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Background Hyperspectral imaging is emerging as a promising approach for plant disease identification. The large and possibly redundant information contained in hyperspectral data cubes makes deep learning based identification of plant diseases a natural fit. Here, we deploy a novel 3D deep convolutional neural network (DCNN) that directly assimilates the hyperspectral data. Furthermore, we interrogate the learnt model to produce physiologically meaningful explanations. We focus on an economically important disease, charcoal rot, which is a soil borne fungal disease that affects the yield of soybean crops worldwide. Results Based on hyperspectral imaging of inoculated and mock-inoculated stem images, our 3D DCNN has a classification accuracy of 95.73% and an infected class F1 score of 0.87. Using the concept of a saliency map, we visualize the most sensitive pixel locations, and show that the spatial regions with visible disease symptoms are overwhelmingly chosen by the model for classification. We also find that the most sensitive wavelengths used by the model for classification are in the near infrared region (NIR), which is also the commonly used spectral range for determining the vegetative health of a plant. Conclusion The use of an explainable deep learning model not only provides high accuracy, but also provides physiological insight into model predictions, thus generating confidence in model predictions. These explained predictions lend themselves for eventual use in precision agriculture and research application using automated phenotyping platforms.

Modern agriculture, based on biparental crop varieties have contributed tremendously to the world’s food supply. However, the strategy is also being challenged due to stagnation in yield growth, climate change, susceptibility to biotic and abiotic stresses etc. Biparental crossing, the conventional cereal breeding approach, is inherently limited in its ability to fully harness the rich genetic diversity available within a crop species. This limitation stems from the restricted number of parental lines involved, which restricts the pool of desirable traits that can be combined. In contrast, cutting-edge multi-parental crossing strategies possess immense potential for generating superior trait combinations by tapping into a vastly broader genetic pool. However, despite the several advantages of this approach, its full potential has not been adequately exploited. The existing research on the development of multi-parent advanced generation inter-cross (MAGIC) populations in crops such as rice, maize, and sorghum has primarily focused on the populations themselves, lacking robust demonstrations of the potential advantages of this approach over biparental crossing in terms of developing superior crop varieties. This study aimed to develop post-rainy season sorghum genotypes with enhanced yield potential and improved tolerance to drought, shoot fly, and charcoal rot through the utilization and demonstration of a multi-parent crossing approach. 17 founder lines were utilized to generate four 8-way crosses. The performance of the resulting progeny was systematically evaluated across multiple locations. The results revealed that the 8-way cross-derived lines exhibited remarkable superiority in both grain and stover yields, outperforming not only the 2-way and 4-way cross derivatives but also their founder parents. Notably, the 8-way cross-derived lines demonstrated substantial yield advantages of over 70% and 30% in grain and stover production, respectively, compared to the bi-parent crosses. These lines also displayed enhanced drought tolerance and improved resistance against key insect pests and diseases. Specifically, two 8-way cross-derived lines, S22086RV and S22085RV, significantly outperformed the national check cultivar CSV 29R, with nearly 70% and 60% higher grain yields, and over 30% and 15% greater stover yields, respectively. Importantly, these high-performing lines also exhibited exceptional drought stress tolerance, characterized by high transpiration rate, transpiration efficiency, shoot biomass, harvest index, and grain yield coupled with low total water use, as well as resistance against shoot fly (< 15% dead hearts) and charcoal rot (< 10 charcoal rot index). These versatile, stress-resilient lines hold immense promise as valuable genetic resources to drive further crop improvement and the development of superior post-rainy sorghum varieties. This innovative breeding strategy demonstrates significant potential for transforming post-rainy sorghum cultivation, particularly in contexts constrained by limited phenotypic diversity that impedes progress.

The mung bean crop ( Vigna radiata (L.) R. Wilczek) is widely recognized as a key source of pulse food worldwide. However, this crop suffers substantial yield losses due to humid environments, particularly from infestations by the fungal pathogen Macrophomina phaseolina , which causes charcoal rot disease. This infestation results in significant agronomic losses, affecting both the crop’s growth characteristics and overall yield. Previous research suggests that these losses can be mitigated through environmentally friendly soil amendments, such as biochar, as well as by applying various nanofungicides. This study aims to explore the potential of biochar and zinc oxide nanoparticles (ZnONPs) to reduce the severity of charcoal rot disease and enhance the agronomic traits and yield of mung bean plants affected by this disease. The experiment was conducted in triplicate, applying ZnONPs at three concentrations (5, 10, and 20 mg. L − 1 ) via foliar spraying, combined with two levels of biochar (20 g and 40 g per pot). Positive and negative control treatments were also included for comparison. The results demonstrated that applying 40 g of biochar per pot and 20 mg. L − 1 of foliar-applied ZnONPs increased the activities of the anti-oxidative defence enzymes. Additionally, this treatment strategy boosted the plants’ disease resistance mechanisms, leading to lower mortality rates and reduced levels of malondialdehyde (MDA) and hydrogen peroxide (H₂O₂) by 61.7% and 49.23%. Moreover, the treatment positively impacted key growth parameters, increasing total chlorophyll content by 43%, plant height by 47%, and legume count per plant by 80.4%. The application of biochar and ZnONPs also improved seed protein content, reflecting an enhancement in nutritional quality. This study supports the use of biochar and ZnONPs as biostimulants to manage yield losses in mung bean crops affected by charcoal rot disease. The future prospects of using ZnONPs and biochar as treatments in agriculture are promising, as they offer innovative, eco-friendly solutions to enhance crop productivity, improve soil health, and reduce reliance on synthetic chemicals, paving the way for more sustainable and resilient agricultural systems.

Endophytes can induce the defence responses and modulates physiological attributes in host plants during pathogen attacks. In the present study, 127 bacterial endophytes (BEs) were isolated from different parts of healthy soybean plant. Among them, two BEs (M-2 and M-4) resulted a significant antagonistic property against Macrophomina phaseolina, causes charcoal rot disease in soybean. The antagonistic potential was evaluated through dual culture plate assay, where M-4 expressed higher antifungal activity than M-2 against M. phaseolina. The M-4 produces cell wall degrading enzymes viz. cellulase (145.71 ± 1.34 μgmL−1), chitinase (0.168 ± 0.0009 unitmL−1) and β,1–3 endoglucanase (162.14 ± 2.5 μgmL−1), which helps in cell wall disintegration of pathogens. Additionally, M-4 also can produce siderophores, indole-3-acetic acid (IAA) (17.03 ± 1.10 μgmL−1) and had a phosphate solubilization potential (19.89 ± 0.26 μgmL−1). Further, GC–MS profiling of M-4 has been carried out to demonstrate the production of lipophilic secondary metabolites which efficiently suppress the M. phaseolina defensive compounds under co-culture conditions. Bio-efficacy study of M-4 strain shown a significant reduction in disease incidence around 60 and 80% in resistant and susceptible varieties of soybean, respectively. The inoculation of M-4 potentially enhances the physiological attributes and triggers various defence responsive enzymes viz. superoxide dismutase (SOD), phenol peroxidase (PPO), peroxidase (PO) and catalase (CAT). The histopathological study also confirmed that M-4 can reduce the persistence of microsclerotia in root and shoot tissue. Conclusively, M-4 revealed as an efficient biocontrol agent that can uses multifaceted measures for charcoal rot disease management, by suppress the M. phaseolina infection and enhance the physiological attributes of soybean.

Charcoal rot disease, caused by the fungus Macrophomina phaseolina, results in major economic losses in soybean production in southern USA. M. phaseolina has been proposed to use the toxin (-)-botryodiplodin in its root infection mechanism to create a necrotic zone in root tissue through which fungal hyphae can readily enter the plant. The majority (51.4%) of M. phaseolina isolates from plants with charcoal rot disease produced a wide range of (-)-botryodiplodin concentrations in a culture medium (0.14–6.11 µg/mL), 37.8% produced traces below the limit of quantification (0.01 µg/mL), and 10.8% produced no detectable (-)-botryodiplodin. Some culture media with traces or no (-)-botryodiplodin were nevertheless strongly phytotoxic in soybean leaf disc cultures, consistent with the production of another unidentified toxin(s). Widely ranging (-)-botryodiplodin levels (traces to 3.14 µg/g) were also observed in the roots, but not in the aerial parts, of soybean plants naturally infected with charcoal rot disease. This is the first report of (-)-botryodiplodin in plant tissues naturally infected with charcoal rot disease. No phaseolinone was detected in M. phaseolina culture media or naturally infected soybean tissues. These results are consistent with (-)-botryodiplodin playing a role in the pathology of some, but not all, M. phaseolina isolates from soybeans with charcoal rot disease in southern USA.

The soil fungus Macrophomina phaseolina, the charcoal rot disease agent, poses a major threat to cotton fields. In Israel, highly infected areas are also inhabited by the maize pathogen Magnaporthiopsis maydis. This study reveals the relationships between the two pathogens and their impact on cotton sprouts. Infecting the soil 14 days before sowing (DBS) with each pathogen or with M. phaseolina before M. maydis caused a strong inhibition (up to 50–65%) of the sprouts’ development and survival, accompanied by each pathogen’s high DNA levels in the plants. However, combined or sequence infection with M. maydis first led to two distinct scenarios. This pathogen acted as a beneficial protective endophyte in one experiment, leading to significantly high emergence and growth indices of the plants and a ca. 10-fold reduction in M. phaseolina DNA in the sprouts’ roots. In contrast, M. maydis showed strong virulence potential (with 43–69% growth and survival suppression) in the other experiment, proving its true nature as an opportunist. Interestingly, soil inoculation with M. phaseolina first, 14 DBS (but not at sowing), shielded the plants from M. maydis’ devastating impact. The results suggest that the two pathogens restrict each other, and this equilibrium may lead to a moderate disease burst.

Charcoal rot caused by the fungal pathogen Macrophomina phaseolina (Tassi) Goid is one of various devastating soybean (Glycine max (L.) Merr.) diseases, which can severely reduce crop yield. The investigation into the genetic potential for charcoal rot resistance of wild soybean (Glycine soja) accessions will enrich our understanding of the impact of soybean domestication on disease resistance; moreover, the identified charcoal rot-resistant lines can be used to improve soybean resistance to charcoal rot. The objective of this study was to evaluate the resistance of wild soybean accessions to M. phaseolina at the seedling stage and thereby select the disease-resistant lines. The results show that the fungal pathogen infection reduced the growth of the root and hypocotyl in most G. soja accessions. The accession PI 507794 displayed the highest level of resistance response to M. phaseolina infection among the tested wild soybean accessions, while PI 487431 and PI 483660B were susceptible to charcoal rot in terms of the reduction in root and hypocotyl growth. The mean values of the root and hypocotyl parameters in PI 507794 were significantly higher (p < 0.05) than those of PI 487431 and PI 483460B. A analysis of the resistance of wild soybean accessions to M. phaseolina using the root and hypocotyl as the assessment parameters at the early seedling stage provides an alternative way to rapidly identify potential resistant genotypes and facilitate breeding for soybean resistance to charcoal rot.

Charcoal rot causes severe yield loss in mungbean. To sustain the crop health, it is vital to include alleles that may be useful in resisting the charcoal rot disease. Therefore, in the present study, genetic divergence using ISSR primers across six samples were studied for charcoal rot resistance. One resistant and one susceptible cultivars of mung bean namely, WBM 4–34-1–1 and PDM-139, respectively were used in the present investigtion. Leaf samples were treated with an elicitor, Salicyclic acid (SA) at 1 milli molar (mM) and Macrophomina phaseolina was inoculated at 15 DAS and untreated seedlings served as a check. Total genomic DNA was isolated from leaf samples of 15 days old seedlings of both the genotypes and ISSR genotyping was performed with six ISSR primers i. e., UBC- 847, ISSCR 2, ISSCR 5, UBC 825, A9 and C6. The primers UBC-847 and ISSCR-2 were observed to show moderate polymorphism of 15.15%. The UPGMA clustering method differentiated the test samples into three clusters i.e ., Cluster I includes only one sample viz., Bireshwar genotype treated with Salicyclic acid @ 1 mM. Cluster II was the major one that included three samples viz . ., Bireshwar genotype (Control), Samrat genotype (Control) and Samrat genotype of mungbean treated with Salicyclic acid @ 1 mM (SA @1 mM) and Cluster III included two samples viz. Bireshwar treated with salicyclic acid @ 1 mM and inoculated with pathogen (SA@1 mM with Pathogen Inoculated), Samrat genotype treated with salicyclic acid @ 1 mM and inoculated with pathogen (SA@1 mM with Pathogen Inoculated). These findings indicate that the mungbean genotypes used in the present study could enrich the local gene pool and provide information for charcoal rot resistance breeding.

An isolate of Macrophomina phaseolina from muskmelons (Cucumis melo) was reported by Dunlap and Bruton to produce red pigment(s) in melons and in culture in the presence of added glycine, alanine, leucine, or asparagine in the medium, but not with some other amino acids and nitrogen-containing compounds. We explored the generality and mechanism of this pigment production response using pathogenic M. phaseolina isolates from soybean plants expressing symptoms of charcoal rot disease. A survey of 42 M. phaseolina isolates growing on Czapek-Dox agar medium supplemented with glycine confirmed pigment production by 71% of isolates at the optimal glycine concentration (10 g/L). Studies in this laboratory have demonstrated that some pathogenic isolates of M. phaseolina produce the mycotoxin (−)-botryodiplodin, which has been reported to react with amino acids, proteins, and other amines to produce red pigments. Time course studies showed a significant positive correlation between pigment and (−)-botryodiplodin production by selected M. phaseolina isolates with maximum production at seven to eight days. Pigments produced in agar culture medium supplemented with glycine, beta-alanine, or other amines exhibited similar UV-vis adsorption spectra as did pigments produced by (±)-botryodiplodin reacting in the same agar medium. In a separate study of 39 M. phaseolina isolates, red pigment production (OD520) on 10 g/L glycine-supplemented Czapek-Dox agar medium correlated significantly with (−)-botryodiplodin production (LC/MS analysis of culture filtrates) in parallel cultures on un-supplemented medium. These results support pigment production on glycine-supplemented agar medium as a simple and inexpensive in-culture method for detecting (−)-botryodiplodin production by M. phaseolina isolates.

Macrophomina phaseolina is a generalist soil-borne fungus present all over the world. It cause diseases such as stem and root rot, charcoal rot and seedling blight. Under high temperatures and low soil moisture, this fungus can cause substantial yield losses in crops such as soybean, sorghum and groundnut. The wide host range and high persistence of M. phaseolina in soil as microsclerotia make disease control challenging. Therefore, understanding the basis of the pathogenicity mechanisms as well as its interactions with host plants is crucial for controlling the pathogen. In this work, we aim to describe the general characteristics and pathogenicity mechanisms of M. phaseolina , as well as the hosts defense response. We also review the current methods and most promising forecoming ones to reach a responsible control of the pathogen, with minimal impacts to the environment and natural resources.