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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 Nitric oxide-mediated modulation of reproductive resilience under cold stress in chickpea(Frontiers Media S.A., 2025) Kaur, Sarbjeet; Padhiar, Deeksha; Jha, Uday Chand; Kumar, Sanjeev; Sharma, Kamal Dev; Parida, Swarup Kumar; Siddique, Kadambot H. M.; Prasad, P. V. Vara; Nayyar, HarshChickpeas are particularly sensitive to cold stress during the reproductive phase, which can significantly impair pod set and yield. This study examined the role of sodium nitroprusside (SNP), a nitric oxide (NO) donor, in mitigating cold-induced reproductive damage in cold-tolerant (CT) and cold-sensitive (CS) chickpea genotypes. After 100 days of outdoor growth, plants were subjected to cold stress (15/8°C day/night; 12 h photoperiod) for 21 days in walk-in growth chambers during the reproductive stage of development. Control plants were maintained at 25/15°C day/night temperature. SNP treatment (1 mM) was applied exogenously each time, first two days prior to stress onset and then at seven-day intervals (three applications total). Cold stress significantly lowered endogenous NO levels in leaves, anthers, and ovules, particularly in CS genotypes, thereby leading to reduced pollen viability and germination. SNP treatment restored NO and improved reproductive performance, with stronger responses in the CS than the CT genotype. For instance, pollen germination increased by 57.9% in CS versus 17.6% in CT, and pollen viability increased by 28.0% and 13.1%, respectively. Enhanced anther function resulted in a 157.2% increase in pod set and 62.0% higher seed yield in CS. SNP also improved physiological traits, including a 43.9% increase in cellular viability, 18.6% in stomatal conductance, and 41.9% in chlorophyll content in CS genotypes. Cryoprotectants (proline, trehalose, and sucrose) accumulated in anthers, reinforcing cold resilience, while oxidative stress was simultaneously alleviated through reduced malondialdehyde, hydrogen peroxide, and electrolyte leakage, together with the upregulation of both enzymatic (superoxide dismutase (SOD), catalase (CAT), ascorbate peroxidase (APx), and glutathione reductase (GR)) and non-enzymatic (ascorbic acid (ASC) and reduced glutathione (GSH)) components. Notably, CS genotypes showed more pronounced improvements from SNP application than CT genotypes, particularly in terms of reproductive success and yield-related traits. These findings highlight the potential of NO donors, such as SNP, to enhance cold tolerance in chickpeas, with promising implications for safeguarding productivity under low-temperature stress, especially in sensitive cultivars.Item Deciphering the dynamics of enzymes associated with the synthesis of cryoprotectants during cold acclimation in contrasting chickpea genotypes(Springer Nature Publishing AG, 2025) Padhiar, Deeksha; Kaur, Sarbjeet; Rani, Anju; Jha, Uday Chand; Prasad, P. V. Vara; Sharma, Kamal Dev; Kumar, Sanjeev; Parida, Swarup K.; Siddique, Kadambot H. M.; Nayyar, HarshChickpea, a vital legume crop, is highly susceptible to cold stress, especially during its reproductive phase, resulting in significant flower and pod abortions and reduced seed yield. Our previous study demonstrated that cold acclimation is effective in enhancing cold tolerance but benefits only cold-tolerant (CT) genotypes, while cold-sensitive (CS) genotypes remain unaffected. In this extended study aimed at probing the detailed mechanisms of this differential response, we further examined the expression profiles of enzymes involved in the synthesis and breakdown of osmolytes (pyrroline-5-carboxylate synthase, proline dehydrogenase (PDH), betaine aldehyde dehydrogenase) and sugars (sucrose synthase, acid invertase, trehalose-6-phosphate synthase, trehalose-6-phosphate phosphatase, and trehalase activity), along with the expression of various antioxidants (superoxide dismutase, catalase, ascorbate peroxidase, and glutathione reductase) in both CT and CS genotypes. Seeds of two contrasting chickpea genotypes, cold-tolerant ICC 17258 and cold-sensitive ICC 15567, were planted in pots during the first week of November in an outdoor field environment. After 40 days, the plants were transferred to walk-in growth chambers for cold acclimation at specific temperatures. Initially, the plants were exposed the plants to 25/18℃ (pre-acclimation stage; PAS) for 2 days, followed by a 21-day cold acclimation period with progressively decreasing temperatures over seven days for each cold acclimation stage (CAS): CAS1 (21/13℃), CAS2 (18/10℃), and CAS3 (15/8℃). Subsequently, the plants were subjected to cold stress at 13/7℃ for 15 days and then exposed to 30/23℃ (12 h day/night) until maturity. Our findings demonstrated that the expression of various enzymes involved in the synthesis of osmolytes and sugars in leaves, anthers, and ovules was significantly upregulated during the cold acclimation process in the CT chickpea genotypes but not in the CS genotypes. This enhanced metabolic activity, coupled with elevated levels of enzymatic antioxidants during the acclimation process, contributed to improved leaf water status, photosynthetic efficiency, and ultimately, superior reproductive performance (pollen germination, pollen viability, stigma receptivity, and ovule viability) under cold stress conditions compared to CS genotypes. The enhanced cold tolerance observed in the CT genotypes is likely attributable to their genetic predisposition and efficient stress defense mechanisms facilitated by the upregulated expression of cold-responsive enzymes.Item Photosynthetic adaptation in poplar under abiotic and biotic stress: integrating molecular, physiological, and biotechnological perspectives(MDPI AG, 2025) Wang, Dong; Jewaria, Pawan Kumar; Xiao, JianweiIn the context of global climate change, the carbon storage and sequestration capacity of terrestrial ecosystems is of increasing concern. Poplars are widely planted because of their fast growth and environmental adaptability. We reviewed the effects of abiotic and biotic stresses on photosynthesis in poplar, focusing on the damage caused by adversity conditions to photosynthetic apparatus, which leads to decreased carbon dioxide (CO2) assimilation and an increase in reactive oxygen species (ROS)-induced oxidative damage. The mechanisms of photosynthesis response to stress in poplar are reviewed, especially the role of genes regulation in regulating photosynthetic efficiency. These findings are particularly important for improving the resilience of poplar under changing environmental conditions. In addition, we discussed a range of strategies to enhance photosynthesis in poplar under stress, such as genetic engineering and synthetic biology. These approaches provide theoretical guidance for improving the resilience of poplar and insights for improving other crops facing similar challenges.Item Deciphering the regulation of transporters and mitogen-activated protein kinase in arsenic and iron exposed rice(Elsevier B.V., 2024) Panthri, Medha; Saini, Himanshu; Banerjee, Gopal; Bhatia, Priyanka; Verma, Neetu; Sinha, Alok Krishna; Gupta, MeetuThis study investigates the influence of arsenic (As) and iron (Fe) on the molecular aspects of rice plants. The mRNA-abundance of As (OsLsi, OsPHT, OsNRAMP1, OsABCC1) and Fe (OsIRT, OsNRAMP1, OsYSL, OsFRDL1, OsVIT2, OsSAMS1, OsNAS, OsNAAT1, OsDMAS1, OsTOM1, OsFER) related genes has been observed in 12-d old As and Fe impacted rice varieties. Analyses of phytosiderophores synthesis and Fe-uptake genes affirm the existence of specialized Fe-uptake strategies in rice with varieties PB-1 and Varsha favouring strategy I and II, respectively. Expression of OsNAS3, OsVIT2, OsFER and OsABCC1 indicated PB-1′s tolerance towards Fe and As. Analysis of mitogen-activated protein kinase cascade members (OsMKK3, OsMKK4, OsMKK6, OsMPK3, OsMPK4, OsMPK7, and OsMPK14) revealed their importance in the fine adjustment of As/Fe in the rice system. A conditional network map was generated based on the gene expression pattern that unfolded the differential dynamics of both rice varieties. The mating based split ubiquitin system determined the interaction of OsIRT1 with OsMPK3, and OsLsi1 with both OsMPK3 and OsMPK4. In-silico tools also confirmed the binding affinities of OsARM1 with OsLsi1, OsMPK3 and OsMPK4, and of OsIDEF1/OsIRO2 with OsIRT1 and OsMPK3, supporting our hypothesis that OsARM1, OsIDEF1, OsIRO2 were active in the connections discovered by mbSUS.Item Plant growth coordination during stress conditions: Role of phytohormones(Elsevier B.V., 2024) Gupta, Shreya; Devi, Loitongbam Lorinda; Singh, Amar PalPlants encounter multiple stresses which are associated with compromised plant growth and yield across the globe. Several studies have been done in the past few years to understand plant acclimatization under numerous stresses like nutrient deficiency, drought, salinity, temperature, and pathogen attack. The shoot and root system architecture in plants seems a promising approach as it is highly sensitive to edaphic and internal signals and plants adapt by modulating them to these stresses. Intrinsic factors such as growth hormones are the key components of the plant whose levels and signaling determine the extent of plant growth and performance. The major phytohormones that are involved in monitoring plant development for optimized plant growth during environmental stresses are auxin, brassinosteroids, cytokinin, abscisic acid, jasmonic acid, gibberellins, and ethylene. In recent years, detailed genetic and biochemical analysis of the signaling and biosynthesis genes and transcription factors of these hormones have been studied from the model plant Arabidopsis to different crops. Genetic studies have shown that these hormones regulate several biological processes of root and shoot growth including cell elongation, division and differentiation, root hair and lateral root formation, and floral and leaf morphology in response to altered environmental conditions. In this chapter, the current understanding of both above- and below-ground plant organs and their developmental plasticity during stress conditions along with the interplay of growth hormones has been summarized and discussed.Item CLAVATA signaling pathway receptors modulate developmental traits and stress responses in crops(Elsevier B.V., 2022) Basu, Udita; Parida, Swarup K.The CLAVATA signaling pathway is one of the most important signaling components in the plant system. The CLE peptides and their receptors play crucial roles in various aspects of plant development and stress responses. The most common receptor types of this signaling system include the leucine-rich repeat (LRR)-receptor-like kinases like the CLAVATA1, BAM receptors, RPK2, and CIKs and the LRR-RLPs like the CLV2 and its coreceptors. The most notable role of the CLAVATA receptors is in meristematic cell maintenance in root and shoot. Their role is well studied in legumes for autoregulation of nodulation and a similar role has been observed in mycorrhizal symbiotic relation establishment and regulation. The CLAVATA receptors are also involved in both biotic and abiotic stress perception and responses in crops. The signaling pathway and its receptors have enormous potential for utilization in crop improvement endeavors. Understanding their role in signal regulation will help in developing better-performing customized crops.Item Potassium (K+) transporters in plants: Regulation and functional role in K+ uptake and homeostasis(Elsevier B.V., 2022) Ankit; Singh, AmarjeetPotassium (K+) is an essential macronutrient for plants and plays an important role in various cellular processes in plants. K+ transporters and channels are responsible for K+ uptake, translocation, as well as maintaining its homeostasis in plants. Other than transportation, these K+ transporters and channels are involved in other physiological processes. Several studies have shown differential expression for K+ transporter genes under abiotic stresses, such as salinity and drought. Plants can sense K+ deficiency through different mechanisms. K+ transporters and channels activity have been regulated by transcriptional as well as post–transcriptional modifications. This chapter discusses various K+ transporters and channels, their function, regulation at different levels, and their role in biotic and abiotic stress responses in plants.Item Molecular characterization, evolutionary analysis, and expression profiling of BOR genes in important cereals(MDPI AG, 2022) Sharma, Himanshu; Sharma, Alok; Rajput, Ruchika; Sidhu, Sukhjeet; Dhillon, Harpal; Verma, Praveen Chandra; Pandey, Ashutosh; Upadhyay, Santosh KumarBoron (B) is an essential micronutrient of plants. Plants grapple with a narrow range of B between its toxicity and deficiency. B homeostasis mechanism is required to rescue plants from such a quagmire. B transporters are specialized proteins involved in the homeostasis of B. In the present study, a total of 29 BOR genes were identified in five major cereals, including three BORs in each Brachypodium distachyon and Sorghum bicolor, four in Oryza sativa, six in Zea mays, and 13 in Triticum aestivum. Multiple sequence alignments, domain structure analyses, and phylogenetic analysis indicated the conserved nature of the BOR protein family. Duplication events and Ka/Ks analysis of TaBORs showed the role of segmental duplication events and purifying selection in the expansion of the BOR family in T. aestivum. Furthermore, in silico expression and co-expression analyses under biotic and abiotic stress conditions depicted their involvement in combating such conditions. Moreover, qRT-PCR of TaBORs in B treatment suggested the roles of BOR genes in B stress management. The present study hints at the conserved nature of BOR proteins and their different aspects. The study will lay down a way for several crop improvement programs.Item Sensing and signalling in plant stress responses: ensuring sustainable food security in an era of climate change(John Wiley & Sons, 2020) Pareek, Ashwani; Joshi, Rohit; Gupta, Kapuganti Jagadis; Singla-Pareek, Sneh L.; Foyer, Christine‘EMBO India Symposium ‘Sensing and signalling in plant stress response’ held in New Delhi, India, 15–17 April 2019 Agriculture in the 21stcentury faces multiple challenges from biotic and abiotic stresses, which impose major constraints on crop yield. Under field conditions, the combined or sequential occurrence of environmental stresses poses a serious threat to global food security. Plants exhibit plasticity in their responses to environmental stresses, which may be attributed to their genetic and/or epigenetic makeup. One of the major challenges facing plant biology today concerns how gene regulatory networks function to generate morphological and adaptive diversity. Gaining a better understanding of the responses of crop plants to environmental stresses will allow the identification of improved genetic markers to increase yield stability and enhance productivity over a wide range of growth conditions. The availability of high-throughput sequencing technologies provides an opportunity to uncover the genetic/epigenetic basis of plant stress responses and adaptation. Furthermore, dissection of the molecular mechanisms underlying resilience will help us understand how plants cope with extreme environmental conditions, and ultimately lead to the development of climatesmart crops. Understanding the sensing and signalling mechanisms that plants use to perceive and respond appropriately to stress is crucial for the development of stress-resistant crops using current strategies and technologies.