Publications of NIPGR Scientists
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Item Induced post-invasive defenses in the nonhost plant Parthenium hysterophorus L. prevent root cortical colonization by Macrophomina phaseolina and impart resistance to dry root rot(Elsevier B.V., 2025) Mirchandani, Rishabh; Kandpal, Manu; Ranjan, Aashish; Sinharoy, Senjuti; Senthil-Kumar, MuthappaDry root rot (DRR) of chickpea is caused by the broad-range necrotrophic fungus Macrophomina phaseolina. Chickpea germplasm does not provide durable resistance to DRR, which is particularly devastating under drought. Even moderately resistant chickpea varieties become susceptible under combined stress. We hypothesized that nonhost resistance (NHR) is durable even under combined stress. Using the blotter paper assay and stereomicroscopic observations, we identified the asterid weed Parthenium hysterophorus as a potential nonhost of M. phaseolina among 82 potential nonhosts. Epidermal necrotic lesions were prevented in P. hysterophorus. In planta fungal load was 0.195 and 0.007 ng/ng total DNA in chickpea and P. hysterophorus, respectively. M. phaseolina could not colonize the P. hysterophorus root while up to 6 cortical cell layers were colonized in chickpea. Further, NHR was durable under combined stress. Dual RNA sequencing revealed that M. phaseolina actively attempted to infect the nonhost and activated specific genes in the xenobiotics degradation pathway. P. hysterophorus also showed an active defense response with1958 and 2294 differentially expressed genes at 2 and 4 DAI, respectively, with 363 upregulated at both time points. Differential expression of cell wall synthesis, phytohormone signaling, and other defense response pathways likely contributes to NHR. Few genes in the phenylpropanoid biosynthesis pathways in P. hysterophorus were also upregulated, possibly because these metabolites are linked to the distinct changes in the fungus during nonhost infection. We therefore conclude that P. hysterophorus exhibits post-invasive NHR to M. phaseolina and that general defense, phytohormone signaling and secondary metabolic pathways contribute to NHR.Item Navigating towards dry root rot resistance in mungbean: impacts, mechanisms, and management strategies(Springer Nature Publishing AG, 2024) Sadhana, Nithyananth Hemanth; Geethanjali, Subramaniam; Mirchandani, Rishabh; Natesan, Senthil; Senthil-Kumar, MuthappaVigna radiata L., commonly referred to as mungbean or green gram, holds significant importance as a pulse crop in India. However, its productivity is severely impacted by the combined incidence of dry root rot disease and drought stress. Dry root rot, caused by Macrophomina phaseolina, manifests as reduced yield and compromised produce quality. M. phaseolina is a necrotrophic fungus with a broad host range. Screening studies in several crops’ germplasms have shown a skewness towards susceptibility. Further, the fungus has augmented virulence and survivability in soil under low moisture and high heat. Thus, concurrent drought and dry root rot leads to significantly higher yield losses. This review highlights the status of the disease in mungbean and its future implications owing to the changing climate scenario. We also highlight the molecular and genomic studies conducted in mungbean and several other crops to elucidate the mechanisms involved in M. phaseolina resistance. The review also suggests management practices which can alleviate yield losses in dry root rot affected fields. Understanding the physiological and molecular mechanisms of dry root rot, drought, and their interaction on disease proliferation can help mitigate the challenges associated with dry root rot management and aid future research.Item Abiotic stress impact on the interaction between Macrophomina phaseolina and crop plants(Springer Nature Publishing AG, 2024) Ranjan, Shubhashish; Mirchandani, Rishabh; Senthil-Kumar, MuthappaMacrophomina phaseolina (Tassi.) Goid is an emerging pathogen that causes diseases like dry root rot and charcoal rot in more than 100 plant families. Abiotic stresses such as drought, salinity, and heat exacerbate this fungal effect and predispose crops to pathogen attacks. Importantly, these combined stresses lead to significant crop yield losses under field conditions. In this, we review the interaction between the devastating pathogen M. phaseolina and several abiotic stresses that are more likely to occur in scenarios of climate change. Drought, heat, and salinity are the major stresses that interact with M. phaseolina in the field. We discuss several field studies, unique physiological and molecular responses, and their mechanisms of control in response to combined stress. The net effect of these interactions depends on a multitude of factors; thus, these interactions modify the impact of biotic stresses on plants by altering their susceptibility. The aim of this review is to provide an overview of what is currently known about M. phaseolina and abiotic stress interactions, as well as several other edaphic factors that interact with plants. We briefly discuss the role of drought, salinity, heat stress, and edaphic factors (such as pH, N, P, K, etc.) that influence pathogen infection in plants. Furthermore, we discuss possible management strategies to combat crop loss due to combined stress. Thus, we suggest the future aspect of combined stress breeding, along with the use of multi-omics techniques and genome editing approaches, to develop cultivars that exhibit stability in a combined stress environment.Item Drought attenuates plant responses to multiple rhizospheric pathogens: A study on a dry root rot-associated disease complex in chickpea fields(Elsevier B.V., 2023) Chilakala, Aswin Reddy; Pandey, Prachi; Durgadevi, Athimoolam; Kandpal, Manu; Patil, Basavanagouda S.; Rangappa, Krishnappa; Reddy, Puli Chandra Obul; Ramegowda, Venkategowda; Senthil-Kumar, MuthappaContext or problem: Root rots, a major factor contributing to yield loss in chickpea, often occur in disease complexes. Objective or research question: Plant responses to disease complexes are not well elucidated. We sought a clear understanding of a newly identified disease complex in chickpea, dry root rot (DRR)–wilt disease complex, in the field and studied the effect of drought on the severity of the complex and its effect on yield. We compared plant responses to DRR alone and the disease complex under drought and determined the phytohormones involved in plant defense against the disease complex. Methods: We compared the effect of 14 environments (two soil moisture regimes at seven locations) on the incidence of the disease complex and yield loss in four chickpea genotypes. We also studied the effect of drought on rhizospheric and root endo-microbial communities by whole-genome and metagenomic sequencing and performed LC-MS-based phytohormonal profiling of chickpea roots. Results: Soil moisture and plant genetic variability were critical in modulating disease incidence in field conditions. DRR was the primary driver of the disease complex under drought stress. Drought aggravated the yield reductions caused by the disease complex from 35% to 60% in susceptible genotypes. Further, drought-tolerant genotypes performed better under combined disease complex infection and drought stress and exhibited lesser yield losses than susceptible genotypes. Pathogenic fungi such as Macrophomina phaseolina, Fusarium oxysporum, and Rhizoctonia solani were enriched in the chickpea rhizosphere, and M. phaseolina was predominant in infected chickpea roots under both well-watered and drought conditions. Symbiotic associations of chickpea with nitrogen-fixing bacteria were suppressed under drought stress. Abscisic acid, jasmonic acid, and salicylic acid were found to be involved in defense against the disease complex across various stages of plant growth. Implications or significance: We highlight the interaction between drought and soil pathogens affecting chickpea yield and suggest the utilization of drought-tolerant root traits as donor traits for improving combined stress resistance. We also demonstrate growth stage–dependent phytohormonal responses elicited by DRR and the DRR–wilt disease complex. The identification and management of root rots is essential, and our findings offer valuable new insights into a lesser-known but highly significant disease complex of chickpea. Data availability statement: Manuscript data is available at Supplementary File S1. The soil microbe whole-genome and metagenome and root-microbe 16 S and ITS sequencing data are available at NCBI PRJNA871091 and PRJNA895851.Item The war for apoplastic water: stomatal control as a key strategy in bacterial pathogenesis(Springer Nature Publishing AG, 2023) Choudhary, Aanchal; Senthil-Kumar, MuthappaIn this commentary, important recent discoveries on effector-mediated manipulation of apoplast hydration and the involvement of ABA machinery that are targeted in later stages of bacterial infection culminating in stomatal closure are highlighted. This article also sheds light on the differences in early and later stages of infection wherein the COR signaling in the initial phase promotes stomatal opening while in later stages ABA signaling overrides and forces the stomata to close. Also, the current understanding of pathogen-driven modulation of leaf water status during infection, in which stomata act as a crucial battleground between pathogens and plants at the post-invasive stage is summarized.Item Investigation of the novel transcriptional changes under combined drought and bacterial stress underpins the role of AtMYB96 in imparting tolerance(Springer Nature Publishing AG, 2021) Choudhary, Aanchal; Senthil-Kumar, MuthappaThe physiological and molecular responses instigated to combat drought and bacterial pathogens often work antagonistically and, in most cases, the impact of combined stress is more detrimental to plant growth. Interestingly, plants exposed to this stress combination show a novel transcriptome fingerprint with a significant set of genes that are uniquely altered under combined stress. Despite this being reported in several transcriptomic datasets, our molecular understanding of these combined stress-specific genes and pathways is still in its nascent stages. These unique genes and the dedicated regulatory pathways are important for understanding the molecular aspects of signaling responses under combined stress. In this study, a previously available microarray dataset was extensively reanalysed to identify the novel genes and pathways specifically altered under combined stress. Using a combination of bioinformatic and data-guided approaches, we identified major biological pathways, transcription factor (TF) network and novel motifs potentially involved in the combined stress-specific responses. The candidate gene analysis using gene expression and mutant analysis identified AtMYB96 as an important TF involved in combined stress response. Taken together, our analysis pinpoints many novel genes that can be used for understanding the molecular mechanism of how plants deal with the combination of drought and bacterial pathogen.Item Morpho-physiological traits and molecular intricacies associated with tolerance to combined drought and pathogen stress in plants(Springer Nature, 2018) Irulappan, Vadivelmurugan; Senthil-Kumar, MuthappaCrops in field conditions are challenged by the simultaneous occurrence of drought and pathogen stress. In the past, research was primarily focused on studying the impact of individual stresses on plants and selection of crop varieties potentially tolerant to particular stress by yield-associated morpho-physiological traits. However, several molecular responses of crop plants underlying morpho-physiological features to concurrent stresses are not similar to that of individual stresses. Certain morpho-physiological traits such as cell membrane stability, leaf water potential, stomatal movement, and root length were shown to be altered distinctly under combined stress to combat the stress condition. However, the relevance of such traits under combined stress tolerance is not precisely known. In this chapter, from the extensive literature survey, we identified several morpho-physiological changes that could be cognate with better plant performance under combined stress and represented them as traits that have potential to impart combined stress tolerance. We have comprehensively explained physiological and molecular basis for each trait and, where possible, suggested the ways to exploit the information for identification of varieties with prospective traits. Also, we proposed the need for systematically studying the underlying regulatory traits under combined stress conditions in the future.Item Transcriptomic changes under combined drought and nonhost bacteria reveal novel and robust defenses in Arabidopsis thaliana(Elsevier B.V., 2017) Choudhary, Aanchal; Gupta, Aarti; Ramegowda, Venkategowda; Senthil-Kumar, MuthappaPlants in the natural conditions are often challenged by a combination of two or more stressors. A combination of drought and pathogen is one of the most pressing threats to the plant’s growth and survival in the field, and thus warrants a mechanistic understanding. Susceptible plant-pathogen interaction, owing to effector-mediated suppression of plant defense responses, limits its scope for combined stress studies. In the present study, we have investigated the morpho-physiological responses of Arabidopsis thaliana to simultaneous drought and nonhost bacterial pathogen Pseudomonas syringae pv. tabaci. Combined stress treatment provoked an early and more pronounced hypersensitive response in the plant as compared to the non-host pathogen treatment. We have further deciphered the molecular basis for the robust defense response observed under combined stress by transcriptomic profiling carried out using whole-genome microarray. We found that the enhanced resistance to the combined stress is accompanied by a massive transcriptional reprogramming involving several transcripts specifically responding to the stress combination. A prominent over-representation of genes involved in basal defense-related machinery was observed under the combined stress. Genes involved in various defense signaling cascades, accumulation of secondary metabolites and those encoding for receptor-like kinases were highly up-regulated under the combined stress. Up-regulated genes related to redox homeostasis and hypersensitive response (HR)-mediated cell death were also found to be markedly enriched under combined stress. We also compared the global gene expression profile of A. thaliana subjected to combined drought-nonhost bacteria to those treated with a combination of drought-host bacteria Pseudomonas syringae pv. tomato DC3000. A significant induction of genes responding to drought as well as bacteria was observed during both the interactions. However, the amplitude of induction was more pronounced under the combination of drought and nonhost bacteria. Our results also indicate that plant activates multiple defense pathways upon exposure to combined stress which strengthens the overall basal immunity of the plant, characterized by a stronger HR response.Item Plant responses to combined drought and pathogen infection: current understanding on the role of phytohormones(Springer, 2017) Pandey, Prachi; Senthil-Kumar, MuthappaPlants under natural conditions encounter a number of abiotic and biotic stresses often being inflicted simultaneously. Plant responses to a stress are governed by intricate network of the hormone signaling pathways. Abscisic acid (ABA) forms the major component of the plant response to drought and cold stress. Salicylic acid (SA), jasmonic acid (JA), and ethylene act as key regulators of plant response to pathogen infection. In fact, the extensive cross talk among the different hormone-mediated signaling pathways determines plant response to a particular stress. A large number of studies focus on hormone signaling under individual drought and pathogen stresses and the cross talk between the two stress responses. However, owing to the relatively few studies on combined drought and pathogen stresses, our understanding of phytohormonal signaling under combined stress is still obscure. Recent studies on combined drought and pathogen infection indicate that plants when simultaneously exposed to the two stresses often exhibit a transcriptional and metabolic response different from that exhibited under single stress conditions. This is also applicable to the phytohormonal signaling. The nature, time, and severity of the two stresses in combination modulate hormonal concentrations as well as the hormone signal transduction pathways involved. In this chapter, we provide a compendious description of the role of the three major hormones, namely, ABA, SA, and JA, in combined drought and pathogen infection. A brief description of the role of auxins, cytokinins, and gibberellins has also been provided. Taking leads from few studies, we have discussed the potential role of hormones in conferring combined drought and pathogen stress tolerance to plants. We also briefly discussed the effect of different “stress elicitors” on hormone signaling.Item Tailored responses to simultaneous drought stress and pathogen infection in plants(Springer, 2016) Choudhary, Aanchal; Pandey, Prachi; Senthil-Kumar, MuthappaUnder field conditions plants are often challenged by combination of biotic and abiotic stressors and they severely affect crop productivity. An increasing number of studies suggest that plants “tailor” their adaptation strategies to combat simultaneously occurring stresses. The stress combat strategies of plants are customized according to the stress combination and vary with the intensity and timing of the stresses involved. While some of the responses seen under combined stress are commonly instigated by individual stresses, some other are uniquely triggered under combined stress. Since some responses are unique only to the combined stress, the outcome of a stress interaction cannot be completely predicted using results from individual stress studies. In this chapter, the effects of combinatorial drought stress and pathogen infection on plants are discussed with an emphasis on the molecular and physiological mechanisms that underpin how plants tolerate simultaneously occurring stresses. We also highlight the complexity involved in the responses of plants to multiple stresses and underscore the importance of studying plant stressors in combination.