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 Stress combinations and their interactions in crop plants(Springer Nature Publishing AG, 2024) Ramegowda, Venkategowda; Senthil, Alagarswamy; Senthil‑Kumar, MuthappaCombined stresses are a common occurrence in agricultural felds. There is a pressing need for empirical understanding of the plant responses and fnd ways to develop stress tolerant plants and stress management strategies to tackle combined stresses in the feld conditions. Here a comprehensive overview of the current understating and recent research on combined stress interactions in plants are presented. Here we comprehend the fndings from various studies focusing on diferent aspects of combined stress, including abiotic-abiotic, abiotic-biotic, and biotic-biotic stress interactions. In general, the studies discussed here highlight the escalating impact of climate change on plants, emphasizing the need for a deeper understanding of plant responses to concurrent abiotic and biotic stresses. Key fndings from the articles published in this issue, include the adverse efects of combined drought and high-temperature stress on crop growth and yield, the exacerbation of pathogen impacts under abiotic stresses, and the potential for melatonin and salicylic acid to mitigate stress-induced damage. Additionally, use of model systems for quicker understanding of combined stress responses and development of methods and technologies which can be extrapolated to crop plants are discussed. Overall, fndings from the articles from this special issue underscore the complexity of combined stress interactions in plants and highlight the importance of interdisciplinary research eforts to address the challenges posed by climate change and ensure global food security.Item Deciphering the role of MIR169d:NF-YA2 module under individual as well as combined drought and heat stress in Arabidopsis(Springer Nature Publishing AG, 2024) Gupta, Apoorva; Ghosh, Debasish; Rao, Sombir; Mathur, SaloniPlants are often subjected to a combination of abiotic stresses under natural environmental conditions. The response of plants to combined stresses can be very diferent from that to the individual stress. Several regulatory mechanisms work in harmony to maintain plant’s homeostasis during stress conditions. Among them the roles of microRNAs (miRNAs) in combined stresses are beginning to be unravelled. In this study, we evaluated the MIR169d: NF-YA2 target module in individual as well as combined drought and heat stress (HS) in Arabidopsis. We found that MIR169d is highly HS inducible, however, contrary to the reported downregulation of MIR169a/c forms in drought stress in literature, MIR169d is upregulated in drought. Moreover, while MIR169d expression is upregulated during combined stress, the response is less than individual stresses. Further, Arabidopsis plants overexpressing MIR169d or target nf-ya2 knockout mutant plants are more tolerant to both individual as well as combined heat and drought stress as indicated by the higher expression of stress responsive genes and less Trypan blue staining, while plants overexpressing NF-YA2 or those in which miR169defg isoform is sponged up (MIM169defg) are more prone to individual as well as combined heat and drought stress. The MIR169d promoter harbours both heat and drought stress-responsive cis-elements. Assessment of GUS expression in MIR169d-promoter:GUS and NF-YA2-promoter:GUS transgenic lines shows increased and reduced reporter expression in all the three stress conditions as compared to control, respectively. This suggests a stress-induced transcriptional regulation of the MIR169d:NF-YA2 pair. Thus, the MIR169d:NF-YA2 module can be potentially exploited to engineer crops for resistance to multiple abiotic stresses.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 Inferring the regulatory network of the miRNA-mediated response to individual and combined heat and drought stress in tomato(Springer Nature Publishing AG, 2021) Bansal, Chandni; Balyan, Sonia; Mathur, SaloniUnder natural environmental conditions, plants are prone to be challenged simultaneously by combination of stresses like heat and drought stress together, thus affecting their overall growth, development and reproduction. Moreover, future climatic conditions are predicted to be warmer and drier, thus, warranting deep understanding of the stress-responsive regulatory networks for developing stress-management strategies. The role of microRNAs (miRNAs) that are key regulators of different stress signalling cascades in such dual stress conditions using varieties growing in warmer climatic conditions is completely lacking. In this study, we have investigated the effect of drought, heat and the two stresses together (combined stress) on a heat-tolerant tomato (Solanum lycopersicum) variety by evaluating physiological parameters as well as, some stress-responsive miRNA-target modules. Taqman-based qRT-PCR miRNA expression analysis showed enhanced expression of sly-miR482d-3p, sly-miR172d-3p, sly-miR164b-3p, sly-miR398b in individual drought and heat stress with an additive upregulation effect under combined stresses. On the other hand, the expression of sly-miR397-5p and sly-miR396b-3p was less when these two stresses co-occurred than the individual stresses and an antagonistic response was observed for sly-miR166a expression in combined versus single stresses. Several high confidence miRNA targets (101) were identified in-silico using degradome data and were functionally annotated using Gene Ontology enrichment analysis into various stress regulatory networks. The comparative analysis confirmed the inverse expression regulation of the miRNA:target pairs for sly-miR398b:Solyc07g006180, sly-miR164b-3p:Solyc08g061500, sly-miR172d:Solyc04g049800, sly-miR396b-3p:Solyc01g102810 and sly-miR396b-3p:Solyc05g017930 under all the three stress conditions. Since miRNAs are highly conserved across diverse plant species, these miRNAs can be candidates for engineering climate resilient crop plants.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.