Institutional Publications

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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, Meetu
Priming, 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.
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.
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, Manoj
Foxtail 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.

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