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Item Genome-wide identification and expression analysis of chickpea U-box E3 ligases identifies CaPUB4 and CaPUB16 as candidate responsive genes for abiotic stress tolerance(Springer Nature Publishing AG, 2026) Fernandes, Nithya; Unnati, G. Meher; Bhattacharjee, Surjit; Pandey, Ashutosh; Mishra, NeelamU-box E3 ubiquitin ligases play a crucial role in post-translational protein modification, stress signaling, and cellular adaptation in plants. In this study, 38 non-redundant CaPUB genes were identified from the chickpea (Cicer arietinum) genome and characterized for their phylogenetic relationships, domain architecture, gene structures, and expression profiles. Synteny and gene ontology analyses revealed evolutionary conservation with Lotus japonicus and Arabidopsis thaliana, and functional involvement in processes such as ubiquitination, signaling, and stress responses. RNA sequencing and qPCR analyses demonstrated distinct tissue-specific expression patterns. Specifically, CaPUB14 and CaPUB2 were predominantly expressed in particular organs, whereas CaPUB4 and CaPUB16 were upregulated under drought and salt stress in the stress-tolerant ICC4958 cultivar. Functional interaction network analysis revealed that CaPUB4 and CaPUB16 proteins interact with an identical set of partner proteins, supporting the hypothesis that these ligases may function collaboratively in stress adaptation. Collectively, these findings provide insights into the diversity, expression patterns, and potential regulatory roles of the CaPUB gene family, highlighting promising candidate genes for future functional characterization and their possible utility in improving crop stress resilience.Item AraNSdb: a dedicated database of stress-responsive non-coding RNAs in Arabidopsis thaliana(Springer Nature Publishing AG, 2026) Vivek, A.T.; Bhatia, Manika; Sahu, Namrata; Kalakoti, Garima; Kaushik, Love; Mukherjee, Kanka; Kumar, ShaileshPlants, as sessile organisms, are constantly exposed to biotic and abiotic stresses, making their ability to respond crucial for survival. Non-coding RNAs (ncRNAs) have emerged as key regulators in these stress responses, with several studies identifying numerous stress-responsive ncRNAs (SRNs). However, a comprehensive collection of SRNs derived from sequencing data in Arabidopsis thaliana has been lacking. To address this, we utilized high-throughput experimental data and mined published studies to construct AraNSdb (Arabidopsis ncRNA Stress Database), a systematic resource for storing and querying SRNs. AraNSdb documents over 1,000 expression profiles from diverse stress datasets, encompassing 6,616 SRNs, including microRNAs (miRNAs), small interfering RNAs (siRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs). The database features an intuitive web interface for exploring SRNs associated with specific stress types and provides detailed ncRNA annotations to support functional and regulatory studies. AraNSdb offers a valuable platform for advancing our understanding of ncRNA-mediated stress responses and is freely accessible at http://www.nipgr.ac.in/AraNSdb.Item OsLdh3 interacts with OsGAPC3 and OsLos2 to maintain the glycolytic continuum for tolerance to multiple abiotic stresses in rice(Oxford University Press, 2026) Chatterjee, Yajnaseni; Babuta, Priyanka; Gupta, Kapuganti Jagadis; Pareek, Ashwani; Singla-Pareek, Sneh LataLactate dehydrogenases are oxidoreductases present in almost all living organisms. They catalyze the interconversion of pyruvate and L-lactate with simultaneous oxidation of NADH and reduction of NAD+. Since their function remains largely unexplored in rice, in this study we deciphered the role of the rice lactate dehydrogenase, OsLdh3. OsLdh3 showed optimum enzyme activity at pH 6.6 for the forward reaction (pyruvate to L-lactate) and pH 9 for the reverse reaction (L-lactate to pyruvate). Protein-protein interaction studies revealed that OsLdh3 interacts with the glycolytic enzymes glyceraldehyde 3-phosphate dehydrogenaseC3 (OsGAPC3) and Enolase2 (OsLos2), suggesting its role in regulating glycolytic flux. Further, overexpression of OsLdh3 in rice showed enhanced abiotic stress tolerance by exhibiting elevated NAD+ levels and OsGAPC3 activity, thereby facilitating an improved glycolytic continuum and higher pyruvate accumulation. Consequently, these lines also showed increased mitochondrial respiration and ATP synthesis, and reduced reactive oxygen species (ROS) accumulation. Further, enhanced photosynthetic efficiency and reduced yield penalty of the stress-imposed OsLdh3 overexpression lines underscore its importance in crop productivity under adverse climatic conditions. Thus, our findings show that OsLdh3 enhances stress tolerance in rice by regulating redox homeostasis and respiration, reducing ROS levels, and maintaining energy balance. This makes OsLdh3 a promising candidate gene for developing climate-resilient rice cultivars with reduced yield gap.Item Genome-wide identification, functional characterization of protein phosphatase 2A (PP2A) gene family in Cicer arietinum reveals the potential role of CaPP2A-A1 under abiotic stress(Springer Nature Publishing AG, 2025) Fernandes, Nithya; Bhattacharjee, Surjit; Anusha, D. M.; Pandey, Ashutosh; Mishra, NeelamDrought and salt stress are among the primary abiotic factors that negatively impact crop productivity. To cope with these adverse conditions, plants have evolved various adaptive mechanisms, often mediated by specific genes that confer tolerance to different stresses. In this study, we performed a genome-wide identification of PP2A genes in Cicer arietinum using Arabidopsis thaliana genome as a reference. This study identified 21 CaPP2A members distributed across seven chromosomes. Phylogenetic analysis grouped these genes into six distinct subfamilies, each characterized by unique intron-exon structures and conserved motifs. Promoter analysis revealed the presence of cis-acting elements associated with hormone regulation and abiotic stress responsiveness. RNA sequencing analysis demonstrated that nine PP2A genes were significantly responsive to drought and salt stress which was corroborated by quantitative PCR. Notably, the CaPP2A-A1 gene was identified as a key stress responsive since it exhibited significant upregulation in a stress tolerant cultivar, whereas it was downregulated in a susceptible cultivar under both drought and salt stress conditions, suggesting its pivotal role in stress adaptation. Overall, these findings enhance our understanding of the PP2A gene family in chickpea providing a foundation for future functional studies to unravel the PP2A-mediated regulatory networks governing stress tolerance in C. arietinum and facilitate the development of improved breeding strategies for stress-resilient cultivars.Item Genomic, structural, and molecular analysis of calmodulin-binding transcriptional activators (CAMTAs) suggests their role in plant development and abiotic stress tolerance in chickpea(Elsevier B.V., 2025) Sonkar, Kamankshi; Kamali, Saravanappriyan; Kumar, Atul; Deepika, Deepika; Ankit, Ankit; Singh, AmarjeetThe calmodulin-binding transcriptional activator (CAMTA) transcription factors regulate the expression of target genes in Ca2 + dependent cellular functions. CAMTAs are known to regulate biotic and abiotic stress tolerance, and development in plants. CAMTA family has been characterized in Arabidopsis, it is yet to be explored in the legume plant chickpea. Here, we have identified and characterized the chickpea CAMTA family. Total seven CAMTA genes (CaCAMTA1–7) were identified in chickpea. Gene and domain structure analyses suggested that CAMTAs are structurally conserved. The phylogenetic analysis demarcated CaCAMTAs into three groups namely; group I, II and III, and indicated that CaCAMTAs have co-evolved in dicot leguminous plants whereas, they have divergent evolution in monocots. Protein homology modeling revealed their three-dimensional structure, and composition & conformations of α-helix, β-sheets and p-loops. Subcellular localization showed that CaCAMTA4 was localized both, in the nucleus and the cytosol whereas, CaCAMTA5 was localized in the nucleus. CaCAMTA promoters contain various cis-regulatory elements related to abiotic stresses and plant development. Expression profiling using RNA-seq data revealed differential expression of CaCAMTAs during various stages of plant development. RT-qPCR expression analysis showed that most CaCAMTA genes are drought, salt, and ABA responsive, suggesting their role in abiotic stress tolerance in chickpea. Moreover, CaCAMTA regulon was identified based on the presence of CAMTA binding motif (CGCG box) in the promoters of target genes, and in-silico interaction analysis of TF and putative targets. Overall, CaCAMTAs are crucial for abiotic stress tolerance and plant development in chickpea. Key CaCAMTA genes will be functionally characterized, and will be exploited for developing stress tolerant chickpea varieties.Item Broadening the epigenetic horizon of abiotic stress response in plants(Springer Nature Publishing AG, 2024) Chhatwal, Himani; Naik, Jogindra; Pandey, Ashutosh; Trivedi, Prabodh KumarPlants, unlike animals, cannot move from one place to another and have to face different climatic disturbances wherever they are growing. So, they have innumerable built-in mechanisms to adapt to various abiotic stressful conditions like drought, heat, cold, and salinity. The changing environmental conditions influence the expression patterns of genes. Epigenetics involves heritable changes in DNA bases or histone proteins, which ultimately create different conformational states of chromatin. The regulatory enzymes of epigenetic modifications are grouped as writers, readers and erasers, which add, recognize and remove the epigenetic marks, respectively. Here, we provide a comprehensive overview of the mechanism of DNA methylation by the RdDM pathway, its maintenance and removal, and different histone modification categories like acetylation, methylation, phosphorylation and ubiquitination. This review further discusses in detail the crucial role these modifications play in adapting to major abiotic stresses and how plants preserve these experiences as stress memory to respond to recurring stresses. It emphasizes the role of epigenetic modifications as a crucial mechanism for building plant’s tolerance and how it can be an important research priority to improve plant growth and development under abiotic stress conditions.Item Major transcription factor families at the nexus of regulating abiotic stress response in millets: a comprehensive review(Springer Nature Publishing AG, 2024) Prusty, Ankita; Panchal, Anurag; Singh, Roshan Kumar; Prasad, ManojMillets stand out as a sustainable crop with the potential to address the issues of food insecurity and malnutrition. These small-seeded, drought-resistant cereals have adapted to survive a broad spectrum of abiotic stresses. Researchers are keen on unravelling the regulatory mechanisms that empower millets to withstand environmental adversities. The aim is to leverage these identified genetic determinants from millets for enhancing the stress tolerance of major cereal crops through genetic engineering or breeding. This review sheds light on transcription factors (TFs) that govern diverse abiotic stress responses and play role in conferring tolerance to various abiotic stresses in millets. Specifically, the molecular functions and expression patterns of investigated TFs from various families, including bHLH, bZIP, DREB, HSF, MYB, NAC, NF-Y and WRKY, are comprehensively discussed. It also explores the potential of TFs in developing stress-tolerant crops, presenting a comprehensive discussion on diverse strategies for their integration.Item Functional diversification of miR172 isoforms in tomato under abiotic stress(Elsevier B.V., 2024) Bansal, Chandni; Kumar, Adesh; Shrivastava, Monika; Mathur, SaloniPlant gene families have expanded many folds as opposed to animals to compensate for being sessile as well as having unique features like ability to photosynthesise. While different protein families are well characterised in plants, similar knowledge on miRNA families is still in its infancy. The MIR172 family plays important role in various plant development processes including vegetative to reproductive phase change, floral patterning, nodulation, and fruit ripening as well as also in response to different environmental cues. However, in-depth analysis of this family in tomato (Solanum lycopersicum) is limited. In this study, we identified four new MIR172 loci (Sly-MIR172a1/a2/e/f) and two new isoforms, other than those reported at the miRBase repository. The MIR172 family has expanded by segmental duplication events and is conserved between the wild (S. pennellii and S. pimpinellifolium) and the cultivated tomato varieties. However, phylogenetic analysis showed that S. pennellii formed the most divergent member within each clade and S. pimpinellifolium is closer to the cultivated varieties. Additionally, investigations in 42 plant species highlighted that miR172a/b is the most abundant form in the plant kingdom. In addition to the classical target Apetala2 (AP2), degradome analysis identified SEC14p-like phosphatidylinositol transfer family protein (SEC14p) as a novel target of Sly-miR172 that was validated using precursor:effector and target:reporter transient assays. Further, we report dual mode of Sly-miR172-mediated silencing of targets Sly-AP2 and Sly-SEC14p by post-transcriptional transcript cleavage as well as translational repression. Different members of Sly-MIR172s:Sly-AP2s and Sly-MIR172s:Sly-SEC14p exhibit inverse expression correlation in response to different abiotic stresses, suggesting their role in stress response. Functional investigation of MIR172 showed that tomato plants performed better in different abiotic stresses (heat, drought, and salt) upon MIR172 overexpression or target knock-down by virus-induced-gene-silencing. Conversely, when miRNA is chelated using short-tandem-target-mimic, the plants exhibit sensitivity to these stresses. Thus, SlymiR172 acts as a positive regulator while its targets Sly-AP2a and Sly-SEC14p as negative regulators of different abiotic stresses.Item Genome-wide identification and molecular characterization of core ABA signaling components under abiotic stresses and during development in chickpea(Springer Nature Publishing AG, 2025) Kamali, Saravanappriyan; Sonkar, Kamankshi; Ankit, Ankit; Deepika, Deepika; Sharma, Ankita; Singh, AmarjeetAbscisic acid (ABA) signaling is vital for plant's response to abiotic stresses and development. Core components of ABA signaling include ABA receptors PYR/PYL/RCAR, group-A PP2Cs (PP2C-As) and SnRK2 serine/threonine kinases. These have been well studied in Arabidopsis, but their knowledge in the legume crop chickpea is missing. Here, we identified 8 PYLs, 11 PP2C-As and 13 SnRK2s genes in the chickpea genome. Gene duplication events have been found to drive their evolution and expansion in chickpea. Protein homology modeling revealed three-dimensional structure, and arrangements of α-helix, β-sheets and p-loops in respective families. In-planta subcellular localization analysis revealed that CaPYL3 and CaPYL5 proteins were localized at the plasma membrane, and CaPP2CA-1 and CaSnRK2.7 were localized in the cytoplasm and the nucleus. RNA sequencing data analysis indicated the regulatory role of CaPYLs, CaPP2C-As and CaSnRK2s in developmental stages particularly, stages of early embryogenesis to seed maturity. Through RT-qPCR analysis drought, salt and ABA responsive CaPYL, CaPP2C-A and CaSnRK2 genes, which might regulate abiotic stress response in chickpea were identified. Importantly, key genes like CaPYL4, CaPP2C-A4, CaPP2C-A11 and CaSnRK2.9 with overlapping expression in drought, ABA and seed development were identified, which might determine chickpea crop yield. In-silico interaction analysis revealed specific and overlapping interaction among ABA signaling proteins indicating their functional relevance. Overall, core ABA signaling components are crucial for abiotic stress tolerance and development in chickpea. These genes will be functionally validated in the future and will be utilized to generate abiotic stress resilience and high-yielding chickpea varieties.Item Dynamics of epigenetic control in plants via SET domain containing proteins: Structural and functional insights(Elsevier B.V., 2023) Seni, Sushmita; Singh, Roshan Kumar; Prasad, ManojPlants control expression of their genes in a way that involves manipulating the chromatin structural dynamics in order to adapt to environmental changes and carry out developmental processes. Histone modifications like histone methylation are significant epigenetic marks which profoundly and globally modify chromatin, potentially affecting the expression of several genes. Methylation of histones is catalyzed by histone lysine methyltransferases (HKMTs), that features an evolutionary conserved domain known as SET [Su(var)3-9, E(Z), Trithorax]. This methylation is directed at particular lysine (K) residues on H3 or H4 histone. Plant SET domain group (SDG) proteins are categorized into different classes that have been conserved through evolution, and each class have specificity that influences how the chromatin structure operates. The domains discovered in plant SET domain proteins have typically been linked to protein-protein interactions, suggesting that majority of the SDGs function in complexes. Additionally, SDG-mediated histone mark deposition also affects alternative splicing events. In present review, we discussed the diversity of SDGs in plants including their structural properties. Additionally, we have provided comprehensive summary of the functions of the SDG-domain containing proteins in plant developmental processes and response to environmental stimuli have also been highlighted.