Publications of NIPGR Scientists
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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 Wax deposition is vital for thermotolerance in rice(Elsevier B.V., 2025) Sonkar, Kamankshi; Singh, AmarjeetRice is a staple food and source of nutrition for over half of the world’s population. Unfortunately, it is highly susceptible to heat stress both, at vegetative and reproductive developmental stages. In the current scenario of climate change and global warming, even a 1°C rise in environmental temperature could decline cereal production by 6–7% (Lesk et al., 2016). Thus, it could be a serious threat for the food security of ever-growing world population. To combat the environmental emergency there is a dire need of enhancing the thermotolerance important crop plant rice.Item Metabolic and physiological functions of patatin-like phospholipase-A in plants(Elsevier B.V., 2025) Sonkar, Kamankshi; Singh, AmarjeetPatatin-like phospholipase-A (pPLA) is a class of lipid acyl hydrolase enzymes found in both the animal and plant kingdoms. Plant pPLAs are related to the potato tuber storage protein patatin in solanaceous plants. Despite extensive investigation of pPLA functions in the animal system, the mechanistic functional details and regulatory roles of pPLA are poorly understood in plants. In recent years, research pertaining to pPLAs has gain some momentum as some of the key members of pPLA family have been characterized functionally. These findings have provided key insights into the structural features, biochemical activities, and functional roles of plant pPLAs. In this review, we are presenting a holistic overview of pPLAs in plants and providing the latest updates on pPLA research. We have highlighted the genomic diversity and structural features of pPLAs in plants. Importantly, we have discussed the role of pPLAs in lipid metabolism, including sphingolipid metabolism, lignin and cellulose accumulation, lipid breakdown and seed oil content enhancement. Moreover, regulatory roles of pPLAs in physiological processes, such as plant stress response, plant-pathogen interactions and plant development have been discussed. This information will be critical in the biotechnological programs for crop improvement.Item Cellular transport and multifaceted roles of jasmonates in nutrient deficiency response in plants(Springer Nature Publishing AG, 2025) Kamali, Saravanappriyan; Sonkar, Kamankshi; Singh, AmarjeetJasmonates (JAs) are well documented for their role in plant defense and growth regulation. Cellular transport of JAs during their biosynthesis and signaling constitutes an important layer of their functional regulation. However, most of the information about JAs transport has been gathered in recent years. Therefore, understanding the mechanism of intracellular transport of JAs in plants is of great importance to comprehend their function. In addition, in recent years, JAs have emerged as key regulators of nutrient deficiency response in plants. Under nutrient deficiency, plants show unique adaptive responses, including altered root growth, remodeling of root system architecture (RSA), triggering nutrient uptake-related genes, and activation of nutrient transporters. JAs have been found to regulate these responses in relation to the variable availability of macro- and micronutrients. Evidence indicates that in response to deficiencies of macronutrients such as nitrogen (N), phosphorus (P), and potassium (K+), the JA biosynthesis pathway is modulated, leading to higher JA accumulation. Furthermore, the JA-signaling pathway has been shown to regulate nutrient deficiency-related transcription factors, transporters, and RSA for optimum plant development. In this review, recent developments and updates on molecular mechanisms of cellular transport of JAs during JA biosynthesis and signaling are presented. In addition, new insights on involvement of JAs in nutrient uptake, homeostasis, deficiency response, and plant development have been provided.Item Genomic and transcriptomic approaches to developing abiotic stress-resilient crops(MDPI AG, 2023) Kamali, Saravanappriyan; Singh, AmarjeetIn the realm of agriculture, a pressing concern remains the abiotic stresses, such as temperature fluctuation, drought, soil salinity, and heavy metal contamination. These adverse growth conditions hamper crop yields and global food security. In this review, we present a comprehensive examination of the recent advancements in utilizing genomics and transcriptomics, tools to enhance crop resilience against these stress factors. Genomics aids in the identification of genes responsive to stress, unravels regulatory networks, and pinpoints genetic variations linked to stress tolerance. Concurrently, transcriptomics sheds light on the intricate dynamics of gene expression during stress conditions, unearthing novel stress-responsive genes and signaling pathways. This wealth of knowledge shapes the development of stress-tolerant crop varieties, achieved through conventional breeding programs and state-of-the-art genetic engineering and gene editing techniques like CRISPR-Cas9. Moreover, the integration of diverse omics data and functional genomics tools empowers precise manipulation of crop genomes to fortify their stress resilience. In summary, the integration of genomics and transcriptomics holds substantial promise in elucidating the molecular mechanisms behind crop stress tolerance, offering a path towards sustainable agriculture and safeguarding food security amidst shifting environmental challenges.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 Phospholipase-mediated regulation of plant's response to nutrient deficiency(Elsevier B.V., 2023) Sonkar, Kamankshi; Singh, AmarjeetThe plant phospholipid signaling network governs a variety of physiological functions as well as response to biotic and abiotic stresses. Various stimuli are perceived and recognized by plasma membrane, where lipid signal transduction is initiated by a molecular receptor. The phospholipid signaling network includes the major phospholipid hydrolyzing enzymes like phospholipases. Phospholipases play important roles in several biological functions such as biotic and abiotic stresses, nutrient deficiency tolerance, and plant growth and development. Plant phospholipases are classified into phospholipase A (PLA), phospholipase C (PLC), and phospholipase D (PLD) based on the position of hydrolysis on a glycerophospholipid molecule. These phospholipases act on different membrane lipids such as phosphatidylcholine (PC), phosphoinositide (PI), phosphatidylethanolamine (PE), and phosphatidyleserine (PS), resulting in lipid remodeling and generation of secondary lipid messengers, which are involved in many physiological processes such as plant growth, development, and stress responses.Item Regulation of plants nutrient deficiency responses by phytohormones(Elsevier B.V., 2023) Deepika, Deepika; Sonkar, Kamankshi; Singh, AmarjeetLiving organisms have the ability to acquire nutrients from their physical environment and subsequently convert them into an energy source for survival and growth. In plants, nutrients are involved in metabolism and physiology either as constituents of metabolites or enzymes for macromolecule biosynthesis. Based on their concentration in plant dry matter, the 14 essential inorganic elements are categorized into macronutrients and micronutrients. Macronutrients include six elements, nitrogen (N), phosphorus (P), potassium (K), sulfur (S), calcium (Ca), and magnesium (Mg), whereas the micronutrients comprised eight elements, chlorine (Cl), iron (Fe), boron (B), manganese (Mn), zinc (Zn), copper (Cu), molybdenum (Mo), and nickel (Ni) (de Bang et al., 2020; Sustr et al., 2019). Nutrients are distributed in a patchy manner in soil due to their variable interactions with spatially and temporally dispersed charged soil particles (Hodge, 2006). This, along with many other factors, leads to either low nutrient concentration in soil or low accessibility for plants. Low availability of a nutrient causes specific deficiency symptoms. But plants usually face multiple nutrient deficiencies simultaneously leading to a complex response and symptoms. Moreover, various biotic and abiotic stress factors, such as pests, pathogens, water deficit, salinity, and light, also interact to cause atypical nutrient deficiency symptoms (Amtmann et al., 2008; Troufflard et al., 2010; Atkinsonand Urwin., 2012). Globally, nutrient deficiencies are major threats to crop production, causing reduced yields and poor food and feed quality. The world food security challenge is being met by the use of chemical fertilizers (natural and anthropogenic).Item Jasmonic acid biosynthesis pathway and its functional role in plants(Elsevier B.V., 2023) Ankit, Ankit; Kamali, Saravanappriyan; Singh, AmarjeetPlants encounter various abiotic and biotic stresses including drought, heat, cold, salinity, osmotic stress, fungal infection, herbivore attacks in their natural habitat. In these unavoidable circumstances various phytohormones play crucial roles in regulating plant growth and development (Khan et al., 2019, 2020a, 2020b; Nazir et al., 2019, 2021, 2022; Poo´r et al., 2021). Jasmonic acid (JA) is a lipid-derived phytohormone which acts as a signal as well as regulator in various physiological processes and stress conditions. Methyl ester of JA (MeJA) is the first active jasmonate which was detected and isolated as an odorant from Jasminium grandiflorum flowers (Demole et al., 1962). Among the conjugates of JA, JA-Ile is the most biologically active form (Fonseca et al., 2009). Recently, cis-(1)-12- oxophytodienoic acid (OPDA) an intermediate in the lipoxygenases (LOX) pathway for JA biosynthesis has been shown to be functional signaling molecule instead of JA in lower plants, such as Marchantia polymorpha (liverworts), Physcomitrella patens (moss) and Selaginella martensii (spikemoss) (Ogorodnikova et al., 2015; Stumpe et al., 2010; Yamamoto et al., 2015). Apart from bryophytes, fungus species such as Fusarium oxysporum have JA and/or JA-Ile conjugate (Miersch et al., 1999). Although, JA and its derivatives are distributed among bryophytes and fungi, most of the homologs of JA biosynthesis enzymes are present in major lineages of land plants (Han, 2017). In last decade, studies have been performed in both monocotyledons as well as dicotyledons plants to better understand the JA biosynthesis mechanism. In Arabidopsis, JA biosynthesis mainly occurs in chloroplast, peroxisome and cytoplasm (Ruan et al., 2019). In chloroplast, OPDA is synthesized from unsaturated fatty acid α-linolenic acid (α-LeA) derived from the chloroplast membrane, followed by its conversion into JA in peroxisome. The conversion of JA into different functional and structural metabolites takes place in the cytoplasm. JA and its other derivatives like MeJA and JA-Ile are collectively known as jasmonates.Item Genome-wide characterization and comparative analysis of the OSCA gene family and identification of its potential stress-responsive members in legumes(Nature Publishing Group, 2023) Chakraborty, Srija; Gangwar, Rashmi; Zahra, Shafaque; Poddar, Nikita; Singh, Amarjeet; Kumar, ShaileshCicer arietinum, Cajanus cajan, Vigna radiata, and Phaseolus vulgaris are economically important legume crops with high nutritional value. They are negatively impacted globally by different biotic and abiotic stresses. Hyperosmolality-gated calcium-permeable channels (OSCA) have been characterized as osmosensors in Arabidopsis thaliana but have not previously reported in legumes. This study provides a genome-wide identification, characterization, and comparative analysis of OSCA genes in legumes. Our study identified and characterized 13 OSCA genes in C. cajan, V. radiata, P. vulgaris, and 12 in C. arietinum, classified into four distinct clades. We found evidence to suggest that the OSCAs might be involved in the interaction between hormone signalling pathways and stress signalling pathways. Furthermore, they play a major role in plant growth and development. The expression levels of the OSCAs vary under different stress conditions in a tissue-specific manner. Our study can be used to develop a detailed understanding of stress regulatory mechanisms of the OSCA gene family in legumes.