Publications of NIPGR Scientists
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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 Integrated assessment of in vitro regeneration, ISSR-Based genetic fidelity, and antifungal properties in Holmskioldia sanguinea(Springer Nature Publishing AG, 2026) Gouda, Triveni; Pandey, Ashutosh; Mishra, NeelamHolmskioldia sanguinea is valued for its ornamental appeal and traditional medicinal uses for treating rheumatism, dysentery, headaches, hypertension, ulcers, and gynecological disorders, but propagation challenges limit wider cultivation and conservation efforts. To overcome the limitations associated with conventional propagation methods, an effective in vitro regeneration protocol was established using nodal explants. Following surface sterilization, explants were cultured on half strength Murashige and Skoog (MS) medium supplemented with varying concentrations of plant growth regulators for shoot bud initiation and multiplication. The best response was observed with 1.0 mg L−1 BA (Benzyladenine) particularly when combined 0.5 mg L−1 2,4-D (2,4- Dichlorophenoxyacetic acid) Shoot formation was evident within 2 to 3 wk, and rooting was successfully achieved in two wk after transferring the explant with initiated shoots on half strength MS medium supplemented with 1.0 mg L−1 IBA (Indolebutyric acid). Acclimatization involved a two-phase hardening process, beginning with a gradual reduction in external nutrients and followed by transfer to sterile peat moss + sand (2:1, v/v) potting mix, resulting in an impressive 98% survival rate of regenerated plantlets within 8 to 10 wk. The genetic fidelity of regenerants was evaluated using ISSR amplification with ten primers, out of which 6 primers yielded consistent and reproducible monomorphic profiles across wild-type and in vitro derived samples, demonstrating the absence of somaclonal variation and confirming genetic fidelity. In addition to micropropagation and ISSR-based genetic fidelity assessment, the antifungal potential of H. sanguinea was also evaluated. The methanolic leaf extract demonstrated the highest antifungal activity, inhibiting mycelial growth of tested fungi by 98%, indicating its strong potential as a natural antifungal agent. This study established a robust and scalable tissue culture regeneration protocol for H. sanguinea, supporting its conservation and offering opportunities for pharmaceutical applications as a source of natural antifungal compounds.Item Chlorpyrifos degradation by Zhihengliuella sp. ISTPL4: An esterase-driven actinobacterial platform for organophosphorus bioremediation(Elsevier B.V., 2026) Aggarwal, Himanshi; Chaudhary, Divya; Kumari, Taruna; Pradhan, Nischal; Mishra, Vaibhav; Kumar, Antresh; Singh, Anamika; Pandey, Ashutosh; Chaturvedi, Navaneet; Dufossé, Laurent; Mishra, Arti; Joshi, Naveen ChandraOrganophosphorus pesticides (OPs) are widely used agrochemicals that pose serious risks to the environmental and human health due to their persistence and toxicity. This study reports, for the first time, chlorpyrifos (CPF) degradation by actinobacterium Zhihengliuella sp. ISTPL4. Strain ISTPL4 utilized various OPs, including dimethoate, monocrotophos, CPF, and malathion, with the highest growth observed in the presence of CPF as the sole carbon and energy source. Optimal growth and degradation occurred at 28 °C, pH 5, and 3% inoculum in minimal salt medium (MSM). Under optimized conditions, strain ISTPL4 degraded 76.95% of 600 mg L-1 CPF within 7 days. GC-MS analysis identified benzene, 1,3-bis(1,1-dimethylethyl) and phenol, 2,4-bis(1,1-dimethylethyl) as intermediates without the formation of toxic metabolite 3,5,6-trichloro-2-pyridinol (TCP). Whole genome analysis revealed five putative esterase genes potentially associated with CPF degradation. Molecular docking identified carboxylesterase B as the most favorable CPF-binding enzyme, while molecular dynamics simulations supported the stability of the enzyme-substrate complex. A putative metabolic pathway for CPF degradation by strain ISTPL4 was proposed. These findings highlight the potential of Zhihengliuella sp. ISTPL4 as a promising candidate for sustainable bioremediation of OP-contaminated environments.Item Polyphenols-rich Indian barberry berries extract alleviates inorganic arsenic exposure-induced cognitive impairments and associated gut microflora alterations(Elsevier B.V., 2026) Vandana; Gupta, Shweta; Sharma, Rajni; Pandey, Ashutosh; Bishnoi, Mahendra; Rawal, Rakesh; Das, Santasabuj; Singh, Dhirendra PratapArsenic, a globally prevalent environmental toxin that can lead to neuro-behavioural changes. Oxidative stress and activation of inflammatory cascades are prominent mechanisms underlying these effects. The present study investigated the effects of polyphenol-rich extracts from Berberis aristata (Indian barberry) against inorganic arsenic-induced cognitive impairments in a murine model and presented mechanistic insights into its functional food properties. Response Surface Methodology (RSM)-guided hydro-alcoholic extracts were prepared and chemically characterized for their antioxidant activity, total phenolic contents (TPC) and free radical scavenging activities (RSA). UHPLC and LC-MS-based profiling of polyphenols, anthocyanins, and proanthocyanidins was performed. In-vitro toxicity studies in hepatic and colonic cancer cell lines, followed by in-vivo evaluation of these extracts in inorganic arsenic-exposed mice for spatial navigation tasks and passive avoidance-based learning were performed. Further assessments included neurotransmitter levels, histopathological investigations, qRT-PCR-based gene expression analysis, inflammatory cytokines and oxido-nitrosative stress markers in the brain and gastrointestinal tract, Evan's blue dye-based ileum permeability, and short chain fatty acids (SCFAs) estimation, along with Oxford Nanopore-based 16S rRNA metagenomics in cecal contents and PICRUSt2-based functional prediction of metagenomic data. RSM-optimized methods for polyphenol extraction yielded extracts with high TPC and RSA, with flavanols, phenolic acids, and proanthocyanidins identified as major polyphenols, and no in-vitro toxicity was observed. The extracts significantly prevented arsenic exposure-induced cognitive impairment, altered neurotransmitter turnover, neuroinflammation and gastrointestinal tract inflammation, oxidative stress-induced damage, increased ileum permeability, SCFA alteration, and gut microbial dysbiosis. These findings underscore the therapeutic/preventive potential of this polyphenol-rich extract against environmental toxicant-induced neurotoxicity, potentially involving gut microbiota-associated pathways.Item Attenuation of inorganic arsenic exposure-induced cognitive impairments by polyphenols-rich fraction of wild Rubus ellipticus berries via reshaping gut microbiota and reduction of oxidative stress-lead neuro-intestinal inflammation(Elsevier B.V., 2026) Vandana; Gupta, Shweta; Sharma, Rajni; Pandey, Ashutosh; Bishnoi, Mahendra; Rawal, Rakesh; Singh, Dhirendra Pratap; Das, SantasabujThe neurotoxic effects of inorganic arsenic exposure and consequential neurobehavioral outcomes involve activation of inflammatory cascades and reactive oxygen species (ROS)-mediated neuronal damage. Functional foods with characterized bioactive(s) are gaining attention in environmental contaminants-exposure induced pathologies. Here, we investigated the use of an ultrasonication-assisted extraction (UAE) and response surface methodology (RSM)-optimized process for polyphenols-rich extract from a Himalayan berry, Rubus ellipticus, against inorganic arsenic [iAs(III)]-induced cognitive impairments in mice. Total phenolic content (TPC), in-vitro antioxidant activity and cytotoxicities, along with UHPLC and LC-MS based polyphenolic profiles were determined. iAs(III)-exposure-induced spatial navigation tasks and passive avoidance-based learning performances were assessed. Neurochemical estimations, oxido-nitrosative stress markers, histological analysis and qRT-PCR-based gene expression in brain, ileum and, colon, pro-inflammatory cytokines and LPS levels, gut permeability, short chain fatty acids (SCFAs) levels, along with nanopore-based 16s rRNA metagenomics were performed. RSM-optimized UAE methods showed high TPC and antioxidant activities in polyphenol-rich (flavanols, phenolic acids and, proanthocyanidins) extract from R. ellipticus. The extract showed no potential cytotoxicity and significantly prevented iAs(III)-exposure-induced cognitive impairment, especially long-term spatial learning and memory. It also prevented altered neurotransmitter turnover, neuro-/ ileal/ colonic inflammation, and ROS-induced damages, increased ileum permeability, reduced SCFA level, and gut perturbations caused by iAs(III)-exposure. These findings suggest that the polyphenol-rich extract from Rubus ellipticus may offer protection against environmental toxicant [iAs(III)]-induced neurotoxicity and behavioral effects, potentially through combined modulation of oxidative stress, neuroinflammation, and gut-related pathways.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 Targeted lipidome analysis reveals nutritionally enhanced foxtail millet genotypes across diverse grain colours(Springer Nature Publishing AG, 2026) Ramesh, Palakurthi; Seni, Sushmita; Singh, Roshan Kumar; Pandey, Ashutosh; Prasad, ManojFoxtail millet (Setaria italica), a small-grained cereal crop, is a rich source of carbohydrates, proteins, minerals, fibers, and lipids, with lipid content ranging from 1–5% of the total grain composition. Whole grain is an excellent natural source of nutraceutical properties and health-beneficial components that significantly reduce chronic inflammation, cardiovascular disease, metabolic syndrome, and type 2 diabetes. Different grain colours in foxtail millet are associated with distinct metabolome composition. However, the relationship between lipid composition and grain colour remains largely unexplored. In this study, a comprehensive metabolomic analysis of eight differently coloured foxtail millet grains led to the identification of 352 distinct metabolites. Among these, 44 metabolites were chemically classified into categories such as fatty acids, steroids, hydrocarbons, benzenes, monoradylglycerols, quinones, and hydroquinones. Linoleic acid was identified as the predominant fatty acid, while lutein emerged as the most abundant carotenoid across all accessions. Gene expression profiling of carotenoid biosynthesis genes revealed significant genotype-specific variations, with SiPSY1, SiPSY2, SiPSY3, SiZDS, SiLCYB, and SiLCYE exhibiting markedly higher expression in the golden yellow genotype SI 101. Furthermore, several unique compounds, including decane 1-iodo, dodecane 4, 6-dimethyl, hexadecane, heptadecane, eicosane, heneicosane, bis (2-ethylhexyl) phthalate, dotriacontane, 2-methylhexacosane, hexatriacontane, squalene, tetrapentacontane, and tetracosane, were identified in foxtail millet grains. These findings provide valuable insights into the metabolic diversity and the differential accumulation of bioactive compounds in among foxtail millet grains with different colours. The study also assists in selecting foxtail millet genotypes with desirable lipid traits for sustainable crop improvement.Item Cytokinin-mediated repression of anthocyanin biosynthesis in banana fruits(John Wiley & Sons, 2025) Rajput, Ruchika; Tyagi, Shivi; Anchal, Kumar; Singh, Samar; Laxmi, Ashverya; Misra, Prashant; Pandey, AshutoshAnthocyanins are pigments responsible for vibrant plant colors and play vital roles in plant physiology. This study compares two banana cultivars, Grand Naine (GN) and Red Banana (RB), which exhibit significant differences in anthocyanin pigmentation. Transcriptomic profiling of peel (PL) and pulp (PP) tissues revealed cytokinin-responsive type-B response regulators (RRs), MaRR_B9 and MaRR_B12, as key modulators of anthocyanin biosynthesis. Cytokinin treatment of PP tissues increased the expression of MaRR_B9 and MaRR_B12, while significantly reducing the expression of dihydroflavanol reductase (MaDFR1, MaDFR2) and anthocyanidin synthase (MaANS) genes along with anthocyanin content. Through a combination of physiological, molecular, and biochemical analyses, we demonstrate that MaRR_B9 and MaRR_B12 exert direct regulatory control over key structural genes of anthocyanin biosynthesis, MaDFRs and MaANS. Additionally, a type B-RRs motif (AGATT) was identified in the promoter regions of MaDFR2 and MaANS, suggesting that MaRRs might directly regulate the transcription of MaDFR2 and MaANS. MaRR_B9 and MaRR_B12 interact with the promoters of MaDFR2 and MaANS, repressing these genes in vivo. Overexpression of MaRR_B9 and MaRR_B12 in banana fruits leads to a reduction in anthocyanin content, notably the cyanidin derivative, accompanied by altered expression patterns of MaDFRs and MaANS. Thus, the present study identifies MaRR_B9 and MaRR_B12 as novel regulators of anthocyanin biosynthesis in banana and provides further evidence that the cytokinin regulatory network modifies anthocyanin accumulation in plants. In conclusion, our findings reveal new molecular targets, in the form of MaRRs, for the genetic optimization aimed at enhancing anthocyanin content, stress resilience, and nutritional value in crop plants.Item Heat-responsive MaHSF11 transcriptional activator positively regulates flavonol biosynthesis and flavonoid B-ring hydroxylation in banana (Musa acuminata)(John Wiley & Sons, 2025) Naik, Jogindra; Rajput, Ruchika; Singh, Samar; Stracke, Ralf; Pandey, AshutoshPlant flavonols act primarily as ultraviolet radiation absorbers, reactive oxygen species scavengers, and phytoalexins, and they contribute to biotic and abiotic stress tolerance in plants. Banana (Musa acuminata), an herbaceous monocot and important fruit crop, accumulates flavonol derivatives in different organs, including the edible fruit pulp. Although flavonol content varies greatly in different organs, the molecular mechanisms involving transcriptional regulation of flavonol synthesis in banana are not known. Here, we characterized three SG7-R2R3 MYB transcription factors (MaMYBFA1, MaMYBFA2, and MaMYBFA3) and heat shock transcription factor (MaHSF11), to elucidate the molecular mechanism involved in transcriptional regulation of flavonol biosynthesis in banana. MaMYBFA positively regulates flavonol synthase 2 (MaFLS2) and downregulates MaFLS1. We show these transcription factors to be weak regulators of flavonol synthesis. Overexpression of MaHSF11 enhances flavonol contents, particularly that of myricetin, and promotes flavonol B-ring hydroxylation, which contributes to the diversity of flavonol derivatives. MaHSF11 directly interacts with the MaFLS1 and flavonoid 3',5'-hydroxylase1 (MaF3'5'H1) promoters, both in vitro and in vivo. MaHSF11 activates the expression of MaDREB1 directly, which is known to promote cold and chilling tolerance in banana fruit. Overall, our study elucidates a regulatory mechanism for flavonol synthesis in banana and suggests possible targets for genetic optimization to enhance nutritional value and stress responses in this globally important fruit crop.Item CRISPR/dCas9-KRAB mediated transcriptional suppression of NtbHLH47 enhances tolerance to iron stress and modulates iron content in tobacco(Elsevier B.V., 2025) Alok, Anshu; Chauhan, Hanny; Rout, Biswaranjan; Pandey, Ashutosh; Singh, KashmirIron homeostasis is a multifaceted regulatory process that needs to be studied to elucidate iron distribution, uptake, and storage in plants. NtbHLH47, a homologue to AtbHLH47, is a negative regulator of iron. The current study deploys CRISPR interference-dCas9-KRAB (Krüppel-associated box) in the transcriptional suppression of NtbHLH47 and its effect on iron uptake by plants. The pHSN6I01 harbouring dCas9-KRAB and gRNA targeting NtbHHLH47 was constructed. Four gRNAs were designed, G1, G2, G3, and G4, located at + 19, + 111, + 232, and + 335 bp upstream from the ATG start codon in the promoter region of NtbHLH47. The NtbHLH47 was repressed in the developed transgenic lines of tobacco and the qRT-PCR analysis showed that target sites G1 and G2 suppressed NtbHLH47 effectively. The transgenic pHSN6I01 +G1 plants were tolerant to the elevated levels of iron, copper, zinc, and magnesium. The root Ferric chelate reductase activity of pHSN6I01 +G1 lines was reduced against wild type. The Perl staining showed high iron content in the roots of the pHSN6I01 +G1 plants. ICP-MS analysis showed increased Fe content in the roots of pHSN6I01 +G1 line suggesting that NtbHLH47 modulates it. The expression of NtbHLH38, NtbHLH100, NtbHLH101, and NtFIT was found to be upregulated in the pHSN6I01 +G1 line. This is the first report of using CRISPRi based on dCas9-KRAB in tobacco and its application in the functional validation of a gene. Using this, NtbHLH47 was transcriptionally suppressed and the generated lines expressed increased levels of iron in the roots of N. tabacum and gave insight in the iron homeostasis.