Institutional Publications

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Start date: 2020Subject: search.filters.subject.Rice

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    Rice PROTEIN L-ISOASPARTYL METHYLTRANSFERASES provides tolerance against sheath blight disease and repairs ALDH and PBZ1
    (Nature Publishing Group, 2026) Gautam, Shikha; Kamble, Nitin Uttam; Achary, Rakesh Kumar; Chandan, Ravindra Kumar; Varshney, Vishal; Hazra, Abhijit; Laha, Saroj; Mahawar, Shivangi; Mehandiratta, Sohela; Singh, Sarvanand; Jha, Gopaljee; Majee, Manoj
    Protein L-isoaspartyl methyltransferase (PIMT) regulates key seed traits and abiotic stress tolerance in plants by repairing isoaspartyl (isoAsp) damaged proteins. However, whether PIMT-mediated repair is induced and is required during biotic stress tolerance remains unknown. Using rice lines with OsPIMT overexpression, RNAi-mediated suppression, and genome editing, we show that PIMT enhances tolerance to sheath blight (ShB) caused by Rhizoctonia solani. OsPIMT restricts fungal penetration and colonization of rice sheaths. Co-immunoprecipitation coupled with LC-MS/MS identify various proteins including antioxidant proteins, aldehyde dehydrogenases (ALDH) and pathogenesis-related protein 10 (PBZ1), that undergo isoAsp modification during R. solani infection and interact with PIMT. We show that OsALDH and OsPBZ1 exhibit intrinsic antifungal activity against R. solani, but isoAsp modification impairs their activity, making PIMT mediated repair important. Further, OsALDH enhances tolerance to R. solani by inhibiting lipid peroxidation and ROS homeostasis in rice and fungus. Overall, our study reveals that PIMT enhances ShB tolerance through the repair of isoAsp-damaged proteins important for disease tolerance.
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    Network-based multiomics and transgenic validation reveal that OsPHR3 modulates phosphate-carbon metabolic trade-offs during rice seed development
    (Elsevier B.V., 2026) Pazhamala, Lekha; Pandey, Mandavi; Deveshwar, Priyanka; Ghatak, Arindam; Weckwerth, Wolfram; Chaturvedi, Palak; Giri, Jitender
    Phosphate (Pi) allocation during the grain-filling stage is a major determinant of crop yield, supporting macromolecule synthesis, energy metabolism, and nutrient storage. However, its storage as phytic acid (PA) reduces nutritional quality by chelating essential minerals. Despite its importance, a comprehensive understanding of the molecular mechanisms integrating Pi transport, carbohydrate metabolism, and PA biosynthesis during seed development remains incomplete. To address this gap, we investigated stage-specific phosphate regulatory networks in rice by integrating transcriptomic, proteomic, and metabolomic approaches. Temporal expression profiling and gene coexpression network analyses of phosphate regulators and transporter genes revealed their distinct roles during early and mid-grain filling stages. PHOSPHATE STARVATION RESPONSE 3 (OsPHR3) emerged as a central regulatory hub, coordinating the balance of Pi, sugar, starch and phytate, along with other metabolites. Network-based multiomics integration further identified 126 genes involved in nutrient storage and stress tolerance, with myo-inositol-1-phosphate synthase (OsMIPS1) and starch synthase 3 (OsSSIII) as key genes. CRISPR/Cas9-generated osphr3 knockout lines confirmed the critical role of OsPHR3 in regulating these target genes. Mutants exhibited significantly reduced seed starch, PA, and total phosphorus contents, while scanning electron microscopy revealed aberrant starch granule morphology. Loss-of-function of OsPHR3 lowered PA levels by 19.46–22.50 %, with moderate trade-offs in yield-related traits. Although, OsPHR3 is known to contribute to nitrogen and phosphorus homeostasis, our findings establish it as a key regulator orchestrating a stage-specific phosphate-carbon allocation during seed development. These insights provide key targets for refining nutrient partitioning to achieve increased yields, reduced phytic acid, and enhanced phosphorus use efficiency for agricultural sustainability.
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    The Mediator complex subunit, OsMED26_2, modulates plant growth, seed set and seed traits related to starch quality in rice
    (Elsevier B.V., 2026) Prusty, Ankita; Malik, Naveen; Ranjan, Rajeev; Agarwal, Pinky; Parida, Swarup K.; Kapoor, Sanjay; Tyagi, Akhilesh K.
    The Mediator (MED) complex is a multi-subunit structure crucial for RNA polymerase II-dependent transcription in eukaryotes. In this study, we investigated the function of a seed-preferential subunit of the rice Mediator complex, namely, OsMED26_2, for the first time. Knockdown of OsMED26_2 in rice reduced plant height and altered panicle morphology with shorter panicles, lesser branching, and fewer seeds per panicle. OsMED26_2 knockdown also led to shorter grains with shorter length and chalky endosperm. A significantly higher percentage of grains with chalkiness (PGWC) and degree of chalky endosperm (DCE) was observed in OsMED26_2 knockdown lines. OsMED26_2-knockdown seeds contained lower starch levels and altered proportions of amylose and amylopectin. Scanning electron microscopy further showed that these changes caused irregular, round, and loosely packed starch granules in the endosperm, contributing to the chalky phenotype. Decreased amylose content and increased grain chalkiness were corroborated by the downregulation of the Waxy (Wx) gene, which is involved in amylose synthesis, and altered expression of AMY3A, CHALK5, FLO4, GPA3, and SUSY3 genes, which regulate grain chalkiness. Our findings demonstrate that OsMED26_2 is critical in regulating panicle architecture, impacting yield, and modulating starch level and composition to control grain chalkiness and thereby suggesting its functional significance especially in manipulating yield attributing grain cooking quality traits of rice.
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    A CRISPR-Cas9 library to target putative redundant gene sets facilitates their functional exploration in grain development in rice
    (Springer Nature Publishing AG, 2025) Yadav, Banita; Sardar, Shaswati; Yadav, Anil; Kumari, Annapurna; Gautam, Mohini; Mandlik, Rushil; Arora, Simran; Kumar, Shailesh; Jewaria, Pawan Kumar; Sonah, Humira; Deshmukh, Rupesh; Chinnusamy, Viswanathan; Ram, Hasthi
    Advent of CRISPR-Cas9 library approach has revolutionized the field of high throughput targeted mutagenesis in plants. By identifying an sgRNA spacer that can target multiple paralogous genes in a genome, higher-order knockout plants can be developed. Using this concept, we developed ten CRISPR-Cas9 pool libraries and generated higher-order knockout plants in rice. Towards this, firstly we identified genome-wide sets of genes which are co-expressed and have high sequence similarity and can be targeted by a single sgRNA. Based on the expression pattern, these genes were divided into ten groups, and subsequently ten CRISPR-Cas9 plasmid libraries were developed. One such library designed against seed-expressed genes was transformed into rice and higher-order knockout plants were developed. Genotyping revealed that around 90% T0 plants had editing, and among the edited plants majority of them were higher-order knockouts. Phenotypic analysis in the next generation discovered functions of several seed specific genes in grain length, width, number and 100-grain weight. By analyzing single and double mutants for two Agenet domain-containing proteins, we have discovered an epistatic interaction between them for grain development. Further application of our approach will help to uncover hidden functions of the targeted genes and accelerate functional genomics research in rice. The CRISPR-Cas9 library is a useful approach to generate higher-order knockout mutants and identify functions of the targeted genes in rice.
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    Method for the measurement of ethylene during hypoxia in rice plants
    (Springer Nature Publishing AG, 2025) Jaiswal, Rekha; Gupta, Kapuganti Jagadis; Praveen, Afsana
    Ethylene is a versatile phytohormone that is involved in the regulation of both growth and development such as senescence, and also it can act as a signaling hormone during hypoxia. Ethylene acts alone or in interaction with different phytohormones and proteins to regulate numerous cellular processes. Accumulating evidence suggest that endogenous ethylene production and emission into atmosphere are modulated by various biotic and abiotic stresses. Since it is a gaseous hormone, a precise detection, particularly under low-oxygen (hypoxic) conditions, is important for understanding its role in regulatory processes and stress signaling pathways. Currently, measurement practices such as gas chromatography, electrochemical sensing, and optical sensing are widely employed to detect ethylene. These methods are distinct from each other in terms of sensitivity, time response, selectivity, and cost. However, each method has its own advantages and limitations. Gas chromatography (GC) is one of the best techniques that is applied for the separation and measurement of ethylene due to its volatile and supersensitive nature. In this chapter, we describe a detailed GC-based procedure specifically optimized for measuring ethylene levels during hypoxic stress application in (Oryza sativa) rice plants.
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    Tolerance of Oryza sativa to low phosphate is associated with adaptive changes in root architecture and metabolic exudates
    (Elsevier B.V., 2025) Srivastava, Akanksha; Gupta, Amber; Bishi, Sujit K.; Akhila, Pole; Latha, P.C.; Subrahmanyam, D.; Brajendra, P.; Anantha, M.S.; Ch, Suvarna Rani; Sakhare, Akshay S.; Bhadana, Vijai Pal; Giri, Jitender; Neeraja, C.N.; Sundaram, R.M.; Mangrauthia, Satendra K.
    The optimum usage of fertilizers is key for the sustainable agriculture. Among nutrients, phosphorus (P) is critical for plant growth and development. Due to complete reliance on natural resources (rock phosphate) for P, the availability of P fertilizers is emerging as a global challenge for crop cultivation. Moreover, the excess application of P fertilizers in rice, mostly grown under flooded conditions, leads to water pollution called eutrophication. In this study, we employed a mutagenesis approach for developing and characterizing rice EMS (ethyl meth anesulfonate) mutants with better adaptation to low soil P conditions. One such mutant of rice cultivar Nagina 22, named NH4824, was characterized comprehensively at seedling and reproductive growth stages under hy droponic and field conditions. The mutant exhibits low soil P tolerance due to combined adaptive changes in root system architecture, anatomy, organic acid exudates, plasma membrane (PM) H+-ATPase activity, induced expression of P transporter genes, and efficient mobilization and partitioning of P in different plant tissues. The activity of antioxidant enzymes and better photosynthesis suggested relatively less stress experienced by NH4824 than N22 under low soil P conditions. These insights are highly useful to develop P use efficient crop cultivars through breeding or genome editing approaches.
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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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    Comprehensive multi-layered analyses of genotype-dependent proteo-metabolic networks reveal organellar crosstalk and biochemical pathways regulating aroma formation in rice
    (Elsevier B.V., 2024) Narula, Kanika; Choudhary, Pooja; Sengupta, Atreyee; Chakraborty, Niranjan; Chakraborty, Subhra
    Molecular basis of rice aroma formation is sparsely known and developmental programs driving biochemical pathways towards aroma is in infancy. Here, discovery and targeted proteo-metabolome of non-aromatic and aromatic rice seeds across developmental stages identified a total of 442 aroma-responsive proteins (ARPs) and 824 aroma-responsive metabolites (ARMs) involved in metabolism, calcium and G-protein signaling. Biochemical examination revealed ARM/Ps were linked to 2-acetylpyrrolidine, γ-aminobutyrate, anthocyanin, tannins, flavonoids and related enzymes. Pairwise correlation and clustering showed positive correlation among ARM/Ps. Consistent with aroma-related QTLs, ARPs were mapped on chromosomes 3,4,5,8 and were mainly compartmentalized in cytoplasm and mitochondria. ARM/P-correlation network identified associations related to metabolism and signaling. Multiple reaction monitoring (MRM) confirmed role of catechins, quinic acid and quercetin in aroma formation. Pathway enrichment, multivariate analysis and qRT-PCR validated that calcium and G-protein signaling, aromatic/branched-chain aminoacid, 2-acetylpyrrolidine, oxylipin, melvonate and prenylpyrophosphate pathways, indole, phenylacetate, flavonoid, cinnamoic ester govern aroma formation in rice.
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    Metabolomic profiling reveals key factors and associated pathways regulating the differential behavior of rice (Oryza sativa L.) genotypes exposed to geogenic arsenic
    (Springer Nature Publishing AG, 2024) Saini, Himanshu; Panthri, Medha; Khan, Ehasanullah; Saxena, Samiksha; Pandey, Ashutosh; Gupta, Meetu
    Arsenic (As) toxicity is an escalating problem; however, information about the metabolic events controlling the varied pattern of As accumulation in rice genotypes within their natural environment is still lacking. The present study is thus an advancement in unravelling the response of such rice genotypes. Soil-water-rice samples were analyzed for As accumulation using ICP-MS. Furthermore, we implemented metabolomics through LC-MS/MS and UHPLC to identify metabolic signatures regulating As content by observing the metalloid's composition in rice agrosystem. Results showed that rice genotypes differed significantly in their levels of metabolites, with Mini mansoori and Pioneer having the highest levels. Mini mansoori contained least As which might have been regulated by Ala, Ser, Glu, Phe, Asn, His, Ile, Lys, Gln, Trp, Tyr, chlorogenic, p-coumaric, trans-ferulic, rutin, morin, naringenin, kampferol, and myricetin, while Asp, Arg, Met, syringic, epigalocatechin, and apigenin contributed to the greater As acclimatization ability of Pioneer. Multivariate tools separated the rice genotypes into two major clusters: Pioneer-Mini mansoori and Damini-Sampoorna-Chintu. KEGG identified three major metabolic pathways (aminoacyl-tRNA, phenylpropanoid, and secondary metabolites biosynthesis route) linked with As tolerance and adaptation mechanisms in rice. Overall, these two genotypes symbolize their As hostile and accommodating attitudes probably due to the accumulated metabolites and the physicochemical attributes of the soil-water. Thus, thorough understanding of the metabolic reactions to As may facilitate the emergence of As tolerant/resilient genotypes. This will aid in the selection of molecular markers to cultivate healthier rice genotypes in As-contaminated areas.
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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.