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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 Novel method for rapid screening of chickpea for combined dry root rot disease and osmotic stress(Springer Nature Publishing AG, 2026) Ranjan, Shubhashish; Chavan, Chaitali Narendra; Senthil-Kumar, MuthappaChickpea (Cicer arietinum L.), confronts substantial challenges from the emerging pathogenic fungus Macrophomina phaseolina (Tassi) Goid, causing dry root rot (DRR) disease. Chickpea plants severely affected by combined DRR and drought stress. Currently sick plot and sick pot method are utilized for germplasm screening to identify tolerant genotypes. These methods are time-consuming; therefore, we propose a novel methodology for the rapid screening of chickpea under combined DRR and osmotic stress conditions. This chapter introduces an adept high-throughput phenotyping methodology, conducted within controlled laboratory conditions, aiming to investigate the interaction between osmotic stress and DRR disease in chickpea crops. The methodology employs an innovative pouch technique for screening combined stress, providing a streamlined temporal investigation process and precise control over stress parameters. The incorporation of polyethylene glycol (PEG) enables the simultaneous imposition of osmotic stress alongside pathogen infection, making the methodology versatile for studying combined stress scenarios. This approach fills a gap in concurrent stress imposition techniques, enhancing germplasm screening by identifying genotypes with varying susceptibility and resistance levels. Thus, we suggest use of high-throughput phenotyping in combination genome-wide association study (GWAS) can take combined stress resistance breeding in chickpea at next level to combat food security and climate change.Item A blotting paper technique for the screening of chickpea genotypes against dry root rot disease(Springer Nature Publishing AG, 2026) Durgadevi, Athimoolam; Pandey, Prachi; Senthil-Kumar, MuthappaDry root rot (DRR) disease is a major threat to chickpea production across the world. This disease is caused by a soil-borne necrotrophic fungal pathogen, Macrophomina phaseolina. The use of disease-resistant varieties paves the way to conquer the disease spread. Though chickpea germplasm with rich genetic diversity is available around the world, its response to DRR is still unexplored. In turn, this demands screening and identification of resistant genotypes for crop protection against the disease. Here we describe an improved blotting paper technique for the large-scale screening of chickpea genotypes for DRR resistance. The method is quick, cost-effective, less labour-intensive, and thus optimized for high-throughput screening and can be efficiently used to screen a large number of chickpea genotypes for resistance against DRR.Item TAIL-PCR for the recovery of Tnt1 flanking sequences in chickpea: a tool for functional genomics studies(Springer Nature Publishing AG, 2026) Chauhan, Chetan; Ranjan, Shubhashish; Jangid, Vinod Kumar; Sinharoy, Senjuti; Senthil-Kumar, MuthappaThermal asymmetric interlaced polymerase chain reaction (TAIL-PCR) is a powerful technique for amplifying genomic regions flanking Tnt1-retortransposon insertions in plants. Here, we present a TAIL-PCR protocol for amplifying Tnt1-flanking genomic sequences in chickpea using Tnt1-transformed hairy roots as the starting material. The amplified products can be cloned and sequenced for the precise mapping of Tnt1-integration sites in the chickpea genome. This method enables the functional characterization of chickpea genes governing root-specific traits and can be easily adapted for flanking sequence tag recovery in chickpea Tnt1-mutant populations.Item A method for isolation and transfection of arabidopsis protoplast for sucrose feeding assay(Springer Nature Publishing AG, 2026) Anjali, Anjali; Senthil-Kumar, MuthappaProtoplasts serve as a powerful system to study various plant physiological processes and to understand crucial signaling pathways within the plant system. The isolation of Arabidopsis protoplasts is a well-established technique and being utilized for wide range of assays. The method described herein includes the precise cutting of Arabidopsis leaves using extraction buffer containing cellulase and macerozyme. Further we present a polyethylene glycol [PEG]-mediated protoplast transformation method. Here, we have elucidated the methodology for isolation of protoplast for the AtSWEET-mediated sucrose uptake assay in control, and Pseudomonas syringe pv tomato DC3000 (Pst DC3000) treated leaves by utilizing GC/MS analysis. Our approach includes certain modifications to the previously published protoplast isolation technique, streamlining the process and providing a more accessible alternative to the highly specialized Xenopus oocyte uptake assay.Item Plant biotic stress: tools and techniques for crop protection(Springer Nature Publishing AG, 2026) Acharya, Krishna Ramakrishnan; Chilakala, Aswin Reddy; Senthil-Kumar, MuthappaAs climate change continues to impact crop yields, developing strategies to enhance plant tolerance to biotic stress has become increasingly important. This requires a thorough evaluation of the tools and methodologies used to manipulate and study biotic stress tolerance. It is crucial to comprehensively understand both conventional and modern techniques, as well as their effectiveness in addressing the specific needs of the crop under study. Detecting diseases at the early stages of plant development can prevent significant losses in large-scale cultivations. Two broad approaches commonly used to mitigate biotic stresses are eliminating causative agents such as fungi, bacteria, nematodes, viruses, or pests, and imparting resistance to the plant. Although there are similarities in the tools and techniques used to address different biotic stresses, each scenario requires dedicated case studies. It is also essential to stay up to date with the latest developments in plant biotechnology to incorporate a cross-disciplinary approach in conducting and validating experiments. This chapter provides an overview of methods covered in this book ranging from molecular breeding to nondestructive techniques that help achieve the goal of safeguarding plant health.Item Extracellular acidification assay to evaluate the effectiveness of antifungal agents on the pathogenicity of Macrophomina phaseolina(Springer Nature Publishing AG, 2026) Acharya, Krishna Ramakrishnan; Chilakala, Aswin Reddy; Senthil-Kumar, MuthappaMacrophomina phaseolina is a fungus that causes dry root rot disease and considerable yield loss worldwide. Fungi exhibit various ways of absorbing nutrients through their plasma membrane, such as free or facilitated diffusion, diffusion channels, or active transport. Glucose, as a preferred carbon source, activates the plasma membrane H+-ATPase, resulting in the release of protons. Consequently, the protons, along with the organic acid metabolites released into the extracellular environment, acidify the cell surroundings. This decrease in pH cues the fungus to shift from saprotrophic to necrotrophic growth, facilitating host invasion. Sustainable dry root rot disease management often relies on the employment of antifungal agents from various biological sources. Despite the discovery of numerous antifungal agents, only a limited number have been evaluated for their efficacy against this phytopathogenic fungus. This scarcity of testing is primarily due to the limitations of existing methods, which often lack standardisation and reproducibility. This chapter introduces a rapid and sensitive method to assess the antifungal activity of various agents against M. phaseolina. By measuring extracellular pH changes after treatment in the presence of a nutrient source, we can determine the inhibitory concentrations of these agents and evaluate their potential for controlling fungal pathogenicity in 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.