Publications of NIPGR Scientists

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    Insect herbivory simulation and insect bioassays to study plant stress memory response
    (Springer Nature Publishing AG, 2026) Meena, Mukesh Kumar
    Plant stress memory response is an emerging field in plant–insect interaction. Recent reports indicate phytohormone jasmonic acid (JA) triggers long-term effects on the defense phenotype, transcriptome, and DNA methylome of Arabidopsis. Long-term JA-mediated induced resistance required MYC2/3/4 transcription factors and epigenetic regulatory components that prepare plants for future insect herbivore threats. Three weeks after transient JA signaling, 5-week-old plants retained induced resistance against herbivory but showed increased susceptibility to pathogens. This mechanism is linked with long-term priming and/or upregulation of JA-dependent defense genes but repression of ethylene- and salicylic acid-dependent genes. Still more research is required to fully understand plant stress memory response in plant–insect interaction. Here, a detailed and reproducible protocol for simulated herbivory and sample collection for transcriptomic and metabolomic studies is described to investigate involved defense signaling pathways. Furthermore, the insect bioassay protocol is described to study insect performance on various plant genotypes. Both protocols are robust and could be useful to study plant stress memory response in plant defense mechanisms through simulated herbivory and direct insect performance and feeding behavior by insect bioassays.
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    Method for the measurement of ethylene during pathogen infection in arabidopsis
    (Springer Nature Publishing AG, 2025) Jaiswal, Rekha; Gupta, Kapuganti Jagadis; Praveen, Afsana
    Ethylene is a gaseous phytohormone that plays an important role as a signaling molecule during pathogen attack, influencing disease resistance and defense responses in plants. A precise measurement of ethylene production upon pathogen challenge is essential to elucidate its role in plant–pathogen interactions. Gas chromatography (GC) is among the most accurate and sensitive techniques for detecting and quantifying ethylene emissions due to its selectivity and effectiveness with gaseous molecules. In this chapter, we provide a detailed procedure employing GC specifically adapted for measuring ethylene levels during pathogen infection (Botrytis cinerea) in Arabidopsis leaflets. Arabidopsis leaflets infected by the necrotrophic pathogen Botrytis cinerea exhibit increased ethylene emission, facilitating the activation of defense pathways and secondary metabolites such as camalexin. The present GC method captures ethylene dynamics at early infection stages, ensuring precise quantification critical for dissecting the molecular mechanisms of plant immunity.
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    Seed germination variability: Why do genetically identical seeds not germinate at the same time?
    (Oxford University Press, 2023) Sharma, Eshan; Majee, Manoj
    For survival in the wild environment, plants prefer a bet-hedging strategy where individual variation is high and also produce a range of phenotypes. When faced with unpredictable environmental conditions, fluctuation in seed behaviour is a beneficial trait that allows the survival of plants, particularly if seedlings from early germinated seeds don't survive. However, this is not a desired trait when agriculture is concerned, where a set of uniformly grown seedlings are required. Even though variability in seed behaviour is unavoidable, over the centuries, humans might have selected seeds with minimum variability for agricultural use. In the model plant Arabidopsis, non-stratified seeds even in the same silique germinate variably. How this variability is manifested from genes to a physiological outcome and what molecular mechanism of bet-hedging facilitates this diversity remains elusive. Will the reintroduction of valuable wild alleles in domesticated crops contribute to this variability between individual seeds by promotion of bet-hedging? Recent advances have shed light on possible molecular pathways of germination that are impacted at the level of single seeds and single cells. Here, we review the hormonal, molecular and cellular mechanisms that may impact the germination outcome of individual genetically identical seeds.
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    OsWAKL21, a putative receptor of rice cell wall damage activates alternate signaling in rice and Arabidopsis to induce immunity
    (American Phytopathological Society, 2019) Malukani, K. K.; Ranjan, A.; Hota, S. J.; Patel, H. K.; Sonti, Ramesh V.
    Xanthomonas oryzae pv. oryzae (Xoo) causes the serious bacterial blight disease of rice. As part of its virulence repertoire, Xoo secretes various cell wall degrading enzymes (CWDEs) such as cellulases, xylanases and a Lipase/esterase (LipA). Conversely, treatment of rice tissues with any of these purified enzymes activates immune responses. Plants sense this cell wall damage as a mark of infection and induce immune responses. Very little information is available about the plant functions that are involved in the elaboration of cell wall damage induced immune responses. Transcriptome analyses revealed a rice cell wall-associated receptor kinase, OsWAKL21 that is upregulated following treatment with either LipA or Xoo. VIGS mediated downregulation of OsWAKL21 attenuates LipA induced immune responses. Overexpression of OsWAKL21 in rice mimics LipA treatment in induction of immune responses, activation of JA pathway and enhanced expression of defence related genes, indicating that it plays an important role in elaboration of LipA induced immune responses. Ectopic expression of OsWAKL21 in Arabidopsis also activates plant immune responses. OsWAKL21 is a moonlighting kinase having in vitro kinase and guanylate cyclase activities. Interestingly, OsWAKL21 needs kinase activity to activate immune responses in rice while in Arabidopsis it needs the guanylate cyclase activity. Thus OsWAKL21 is activating similar immune responses in two different species but via different mechanisms.
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    Whole mount in situ localization of miRNAs and target mRNA transcripts in plants
    (Springer Nature Publishing AG, 2019) Gautam, Vibhav; Singh, Archita; Verma, Swati; Singh, Sharmila; Chatterjee, Sourav; Sarkar, Ananda K.
    The functional characterization of miRNAs often involves understanding of their spatiotemporal expression, which mostly relies on reporter-based or in situ hybridization studies. The available in situ localization methods follow separate protocols for pre-hybridization, hybridization, post-hybridization, and detection steps for both miRNA and mRNA transcripts in plants. In this study, we present a single method which can be used for whole mount in situ localization of both miRNAs and mRNAs in different plant tissues. Our modified method provides enhanced sensitivity for the localization of miRNA and their target transcripts. Consequently, a less laborious, time-saving, economic and efficient method has been proposed by the modification of pre-hybridization, hybridization, post-hybridization and detection steps.
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    Role of plant mediator complex in stress response
    (Springer, 2015) Samanta, Subhasis; Thakur, Jitendra K.
    Class II gene loci of eukaryotes are transcribed by RNA Polymerase II, which functions in coordination with several other proteins like transcription factors, general transcription factors, and cofactors. Recently, Mediator complex, a multi-subunit, megadalton size protein complex has gained lots of attention as an important component of RNA pol II transcriptional machinery because of its essentiality in the regulation of most of the class II genes. Like yeast and other metazoans, plants also possess the Mediator complex across the kingdom, and its isolation and subunit analyses have been reported from the model plant, Arabidopsis. Recent times have experienced a flurry of scientific papers containing the functional information of individual Mediator subunits in plants, although many were reported earlier without consideration of their association with the Mediator complex. Among its diverse functional aspects, several reports have established the Mediator complex as an important integrative hub of different biotic and abiotic stress signaling pathways, which have been discussed in this chapter from the functional genomics perspectives. Although reports are emerging in support of its inclusion as a component of the basic transcriptional machinery, the gene selective roles of the individual Mediator subunits are proven and indisputably accepted.
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    Simultaneous isolation of root and leaf mitochondria from Arabidopsis
    (John Wiley & Sons, 2015) Gupta, Kapuganti Jagadis; Ewald, Ralph
    In all aerobic organisms mitochondria generate ATP via oxidative phosphorylation. For bulky tissues such as potato tubers and cauliflower and for larger crop plants such as tobacco, pea, soybean or etiolated seedlings it is possible to get a good yield of mitochondria. However, for tiny model plants like Arabidopsis it is very difficult to get sufficient quantities of mitochondria for various studies. Moreover, for comparative studies it is very important to isolate leaf and root mitochondria. Due to the lack of chlorophyll, root mitochondria isolation is often an easy task. Leaf mitochondria isolation has the advantage that higher amounts of tissues can be obtained from the plants in comparison to root material, but chlorophyll contamination can be a problem. This chapter describes how to isolate root mitochondria with sufficiently high yields, and how to obtain chlorophyll-free leaf mitochondria simultaneously.