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Item Functional characterization of WsPR-1 reveals its interplay with cytokinin and gibberellin signaling pathways(Elsevier B.V., 2024) Singh, Varinder; Kumar, Paramdeep; Pandey, Ashutosh; Hallan, Vipin; Pati, Pratap KumarPathogenesis-related protein 1 (PR-1) is an antimicrobial protein involved in systemic acquired resistance (SAR) in plants, but its regulatory role and interactions with other pathways remain unclear. In this study, we functionally characterize WsPR-1 gene of Withania somnifera in Nicotiana tabacum to elucidate its role in plant defense, growth, and development. Interestingly, transgenic tobacco plants with increased levels of cytokinin (CK) and decreased gibberellins (GAs) exhibited stunted shoot growth, an underdeveloped root system, modified leaf morphology, reduced seed pod production, and delayed leaf senescence. Transcriptional analysis revealed that WsPR-1 overexpression downregulated the GA 20-oxidase (GA20ox) gene involved in GA biosynthesis while upregulating GA 2-oxidase (GA2ox), a GA catabolic enzyme. Moreover, transcript levels of FRUITFULL (FUL) and LEAFY (NFL2) flowering genes exhibited a decrease in WsPR-1 plants, which could explain the delayed flowering and reduced seed pod development in transgenic plants. Confocal microscopy confirmed increased lignin deposition in stem cross-sections of WsPR-1 transgenic plants, supported by gene expression analysis and lignin content quantification. Additionally, our findings also suggest the involvement of Knotted1-like homeobox (KNOX) gene in enhancing cytokinin levels. This study highlights PR-1's regulatory role in plant growth and development, with potential to boost crop yields and enhance resilience.Item Comparative investigation on chemical and green synthesized titanium dioxide nanoparticles against chromium (VI) stress eliciting differential physiological, biochemical, and cellular attributes in Helianthus annuus L.(Elsevier B.V., 2024) Kumar, Dharmendra; Mariyam, Safoora; Gupta, Kapuganti Jagadis; Thiruvengadam, Muthu; Ghodake, Gajanan Sampatrao; Xing, Baoshan; Seth, Chandra ShekharNanotechnology is a new scientific area that promotes unique concepts to comprehend the optimal mechanics of nanoparticles (NPs) in plants under heavy metal stress. The present investigation focuses on effects of synthetic and green synthesized titanium dioxide nanoparticles (TiO2 NPs and gTiO2 NPs) against Cr(VI). Green TiO2 NPs have been produced from plant leaf extract (Ricinus communis L.). Synthesis was confirmed employing an array of optical spectroscopic and electron microscopic techniques. Chromium strongly accelerated H2O2 and MDA productions by 227 % and 266 % at highest chromium concentration (60 mg/kg of soil), respectively, and also caused DNA damage, and decline in photosynthesis. Additionally, anomalies were observed in stomatal cells with gradual increment in chromium concentrations. Conversely, foliar applications of TiO2 NPs and gTiO2 NPs considerably mitigated chromium stress. Sunflower plants treated with modest amounts of green TiO2 NPs had significantly better growth index compared to chemically synthesized ones. Principal component analysis highlighted the variations among photosynthetic attributes, oxidative stress markers, and antioxidant defense systems. Notably, gTiO2 supplementation to the Cr(VI) strained plants minimized PC3 production which is a rare report so far. Conclusively, gTiO2 NPs have been identified to be promising nano-based nutrition resource for farming applications.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 Meta-analysis of transcriptomics studies identifies novel attributes and set of genes involved in iron homeostasis in rice(Springer Nature Publishing AG, 2023) Shekhawat, Pooja Kanwar; Sardar, Shaswati; Yadav, Banita; Salvi, Prafull; Soni, Praveen; Ram, HasthiIron (Fe) is an important micronutrient for humans as well as for plant growth and development. Rice employs multiple mechanisms to counteract the negative effects of Fe deficiency and Fe toxicity. Previously, many transcriptomics studies have identified hundreds of genes affected by Fe deficiency and/or Fe toxicity. These studies are highly valuable to identify novel genes involved in Fe homeostasis. However, in the absence of their systematic integration, they remain underutilized. A systematic meta-analysis of transcriptomics data from such ten previous studies was performed here to identify various common attributes. From this meta-analysis, it is revealed that under Fe deficiency conditions, root transcriptome is more sensitive and exhibits greater similarity across multiple studies than the shoot transcriptome. Furthermore, under Fe toxicity conditions, upregulated genes are more reliable and consistent than downregulated genes in susceptible cultivars. The integration of data from Fe deficiency and Fe toxicity conditions helped to identify key marker genes for Fe stress. As a proof-of-concept of the analysis, among the genes consistently regulated in opposite directions under Fe deficiency and toxicity conditions, two genes were selected: a proton-dependent oligopeptide transporter (POT) family protein and Vacuolar Iron Transporter (VIT)-Like (VTL) gene, and validated their expression and sub-cellular localization. Since VIT genes are known to play an important role in Fe homeostasis in plants, the entire OsVTL gene family in rice was characterized. This meta-analysis has identified many novel candidate genes that exhibit consistent expression patterns across multiple tissues, conditions, and studies. This makes them potential targets for future research aimed at developing Fe-biofortified rice varieties, as well as varieties tolerant to sub-optimal Fe levels in soil.Item Rice lipases: a conundrum in rice bran stabilization: a review on their impact and biotechnological interventions(Springer Nature Publishing AG, 2023) Bansal, Sakshi; Sundararajan, Sathish; Shekhawat, Pooja Kanwar; Singh, Shivangi; Soni, Praveen; Tripathy, Manas K.; Ram, HasthiRice is a primary food and is one of the most important constituents of diets all around the world. Rice bran is a valuable component of rice, containing many oil-soluble vitamins, minerals, and oil. It is known for its ability to improve the economic value of rice. Further, it contains substantial quantities of minerals like potassium, calcium, magnesium, iron and antioxidants like tocopherols, tocotrienols, and γ-oryzanol, indicating that rice bran can be utilized efectively against several life-threatening disorders. It is difcult to fully utilize the necessary nutrients due to the presence of lipases in rice bran. These lipases break down lipids, specifcally Triacylglycerol, into free fatty acids and glycerol. This review discusses physicochemical properties, mechanism of action, distribution, and activity of lipases in various components of rice seeds. The phylogenetic and gene expression analysis helped to understand the diferential expression pattern of lipase genes at diferent growth phases of rice plant. Further, this review discusses various genetic and biotechnological approaches to decrease lipase activity in rice and other plants, which could potentially prevent the degradation of bran oil. The goal is to establish whether lipases are a major contributor to this issue and to develop rice varieties with improved bran stability. This information sets the stage for upcoming molecular research in this area.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.Item Comparative transcriptome profiling of two contrasting foxtail millet cultivars provides insights into molecular mechanisms underlying dehydration stress response(Springer Nature Publishing AG, 2023) Muthamilarasan, Mehanathan; Suresh, Bonthala Venkata; Singh, Roshan Kumar; Choudhary, Pooja; Aggarwal, Pooja Rani; Prasad, ManojFoxtail millet (Setaria italica L.) has emerged as a model system to understand its adaptation to environmental stresses in the past decade. However, studies on understanding the molecular mechanism underlying the adaptation to dehydration stress and the regulatory network involved in the process remain elusive. In the present study, RNA-seq was performed during dehydration stress in the tolerant (IC4) and sensitive (IC41) cultivars at different time points (0, 6, and 12 h). A total of 2467 and 3318 differentially expressed genes (DEGs) were identified in IC4, and 2535 and 5572 in IC41 at 6 h and 12 h compared to control (0 h), respectively. Gene ontology (GO) analysis revealed that the DEGs were enriched in water transport, response to water deprivation, oxidative stress, amino acid and sugar transport, lipid biosynthesis, and regulation of stomatal opening. Pathway analysis suggested a significant modulation of genes involved in the metabolism of glutathione and tryptophan and biosynthesis of flavonoid, ascorbate, arginine, and proline in IC4 compared to IC41. Genes encoding for DIVARICATA, SBP family protein (teosinte glume architecture 1), and SRS family proteins (LATERAL ROOT PRIMORDIUM 1 and SHI-RELATED SEQUENCE 1) were found to be exclusively upregulated in IC4 during dehydration stress. Gene co-expression networks constructed based on the expression data showed the key modules and hubs that play critical roles during dehydration stress. Altogether, the present study has identified key genes, pathways, and regulatory modules that would serve as a base for further studies to gain insights into the dehydration-responsive molecular circuitry in foxtail millet.Item De novo transcriptome analysis identifies key genes involved in dehydration stress response in kodo millet (Paspalum scrobiculatum L.)(Elsevier B.V., 2022) Suresh, Bonthala Venkata; Choudhary, Pooja; Aggarwal, Pooja Rani; Rana, Sumi; Singh, Roshan Kumar; Ravikesavan, Rajasekaran; Prasad, Manoj; Muthamilarasan, MehanathanKodo millet (Paspalum scrobiculatum L.) is a small millet species known for its excellent nutritional and climate-resilient traits. To understand the genes and pathways underlying dehydration stress tolerance of kodo millet, the transcriptome of cultivar ‘CO3’ subjected to dehydration stress (0 h, 3 h, and 6 h) was sequenced. The study generated 239.1 million clean reads that identified 9201, 9814, and 2346 differentially expressed genes (DEGs) in 0 h vs. 3 h, 0 h vs. 6 h, and 3 h vs. 6 h libraries, respectively. The DEGs were found to be associated with vital molecular pathways, including hormone metabolism and signaling, antioxidant scavenging, photosynthesis, and cellular metabolism, and were validated using qRT-PCR. Also, a higher abundance of uncharacterized genes expressed during stress warrants further studies to characterize this class of genes to understand their role in dehydration stress response. Altogether, the study provides insights into the transcriptomic response of kodo millet during dehydration stress.Item GWAS identifies genetic loci underlying nitrogen responsiveness in the climate resilient C4 model Setaria italica (L.)(Elsevier B.V., 2022) Bandyopadhyay, Tirthankar; Swarbreck, Stéphanie M; Jaiswal, Vandana; Maurya, Jyoti; Gupta, Rajeev; Bentley, Alison R.; Griffiths, Howard; Prasad, ManojIntroduction N responsiveness is the capacity to perceive and induce morpho-physiological adaptation to external and internal Nitrogen (N). Crop productivity is propelled by N fertilizer and requires the breeding/selection of cultivars with intrinsically high N responsiveness. This trait has many advantages in being more meaningful in commercial/environmental context, facilitating in-season N management and not being inversely correlated with N availability over processes regulating NUE. Current lack of its understanding at the physio-genetic basis is an impediment to select for cultivars with a predictably high N response. Objectives To dissect physio-genetic basis of N responsiveness in 142 diverse population of foxtail millet, Setaria italica (L.) by employing contrasting N fertilizer nutrition regimes. Methods We phenotyped S. italica accessions for major yield related traits under low (N10, N25) and optimal (N100) growth conditions and genotyped them to subsequently perform a genome-wide association study to identify genetic loci associated with nitrogen responsiveness trait. Groups of accessions showing contrasting trait performance and allelic forms of specific linked genetic loci (showing haplotypes) were further accessed for N dependent transcript abundances of their proximal genes. Results Our study show that N dependent yield rise in S. italica is driven by grain number whose responsiveness to N availability is genetically underlined. We identify 22 unique SNP loci strongly associated with this trait out of which six exhibit haplotypes and consistent allelic variation between lines with contrasting N dependent grain number response and panicle architectures. Furthermore, differential transcript abundances of specific genes proximally linked to these SNPs in same lines is indicative of their N dependence in a genotype specific manner. Conclusion The study demonstrates the value/ potential of N responsiveness as a selection trait and identifies key genetic components underlying the trait in S. italica. This has major implications for improving crop N sustainability and food security.Item Molecular components associated with the regulation of flavonoid biosynthesis(Elsevier B.V., 2022) Naik, Jogindra; Misra, Prashant; Trivedi, Prabodh Kumar; Pandey, AshutoshFlavonoids exhibit amazing structural diversity and play different roles in plants. Besides, these compounds have been associated with several health benefits in humans. Several exogenous and endogenous cues, for example, light, temperature, nutrient status, and phytohormones have been reported as modulators of biosynthesis and accumulation of flavonoids. Thus, multiple hormones and stress-related signaling pathways are involved in the regulation of gene expression associated with this pathway. The transcriptional regulators belonging to the MYB and bHLH family transcription factors are well documented as the direct regulators of the structural genes associated with flavonoid biosynthesis. Recent studies also suggest that some of these factors are regulated by molecular components involved in stress and hormone signaling pathways. Adapter proteins for transcriptional activation or repression via recruitment of co-activators and co-repressors, respectively, E2 ubiquitin ligases, miRNA processing complex, and DNA methylation/demethylation factors have been recently discovered in various plants to play key roles in fine-tuning flavonoids synthesis. In the present review, we aim to provide comprehensive information about the role of different factors in the regulation of flavonoid biosynthesis. Besides, we describe the potential upstream regulators involved in the regulation of flavonoid biosynthesis within the context of available information. To sum up, the present review furnishes an updated account of signal transduction pathways modulating the biosynthesis of flavonoids.