Publications of NIPGR Scientists
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Item Transcriptomic and OsWAK24-MPK3 crosstalk reveal resistance mechanism of primed rice seedlings against Arsenic-Iron(Oxford University Press, 2026) Bhatia, Priyanka; Mittal, Lavanya; Pandey, Shubhangi; Khatoon, Narjis Saba; Sinha, Alok Krishna; Gupta, MeetuPriming, elucidated as "memory," refers to the preconditioning of plant's stress responses to enhance resilience toward future stressors, including arsenic (As) contamination. This adaptive preparedness becomes further complex under As-Fe(iron) interplay, which remains scarcely delineated within priming background. Here, we employed Illumina sequencing to acquire global transcriptome alterations and heterologous interaction approach to chart the molecular reprogramming associated with As and As-Fe-dynamics in primed rice. The transcriptome revealed 3005 and 3650 genes to be differentially regulated in As and As-Fe-exposed primed seedlings. Comprehensive elucidation of expression profiling revealed that key genes were involved in transportation (OsNramp, OsFCR, OsNAS), signalling (OsWRKY, OsMYB, OsAP2, OsZF-TF), and defence (OsHSP, OsPRX, OsCyt P450). The antioxidant (OsGST, OsAPX) expression correlated well with their respective physiological enzyme activity. The entire WAK module, transducing extracellular signals to intercellular pathways, was differentially regulated under As and As-Fe influence. Notably, OsWAK24 revealed higher expression under As-Fe, reflecting its association with seedlings' tolerance behaviour. The computational protein network and docking unfolded OsMPK3 as an interactor of OsWAK24. The split-ubiquitin-based yeast-hybrid assay and immunoblot revealed OsWAK24-OsMPK3 association, suggesting OsMPK3 phosphorylates OsWAK24 at serine residue. Overall, the results decoded the seedling's resilience mechanism and aid in developing rice varieties with desired traits.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 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 Multi-omics approaches for strategic improvement of stress tolerance in underutilized crop species: A climate change perspective(Elsevier B.V., 2019) Muthamilarasan, Mehanathan; Singh, Nagendra Kumar; Prasad, ManojFor several decades, researchers are working toward improving the “major” crops for better adaptability and tolerance to environmental stresses. However, little or no research attention is given toward neglected and underutilized crop species (NUCS) which hold the potential to ensure food and nutritional security among the ever-growing global population. NUCS are predominantly climate resilient, but their yield and quality are compromised due to selective breeding. In this context, the importance of omics technologies namely genomics, transcriptomics, proteomics, phenomics and ionomics in delineating the complex molecular machinery governing growth, development and stress responses of NUCS is underlined. However, gaining insights through individual omics approaches will not be sufficient to address the research questions, whereas integrating these technologies could be an effective strategy to decipher the gene function, genome structures, biological pathways, metabolic and regulatory networks underlying complex traits. Given this, the chapter enlists the importance of NUCS in food and nutritional security and provides an overview of deploying omics approaches to study the NUCS. Also, the chapter enumerates the status of crop improvement programs in NUCS and suggests implementing “integrating omics” for gaining a better understanding of crops' response to abiotic and biotic stresses.Item Integrative network analyses of wilt transcriptome in chickpea reveal genotype dependent regulatory hubs in immunity and susceptibility(Springer Nature, 2018) Ashraf, Nasheeman; Basu, Swaraj; Narula, Kanika; Ghosh, Sudip; Tayal, Rajul; Gangisetty, Nagaraju; Biswas, Sushmita; Aggarwal, Pooja R.; Chakraborty, Niranjan; Chakraborty, SubhraHost specific resistance and non-host resistance are two plant immune responses to counter pathogen invasion. Gene network organizing principles leading to quantitative differences in resistant and susceptible host during host specific resistance are poorly understood. Vascular wilt caused by root pathogen Fusarium species is complex and governed by host specific resistance in crop plants, including chickpea. Here, we temporally profiled two contrasting chickpea genotypes in disease and immune state to better understand gene expression switches in host specific resistance. Integrative gene-regulatory network elucidated tangible insight into interaction coordinators leading to pathway determination governing distinct (disease or immune) phenotypes. Global network analysis identified five major hubs with 389 co-regulated genes. Functional enrichment revealed immunome containing three subnetworks involving CTI, PTI and ETI and wilt diseasome encompassing four subnetworks highlighting pathogen perception, penetration, colonization and disease establishment. These subnetworks likely represent key components that coordinate various biological processes favouring defence or disease. Furthermore, we identified core 76 disease/immunity related genes through subcellular analysis. Our regularized network with robust statistical assessment captured known and unexpected gene interaction, candidate novel regulators as future biomarkers and first time showed system-wide quantitative architecture corresponding to genotypic characteristics in wilt landscape.Item Interplay of neuronal and non-neuronal genes regulates intestinal DAF-16-mediated immune response during Fusarium infection of Caenorhabditis elegans(Nature Publishing Group, 2017) Nag, Papri; Aggarwal, Pooja Rani; Ghosh, Sudip; Narula, Kanika; Tayal, Rajul; Maheshwari, Nidhi; Chakraborty, Niranjan; Chakraborty, SubhraAlthough precisely controlled innate immune response is governed by conserved cellular events in phylogenetically diverse hosts, the underlying molecular mechanisms by which this process is regulated against a multi-host pathogen remain unknown. Fusarium oxysporum is a model multi-host pathogen, known to be associated with neuronal stress in humans and vascular wilt in plants. The interaction between innate immune and neuronal pathways is the basis of many diverse biological responses. How these processes are coordinated in response to fungal disease is not well understood. Here, we show that F. oxysporum f. sp. ciceri causes neuronal stress and intestinal disintegration, ultimately leading to the death of Caenorhabditis elegans. To explore the regulatory framework of Fusarium-associated disease, we analysed the gene expression during infection, integrated temporal gene expression, and network analysis with genetic inactivation data in Caenorhabditis elegans. We identified 1024 genes showing significant changes in expression (corrected P-values <0.05) in response to Fusarium infection. Co-expression network analysis of our data identified prognostic genes related to disease progression. These genes were dynamically expressed in various neuronal and non-neuronal tissues exhibiting diverse biological functions, including cellular homeostasis, organ patterning, stress response, and lipid metabolism. The RNA-seq analysis further identified shared and unique signalling pathways regulated by DAF-16/FOXO and SIR-2.1 linking neuronal stress, which facilitates negative regulation of intestinal innate immunity. Genetic analysis revealed that GCY-5 in ASE functions upstream of DAF-16, whereas ASI-specific SRD-1 regulates behavioural immunity. Overall, our results indicate that a ubiquitous response occurs during Fusarium infection mediated by highly conserved regulatory components and pathways, which can be exploited further for the identification of disease-responsive genes conserved among animals and plants. Finally, this study provided a novel insight into cross-species immune signalling and may facilitate the discovery of cellular therapeutic targets for Fusarium-associated disease.Item A novel FIKK kinase regulates the development of mosquito and liver stages of the malaria(Nature Publishing Group, 2016) Jaijyan, Dabbu Kumar; Verma, Praveen K.; Singh, Agam PrasadProtein phosphorylation is the most important post-translational event in the regulation of various essential signaling pathways in a cell. Here, we show the functional characterization of a FIKK family protein kinase of the rodent malaria parasite (PbMLFK), which is expressed only in mosquito and liver stages and contains two functional C-terminal PEXEL motifs. We demonstrate that this protein plays a role in mosquito and liver stages of parasite growth. The oocysts of PbMLFK-deficient parasites produced 4-fold fewer sporozoites. In the liver of infected mice, PbMLFK-deficient parasites grew 100-fold less than did wild type parasites. We also show that the C-terminal domain of this protein has a functional serine-threonine kinase and that its activity was inhibited by a known PKA inhibitor. Transcriptome analysis of infected host cells suggests that in absence of this protein expression of the 288 host mRNAs are perturbed which are primarily associated with the immune system, cell cycle and metabolism.Item Rice improvement through genome-based functional analysis and molecular breeding in India(Springer, 2016) Agarwal, Pinky; Parida, Swarup K.; Raghuvanshi, Saurabh; Kapoor, Sanjay; Khurana, Paramjit; Khurana, Jitendra P.; Tyagi, Akhilesh K.Rice is one of the main pillars of food security in India. Its improvement for higher yield in sustainable agriculture system is also vital to provide energy and nutritional needs of growing world population, expected to reach more than 9 billion by 2050. The high quality genome sequence of rice has provided a rich resource to mine information about diversity of genes and alleles which can contribute to improvement of useful agronomic traits. Defining the function of each gene and regulatory element of rice remains a challenge for the rice community in the coming years. Subsequent to participation in IRGSP, India has continued to contribute in the areas of diversity analysis, transcriptomics, functional genomics, marker development, QTL mapping and molecular breeding, through national and multi-national research programs. These efforts have helped generate resources for rice improvement, some of which have already been deployed to mitigate loss due to environmental stress and pathogens. With renewed efforts, Indian researchers are making new strides, along with the international scientific community, in both basic research and realization of its translational impact.Item Laser assisted microdissection, an efficient technique to understand tissue specific gene expression patterns and functional genomics in plants(Springer, 2015) Gautam, Vibhav; Sarkar, Ananda K.Laser assisted microdissection (LAM) is an advanced technology used to perform tissue or cell-specific expression profiling of genes and proteins, owing to its ability to isolate the desired tissue or cell type from a heterogeneous population. Due to the specificity and high efficiency acquired during its pioneering use in medical science, the LAM technique has quickly been adopted for use in many biological researches. Today, it has become a potent tool to address a wide range of questions in diverse field of plant biology. Beginning with comparative transcriptome analysis of different tissues such as reproductive parts, meristems, lateral organs, roots etc., LAM has also been extensively used in plant-pathogen interaction studies, proteomics, and metabolomics. In combination with next generation sequencing and proteomics analysis, LAM has opened up promising opportunities in the area of large scale functional studies in plants. Ever since the advent of this technique, significant improvements have been achieved in term of its instrumentation and method, which has made LAM a more efficient tool applicable in wider research areas. Here, we discuss the advancement of LAM technique with special emphasis on its methodology and highlight its scope in modern research areas of plant biology. Although we put emphasis on use of LAM in transcriptome studies, which is mostly used, we also discuss its recent application and scope in proteome and metabolome studies.Item Genome-wide strategies for genetic enhancement of rice(2011) Kapoor, S; Khurana, R; Baranwal, V; Agarwal, Pinky; Ray, S; Tyagi, Akhilesh K.