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Item Plant responses to combined abiotic and biotic stresses(Springer Nature Publishing AG, 2026) Preethi, V; Senthil, A; Senthil-Kumar, Muthappa; Raveendran, M; Anitha, K; Boominathan, P; Johnson, I; Karthikeyan, RClimate change has increased the frequency of extreme weather events, leading to the widespread occurrence of various abiotic stresses such as drought, salinity and temperature. Abiotic challenges often coincide with biotic stresses including pathogen and pest infestations. The frequent occurrence of such stresses, either individually or in combination, hinders crop growth, development, yield and quality. Plants have evolved diverse physiological and molecular adaptations to safeguard themselves against various stresses. However, plant responses to combined biotic and abiotic stresses are more complex and variable than responses to individual stresses, due to the intricate interactions among signaling networks and defense pathways. A clear understanding of how abiotic stresses influence pest and disease incidence as well as their severity is essential for developing strategies to mitigate the effect of combined stresses. Despite progress in individual stresses, there is a lack of comprehensive studies on the alterations in physiological, biochemical and molecular mechanisms of plants under combined stress conditions. This review aims to provide insights into plant responses to combined abiotic and biotic stress interactions and highlights the key morpho-physiological, biochemical, and molecular mechanisms, and presents recent case studies illustrating plant responses and effects under such combined stresses. In addition, this review highlights the integration of mechanistic insights with modern biotechnological and breeding strategies for enhancing plant tolerance to combined abiotic and biotic stresses. By providing a multi-dimensional framework that connects physiological, molecular, and computational analyses, it enables the identification of tolerant genotypes and serves as a comprehensive resource for plant breeders, molecular biologists, and agronomists to develop targeted strategies for improving crop resilience under combined stress conditions.Item An artificial neural network–based deep learning model to predict combined stress impact and interaction in plants(John Wiley & Sons, 2026) Priya, Piyush; Pandey, Prachi; Jain, Rubi; Kandpal, Manu; Jain, Shradha; Chaudhury, Rim; Ramegowda, Venkategowda; Senthil-Kumar, MuthappaPremise: Plants are frequently exposed to combinations of abiotic and biotic stresses that pose a greater threat to yield and productivity than individual stresses. However, knowledge of the impact of many stress combinations in numerous plants is limited due to the lack of experimental data, which could take decades to generate. To overcome this limitation, we utilized existing literature data from various plant species and stress combinations to derive biological inferences, thereby gaining a comprehensive understanding of plant responses through a computational tool. Methods: Public databases were used to gather literature on the impact of various abiotic and biotic stress combinations. Then, a composite artificial neural network (ANN)–based multi-target classification and regression deep learning model was developed using machine learning algorithms. Results: The model predicted the impact of stress interactions in plants, including the morphological parameters affected and percentage changes in those parameters, with an overall accuracy of 76.33%. Predicted reductions in yield were validated in rice under combined drought and heat stress. Discussion: The ANN-based model developed in this study is a valuable resource for plant researchers seeking to understand the impact of stress combinations. The tool can make use of multivariate and complex combined stress datasets.Item Dual localization of JA receptor, CaCOI2, explains JA perception dynamics in chickpea(John Wiley & Sons, 2025) Singh, Ajit Pal; Bhatia, Chitra; Singh, Ekampreet; Singh, Amit Kumar; Fatima, Urooj; Senthil-Kumar, Muthappa; Giri, JitenderJasmonates (JAs) are a group of oxylipin-derived phytohormones involved in various biotic and abiotic stress responses and regulate plant development. JAs are perceived by receptor proteins called coronatine insensitive (COI). These JA receptors encode F-box proteins that form the SCFCOI ubiquitin ligase complex (comprising Skp, Cullin, and F-box) and activate JA signaling by promoting the degradation of the transcriptional repressor JAZ (JA associated ZIM domain containing) proteins via the 26S proteasomal pathway. However, JA signaling is not well understood in chickpea, a vital legume. In this study, we identified two potential chickpea JA receptors, named CaCOI1 and CaCOI2, and characterized CaCOI2 as a functional JA receptor. Subcellular localization experiments revealed that CaCOI2 is localized outside the nucleus but moves into the nucleus upon JA perception to activate signaling. Using domain-swapping experiments between CaCOI1 and CaCOI2, we demonstrated that the leucine-rich repeat region of the receptors, which interacts with bioactive JA such as JA-Isoleucine, also plays a crucial role in controlling the subcellular localization of CaCOI proteins. Our findings identify a functional JA receptor in chickpea and reveal new aspects of JA signaling and perception, which may also be relevant to other plants.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 From combined stress to climate resilience: harnessing the power of a knowledge resource(Current Science Association, 2024) Maitraya, Bharat; Pandey, Prachi; Senthil-Kumar, MuthappaUnderstanding the intricate dynamic impact of combined stresses on plant growth and productivity amidst escalating climate change is one of the most prevalent challenges for today’s plant stress biologists. This commentary emphasizes the necessity of employing a centralized resource to collect and analyse scattered data on combined and individual abiotic and biotic stresses in plants. Introducing the Stress Combinations and their Interactions in Plants Database, we underscore its role in consolidating and comprehending diverse omics datasets and facilitating interdisciplinary research efforts to advance agricultural research.Item Unmasking complexities of combined stresses for creating climate-smart crops(Elsevier B.V., 2024) Pandey, Prachi; Senthil-Kumar, MuthappaUnderstanding the complex challenges that plants face from multiple stresses is key to developing climate-ready crops. We highlight the significance of the Stress Combinations and their Interactions in Plants database (SCIPdb) for studying the impact of stress combinations on plants and the importance of aligning thematic research programs to create crops aligned with achieving sustainable development goals.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 Drought: A context-dependent damper and aggravator of plant diseases(John Wiley & Sons, 2024) Choudhary, Aanchal; Senthil-Kumar, MuthappaDrought dynamically influences the interactions between plants and pathogens, thereby affecting disease outbreaks. Understanding the intricate mechanistic aspects of the multiscale interactions among plants, pathogens, and the environment—known as the disease triangle—is paramount for enhancing the climate resilience of crop plants. In this review, we systematically compile and comprehensively analyse current knowledge on the influence of drought on the severity of plant diseases. We emphasise that studying these stresses in isolation is not sufficient to predict how plants respond to combined stress from both drought and pathogens. The impact of drought and pathogens on plants is complex and multifaceted, encompassing the activation of antagonistic signalling cascades in response to stress factors. The nature, intensity, and temporality of drought and pathogen stress occurrence significantly influence the outcome of diseases. We delineate the drought-sensitive nodes of plant immunity and highlight the emerging points of crosstalk between drought and defence signalling under combined stress. The limited mechanistic understanding of these interactions is acknowledged as a key research gap in this area. The information synthesised herein will be crucial for crafting strategies for the accurate prediction and mitigation of future crop disease risks, particularly in the context of a changing climate.Item Comparative transcriptome profiling reveals differential defense responses among Alternaria brassicicola resistant Sinapis alba and susceptible Brassica rapa(Frontiers Media S.A., 2024) Ahmed, Reshma; Dey, Kuntal Kumar; Senthil-Kumar, Muthappa; Modi, Mahendra Kumar; Sarmah, Bidyut Kumar; Bhorali, PriyadarshiniAlternaria blight is a devastating disease that causes significant crop losses in oilseed Brassicas every year. Adoption of conventional breeding to generate disease-resistant varieties has so far been unsuccessful due to the lack of suitable resistant source germplasms of cultivated Brassica spp. A thorough understanding of the molecular basis of resistance, as well as the identification of defense-related genes involved in resistance responses in closely related wild germplasms, would substantially aid in disease management. In the current study, a comparative transcriptome profiling was performed using Illumina based RNA-seq to detect differentially expressed genes (DEGs) specifically modulated in response to Alternaria brassicicola infection in resistant Sinapis alba, a close relative of Brassicas, and the highly susceptible Brassica rapa. The analysis revealed that, at 48 hpi (hours post inoculation), 3396 genes were upregulated and 23239 were downregulated, whereas at 72 hpi, 4023 genes were upregulated and 21116 were downregulated. Furthermore, a large number of defense response genes were detected to be specifically regulated as a result of Alternaria infection. The transcriptome data was validated using qPCR-based expression profiling for selected defense-related DEGs, that revealed significantly higher fold change in gene expression in S. alba when compared to B. rapa. Expression of most of the selected genes was elevated across all the time points under study with significantly higher expression towards the later time point of 72 hpi in the resistant germplasm. S. alba activates a stronger defense response reaction against the disease by deploying an array of genes and transcription factors involved in a wide range of biological processes such as pathogen recognition, signal transduction, cell wall modification, antioxidation, transcription regulation, etc. Overall, the study provides new insights on resistance of S. alba against A. brassicicola, which will aid in devising strategies for breeding resistant varieties of oilseed Brassica.Item Callus induction and efficient in vitro plant regeneration protocol for Chickpea(Springer Nature Publishing AG, 2024) Jangid, Vinod Kumar; Senthil-Kumar, Muthappa; Chandran, Divya; Sinharoy, SenjutiThe development of an efficient and consistent callus-mediated in vitro regeneration protocol is crucial for biotechnological approaches aimed at improving chickpea, an economically important crop legume. In this study, we assess the effectiveness of callus-mediated regeneration in different chickpea genotypes. Through in vitro screening of explants, we identified the Indian cultivar Pusa 240 as a favourable genotype with higher efficiency of somatic embryogenesis and in vitro plant regeneration. Building upon this finding, we have successfully established two distinct protocols for chickpea callus-mediated somatic embryogenesis, utilizing leaf and hypocotyl explants obtained from the Pusa 240 genotype. These protocols achieved plant regeneration efficiencies of 27% using leaf explants and 46.6 − 66% using hypocotyl explants. Extensive literature review and comparative analysis underscored the superiority of our current protocol. Subsequently, the regenerated plants were successfully acclimatized and transferred to the greenhouse, exhibiting normal phenotypic growth. This detailed regeneration method will provide a valuable resource for chickpea genetic transformations and the generation of large mutant populations where embryogenesis via callus formation is required. The protocol presented here establishes a powerful tool for studying the functional genomics of chickpea plants and lays the foundation for future advancements in this field.