Publications of NIPGR Scientists

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    Genome-wide identification, in-silico characterisation and expression analysis of multiprotein bridging factor 1 gene family members in rice
    (Springer Nature Publishing AG, 2025) Bishnoi, Alka; Ram, Hasthi; Soni, Praveen
    The multiprotein bridging factor 1 (MBF1) proteins are evolutionarily conserved transcription co-factors. However, little is known about rice MBF1 gene family and its role. A genome-wide search led to the identification of two MBF1 genes in the rice genome. Their proteins contained characteristic MBF1 and helix-turn-helix domains. Phylogenetic analysis showed that they belong to two different groups. Exploration of publicly available rice transcriptome data revealed that OsMBF1b exhibits constitutively high transcript abundance in all tissues and developmental stages of rice with a little alteration in its expression. Contrarily, OsMBF1c exhibited a prominent alteration in its expression in response to environmental perturbations. Both OsMBF1s showed the highest expression in endosperm. Analysis of publicly-available rice transcriptome data also showed that both OsMBF1s have a role in response to different stresses, especially in heat. Transcript analysis using qRT-PCR confirmed heat inducibility of OsMBF1c in contrasting genotypes i.e. IR64 (heat sensitive) and Nagina 22 (heat tolerant). qRT-PCR also confirmed the drought inducibility of both genes in the IR64 genotype which is sensitive to drought stress also as revealed by analysis of different parameters. In-silico interaction study also indicated their role in heat response as a number of proteins required to cope with high temperatures were predicated to be their interacting partners. Several heat-responsive genes were found to co-express with OsMBF1s. In-silico promoter analysis revealed the occurrence of stress-responsive elements in their putative promoters. Interestingly, both OsMBF1s showed diurnal rhythmic expressions having peaks during the daytime when the temperature rises. Altogether, this study indicates an active role of OsMBF1s in thermotolerance in rice. This is the first report regarding the characterization of rice MBF1 members.
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    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, Hasthi
    Iron (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.
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    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, Hasthi
    Rice 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.
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    Regulation of metalloid uptake in plants by transporters and their solute specificity
    (Elsevier B.V., 2023) Sharma, Yogesh; Soni, Praveen; Raturi, Gaurav; Mandlik, Rushil; Rachappanavar, Vinay Kumar; Kumar, Manish; Salvi, Prafull; Tripathi, Durgesh Kumar; Ram, Hasthi; Deshmukh, Rupesh
    Metalloids are a class of elements having properties like metals and non-metals which act as beneficial as well as hazardous for plant growth. Here, the precise role and molecular mechanism involved in the uptake and transport of different metalloids to different plant tissues is discussed. We have also described the efforts made to engineer the metalloid transport i.e. influx/efflux of metalloids that improve the uptake of beneficial metalloids and reduce hazardous metalloids. Metalloids like boron (B) and silicon (Si) play a beneficial role in plant growth and development. Optimum levels of these metalloids improve plant growth and immunity by various direct and indirect effects. On the other hand, metalloids like arsenic (As) and germanium (Ge) are detrimental for plants even at lower concentrations. The presence of these toxic entities inside cells disrupts cellular homeostasis by affecting the molecular, biochemical and physiological processes. The prospect to increase the uptake of beneficial metalloids and limit the hazardous metalloids and the challenges associated with the structural analogy and common transport mechanism is also discussed. The molecular insights into the biochemical and physiological aspects of metalloid transport and detoxification mechanisms will be helpful to exploit metalloid-derived benefits for crop improvement and accomplish food safety.
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    Role of Serendipita indica in enhancing drought tolerance in crops
    (Elsevier B.V., 2021) Jangir, Pooja; Shekhawat, Pooja Kanwar; Bishnoi, Alka; Ram, Hasthi; Soni, Praveen
    The root endophytic fungus Serendipita indica (S. indica) acts as a bio-fertilizer, immuno-modulator, stress-buster and enhances plant growth, and protects the host plant from various biotic and abiotic stresses. Recent high-throughput omics approaches have helped in understanding the role of S. indica in host plants under stress conditions. The present review focuses on the mechanism of S. indica mediated drought-tolerance in crops by analyzing morphological, physiological, biochemical, and molecular processes. Interactions of S. indica with other plant growth-promoting microorganisms have been discussed. The knowledge gap and future prospects have been pointed out.
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    Serendipita indica: Harnessing its versatile potential for food and nutritional security
    (Elsevier B.V., 2021) Shekhawat, Pooja Kanwar; Jangir, Pooja; Bishnoi, Alka; Roy, Shweta; Ram, Hasthi; Soni, Praveen
    Quantity as well as quality of food is a major concern for increasing human population. Serendipita indica, a root endophytic fungus, has multifarious applications in agriculture. It increases nutrient and water uptake, carbon assimilation efficiency and stress-resistance which in turn enhances the growth and yield of plants. Moreover, it improves contents of minerals, fatty acids and essential oil, composition of oil, and fruit firmness in different plants. It also enhances the production of secondary metabolites having medicinal properties. This review highlights the role of Serendipita indica in increasing crop production and improving food quality. The underlying mechanism has also been illustrated.
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    Reference gene identification for gene expression analysis in rice under different metal stress
    (Elsevier B.V., 2021) Soni, Praveen; Shivhare, Radha; Kaur, Amandeep; Bansal, Sakshi; Sonah, Humira; Deshmukh, Rupesh; Giri, Jitender; Lata, Charu; Ram, Hasthi
    Real-time quantitative polymerase chain reaction (RT-qPCR) is the most common approach to quantify changes in gene expression. Appropriate internal reference genes are essential for normalization of data of RT-qPCR. In the present study, we identified suitable reference genes for gene expression analysis in rice seedlings subjected to different heavy metal stresses such as deficiencies of iron and zinc and toxicities of cobalt, cadmium and nickel. First, from publically available RNA-Seq data we identified 10 candidate genes having stable expression. We also included commonly used house-keeping gene OsUBQ5 (Ubiquitin 5) in our analysis. Expression stability of all the 11 genes was determined by two independent tools, NormFinder and geNorm. Our results show that selected candidate reference genes have higher stability in their expression compared to that of OsUBQ5. Genes with locus ID LOC_Os03g16690, encoding an oxysterol-binding protein (OsOBP) and LOC_Os01g56580, encoding Casein Kinase_1a.3 (OsCK1a.3) were identified to be the most stably expressed reference genes under most of the conditions tested. Finally, the study reveals that it is better to use a specific reference gene for a specific heavy metal stress condition rather than using a common reference gene for multiple heavy metal stress conditions. The reference genes identified here would be very useful for gene expression studies under heavy metal stresses in rice.