformative potential of CRISPR/Cas9 and related genome-editing platforms in advancing seed biology and crop improvement, paving the way for next-generation seed technologies.Item The confluence of TOR signaling and plant growth regulators in development and stress responses(Oxford University Press, 2026) Saksena, Harshita B; Kumar, Mukesh; Samtani, Harsha; Sharma, Aishwarye; Rawat, Sanjay Singh; Awasthi, Prakhar; Botta, Halidev Krishna; Sandhya, Shital; Pande, Anjali; Naaz, Sheeba; Kushwah, Sunita; Shukla, Brihaspati N; Laxmi, AshveryaThe Target of Rapamycin (TOR) is an evolutionarily conserved protein kinase that serves as a crucial signaling hub, seamlessly integrating a wide range of internal and external signals to meticulously regulate cellular and organismal physiology. TOR is crucial in regulating the different phases of lifecycle in plants including embryogenesis, seed germination, meristem activation, root and leaf development, flowering and senescence. Beyond its central role in growth and development, emerging research has revealed its significant involvement in the response to environmental stresses. Even though plant growth regulators such as auxin, cytokinin (CK), brassinosteroid (BR), gibberellin (GA), abscisic acid (ABA), ethylene (ET), salicylic acid (SA), jasmonic acid (JA) and nitric oxide (NO) function as pivotal signaling molecules in modulating plant development and stress responses, how they coordinate with the energy status still remains obscure. Here we summarize the current findings on the dynamic interconnection between TOR and these discrete phytoregulators and their potential role in executing diverse biological processes in plants.Item Diverse roles of phytohormonal signaling in modulating plant-virus interaction(Oxford University Press, 2025) Sharma, Shambhavi; Prasad, ManojVirus infection brings about changes in the transcriptome, proteome and metabolome status of the infected plant wherein substantial alterations in the abundance of phytohormones and associated components involved in their signaling pathways have been observed. In the recent years, extensive research in the field of plant virology has showcased the undisputable significance of phytohormone signaling during plant-virus interactions. Apart from acting as growth regulators, phytohormones elicit robust immune response, which restricts the viral multiplication within the plant as well as its propagation by vector. Interestingly, these pathways have been shown to not only act as isolated mechanisms but as complex intertwined regulatory cascades where, the cross-talk among different phytohormones and with other antiviral pathways takes place during plant-virus interplay. Viruses cleverly disrupt phytohormone homeostasis via their multifunctional effectors that seems to be smart approach adopted by viruses to circumvent phytohormone-mediated plant immune responses. In this review, we summarize the current understanding of role of phytohormone signaling pathways during plant-virus interaction in activating antiviral immune responses of plant and also, how viruses exploit these signaling pathways favoring their pathogenesis.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 Role of ubiquitination enzymes in abiotic environmental interactions with plants(Elsevier B.V., 2021) Sharma, Shambhavi; Prasad, Ashish; Sharma, Namisha; Prasad, ManojUbiquitination, a post-translational modification, plays a crucial role in various aspects of plant development and stress responses. Protein degradation by ubiquitination is well established and ubiquitin is the main underlying component directing the turnover of proteins. Recent reports have also revealed the non-proteolytic roles of ubiquitination in plants. In the past decade, ubiquitination has emerged to be one of the most important players in modulating plant's responses to abiotic stresses, which led to identification of specific E3 ligases and their targets involved in the process. Most of the E3 ligases play regulatory roles by modifying the stability and accumulation of stress responsive regulatory proteins, such as transcription factors, thus, modifying the downstream responses, or by degrading the proteins involved in the downstream cascade itself. In this review, we summarize and highlight the recent advances in the field of ubiquitination-mediated regulation of plant's responses to various abiotic stresses including limited nutrient availability and metal toxicity. The non-proteolytic role of ubiquitination in epigenetic regulation of abiotic stress induced response has also been discussed.Item Plant responses to combined drought and pathogen infection: current understanding on the role of phytohormones(Springer, 2017) Pandey, Prachi; Senthil-Kumar, MuthappaPlants under natural conditions encounter a number of abiotic and biotic stresses often being inflicted simultaneously. Plant responses to a stress are governed by intricate network of the hormone signaling pathways. Abscisic acid (ABA) forms the major component of the plant response to drought and cold stress. Salicylic acid (SA), jasmonic acid (JA), and ethylene act as key regulators of plant response to pathogen infection. In fact, the extensive cross talk among the different hormone-mediated signaling pathways determines plant response to a particular stress. A large number of studies focus on hormone signaling under individual drought and pathogen stresses and the cross talk between the two stress responses. However, owing to the relatively few studies on combined drought and pathogen stresses, our understanding of phytohormonal signaling under combined stress is still obscure. Recent studies on combined drought and pathogen infection indicate that plants when simultaneously exposed to the two stresses often exhibit a transcriptional and metabolic response different from that exhibited under single stress conditions. This is also applicable to the phytohormonal signaling. The nature, time, and severity of the two stresses in combination modulate hormonal concentrations as well as the hormone signal transduction pathways involved. In this chapter, we provide a compendious description of the role of the three major hormones, namely, ABA, SA, and JA, in combined drought and pathogen infection. A brief description of the role of auxins, cytokinins, and gibberellins has also been provided. Taking leads from few studies, we have discussed the potential role of hormones in conferring combined drought and pathogen stress tolerance to plants. We also briefly discussed the effect of different “stress elicitors” on hormone signaling.Item Rice OsiSAP7 negatively regulates ABA stress signalling and imparts sensitivity to water-deficit stress in Arabidopsis(Elsevier B.V., 2015) Sharma, Gunjan; Giri, Jitender; Tyagi, Akhilesh K.Stress associated protein (SAP) genes in plants regulate abiotic stress responses. SAP gene family consists of 18 members in rice. Although their abiotic stress responsiveness is well established, the mechanism of their action is poorly understood. OsiSAP7 was chosen to investigate the mechanism of its action based on the dual nature of its sub-cellular localization preferentially in the nucleus or sub-nuclear speckles upon transient expression in onion epidermal cells. Its expression was down-regulated in rice seedlings under abiotic stresses. OsiSAP7 was localized evenly in the nucleus under unstressed conditions and in sub-nuclear speckles on MG132 treatment. OsiSAP7 exhibits E3 ubiquitin ligase activity in vitro. Abiotic stress responses of OsiSAP7 were assessed by its overexpression in Arabidopsis under the control of a stress inducible promoter rd29A. Stress response assessment was done at seed germination and advanced stages of development. Transgenics were ABA insensitive at seed germination stage and sensitive to water-deficit stress at advanced stage as compared to wild type (WT). They were also impaired in ABA and stress-responsive gene expression. Our study suggests that OsiSAP7 acts as a negative regulator of ABA and water-deficit stress signalling by acting as an E3 ubiquitin ligase.Item Drought stress responses and signal transduction in plants(Springer, 2015) Lata, Charu; Muthamilarasan, Mehanathan; Prasad, ManojNature provides all necessary components for healthy growth and development of plants in the form of air, water, light, nutrients, and soil. Any imbalance in the environmental harmony may cause stress to them. Stresses encountered by plants can broadly be categorized into biotic and abiotic stresses. Biotic stresses are mainly caused by pathogens and herbivory, whereas abiotic stresses include the threat imposed by drought, salinity, and extremes of temperature, heavy metals, and pollution. Drought stress is a major cause of yield instability in crops across diverse eco-geographic regions worldwide. A variety of biochemical, molecular, and physiological changes are manifested by plants in response to drought stress. The cellular abscisic acid (ABA) concentration increases on water deficit leading to the activation of a number of stress-responsive genes and the patterns of expression of these genes are very complex, with some genes being induced early while others respond slowly. In general, drought-responsive genes respond to salt and cold stresses as well as to exogenous ABA treatment. However, there are several genes, which express themselves in an ABA-independent manner suggesting that both ABA-dependent and -independent signal transduction cascades exist for drought stress perception, response, and adaptation. Drought stress response and adaptation in plants involves an array of pathways for signal perception, transduction, gene expression and synthesis of proteins, and other stress metabolites. Drought-responsive genes can mainly be classified into two groups. First group constitutes genes whose products provide osmotolerance and protection to plants thus directly functioning in tolerance to stress, while the second group includes genes playing a role in signal transduction as well as regulation of gene expression. This chapter summarizes the complex molecular mechanisms of drought stress response and adaptation in plants, highlighting the transcriptional regulation of stress-responsive gene expression. It also focuses on the recent advances in analyzing various stress-responsive pathways with prime emphasis on ABA-dependent and -independent pathways.Item Role of DREBs in regulation of abiotic stress responses in plants(Oxford University Press, 2011) Lata, Charu; Prasad, ManojAbiotic stresses such as drought, high salinity, and cold are common adverse environmental conditions that significantly influence plant growth and productivity worldwide. The phytohormone abscisic acid (ABA) plays an important role in physiological and developmental responses as well as in co-ordinating various stress signal transduction pathways in plants. DREBs (dehydration responsive element binding) are important plant transcription factors (TFs) that regulate the expression of many stress-inducible genes mostly in an ABA-independent manner and play a critical role in improving the abiotic stress tolerance of plants by interacting with a DRE/CRT cis-element present in the promoter region of various abiotic stress-responsive genes. This review summarizes recent studies highlighting the role of the DRE-binding family of TFs in the adaptive responses to different abiotic stresses and their structural and functional characters with emphasis on the expression and regulation of DREBs. The practical and application value of DREBs in crop improvement, such as stress tolerance engineering as well as marker-assisted selection (MAS), has also been discussed.