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Among the many biotic factors with adverse effects on Solanum lycopersicum (tomato), diseases caused by fungi, viruses and nematodes are notable. Since the genome of S. lycopersicum became available, efforts have continued to identify the genes and proteins associated with the plant defence activity. One such gene family belongs to TIR-NBS-LRR (TNL), a subfamily of larger NBS-LRR genes. In total, 27 full-length TNLs were identified via genome wide analysis. Four pairs of segmental duplication events were observed involving different pairs of chromosomes, except the pairing of Solyc02g082050-Solyc02g032650, which were both present on chromosome 2. More than twenty nine percent (29.63%) of the genes were localised on chromosome 1 alone. Hormone-mediated biotic stress-responsive cis-regulatory elements were detected for methyl-jasmonate, salicylic acid (TCA motif) and ethylene (ERE motif). Differential gene expression was observed for many genes under different plant tissues and biotic stresses. The upregulation of many genes including SlBS4 was observed against Alternaria solani attacks in the disease tolerant varieties. Altogether, the results suggested that TNLs play a significant role in plant defence under biotic stress.

Abstract Early blight (EB), caused by Alternaria solani, is a serious problem in tomato production. Plant growth-promoting rhizobacteria promote plant growth and inhibit plant disease. The present study explored the bio-efficacy of synergistic effect of rhizobacterial isolates and ginger powder extract (GPE) against tomato EB disease, singly and in combination. Six fungal isolates from symptomatic tomato plants were identified as A. solani on the basis of morphological features i.e., horizontal septation (6.96 to 7.93 µm), vertical septation (1.50 to 2.22 µm), conidia length (174.2 to 187.6 µm), conidial width (14.09 to 16.52 µm), beak length (93.06 to 102.26 µm), and sporulation. Five of the twenty-three bacterial isolates recovered from tomato rhizosphere soil were nonpathogenic to tomato seedlings and were compatible with each other and with GPE. Out of five isolates tested individually, three isolates (St-149D, Hyd-13Z, and Gb-T23) showed maximum inhibition (56.3%, 48.3%, and 42.0% respectively) against mycelial growth of A. solani. Among combinations, St-149D + GPE had the highest mycelial growth inhibition (76.9%) over the untreated control. Bacterial strains molecularly characterized as Pseudomonas putida, Bacillus subtilis, and Bacillus cereus and were further tested in pot trials through seed bacterization for disease control. Seeds treated with bacterial consortia + GPE had the highest disease suppression percentage (78.1%), followed by St-149D + GPE (72.2%) and Hyd-13Z + GPE (67.5%). Maximum seed germination was obtained in the bacterial consortia + GPE (95.0 ± 2.04) followed by St-149D + GPE (92.5 ± 1.44) and Hyd-13Z + GPE (90.0 ± 2.04) over control (73.8 ± 2.39) and chemical control as standard treatment (90.0 ± 2). Ginger powder extracts also induce the activation of defence-related enzymes (TPC, PO, PPO, PAL, and CAT) activity in tomato plants. These were highly significant in the testing bacterial inoculants against A. solani infection in tomato crops.

Early blight (EB) disease, caused mainly by Alternaria solani, is an economic threat to potato and tomato production worldwide. Thus, accurate and sensitive detection of the fungal pathogen of this disease in plants at the early infection stage is important for forecasting EB epidemics. In this study, we developed an RNA-based method that enables highly accurate and sensitive A. solani detection in a whole potato leaf at a single spore level based on quantitative real-time polymerase chain reaction (qPCR). We discovered jg1677, a highly expressed gene whose full-length coding sequence is very specific for A. solani, by analyzing A. solani transcripts isolated from enhanced high throughput transcriptome of infected potato leaves by A. solani and using the National Center for Biotechnology Information’s basic local alignment search tool. The specificity of the primers derived from jg1677 was determined using 22 isolates of common potato pathogens, including seven Alternaria isolates. Detecting jg1677 transcripts with qPCR is 1,295 times more sensitive than detecting genomic DNA. In addition, the expression pattern of jg1677 at different infection stages was determined by qPCR. What is more, jg1677 was expressed relatively stable between 15 and 35°C in infected leaves, and its expression was virtually unaffected in isolated leaves left at room temperature for 24 h. Our work provides a much more sensitive and accurate method compared to conditional DNA-based ones, permitting a very early diagnosis of EB and lowering the risk of EB epidemics.

In this study, efficiency of the endophytic fungal isolate Msh5 was evaluated on promoting tomato plant growth and controlling Alternaria alternata, the causal agent of early blight in tomatoes. Morphological and molecular (ITS and tub2 sequences) analyses revealed that the fungal isolate, Msh5, was Acrophialophora jodhpurensis (Chaetomium jodhpurense Lodha). This beneficial fungus was capable of producing indole-3-acetic acid (IAA), urease, siderophore, extracellular enzymes, and solubilized phosphate. Under laboratory conditions, the Msh5 isolate of A. jodhpurensis inhibited A. alternata growth in dual culture, volatile and non-volatile metabolites assays. The supernatant of this endophytic fungus was capable of reducing spore germination and altering the hyphal structure of A. alternata and the spores produced germ tubes showed vacuolization and abnormal structure compared to the control. Also, the effect of A. jodhpurensis on plant growth parameters (such as shoot and root weight and length) and suppressing A. alternata was investigated in vivo via seed inoculation with spores of A. jodhpurensis using 1% sugar, 0.5% carboxymethyl cellulose (CMC) or 0.5% molasses solution as stickers. Colonization of tomato roots by the endophytic fungus resulted in significant increasing plant growth parameters and reduction in the progress of the diseases caused by A. alternata compared to the controls. Among the different coating materials used as stickers, sugar was found to be the most effective for enhancing plant growth parameters and decreasing the disease progress. Therefore, A. jodhpurensis isolate Msh5 can be suggested as a potential biofertilizer and biocontrol agent for protecting tomato plants against A. alternata.

Resistance gene analogs (RGAs) comprising NBS-LRR gene family members are considered prominent candidates in the development of disease-resistant genotypes. NBS-LRR gene family comprised a very large number of genes; therefore, members of one subfamily TIR-NBS-LRR (TNL) are identified in the present study from Solanum tuberosum genome, followed by their bioinformatics characterization. The study identified a total of 44 genes encoding 60 TNL transcripts with two prominent clusters at chromosome 1 and chromosome 11. Expression analysis of 14 TNL genes after Alternaria solani infection at 1, 2, 3, 5, and 7 days post inoculation in two disease-tolerant varieties, Kufri Jyoti and Kufri Pukhraj, and one relatively susceptible variety, Kufri Chandramukhi, showed differential expression of many genes including a high expression (>15-fold) of StTNLC6G2T1 and StTNLC11G9T1. Functional characterization of one such gene, StTNLC7G2, reveals involvement in the generation of reactive oxygen species under A. solani attack, implicating its putative role in plant defense via hypersensitive response.

Silver nanoparticles have gained considerable interest in recent decades due to their antimicrobial activity and are used in water disinfection, wound healing, food packaging, and plant protection. This study tested the potential of silver nanoparticles synthesized using the neem (Azadirachta indica) leaf extract against Alternaria solani causes early blight disease in tomato plants. The pathogen was isolated from infected tomato plants and identified using morphological and molecular features. The results showed significant variation among isolates. Isolates, Shk-1 and Ksr-1 were highly pathogenic, causing up to 80% disease incidence. The potential of silver nanoparticles against each isolate was determined using different concentrations of silver nanoparticles. During in vitro and in vivo experiments, the growth inhibition rate of the pathogen was 70–100% at 50 ppm. Lower concentrations of silver nanoparticles (5 and 10 ppm) increased phenolics, PO, PPO, and PAL production by more than 50% as compared to the untreated control. These defensive mechanisms clearly demonstrate the fungicidal potential of AgNPs and recommend their utilization in different crop protection programs.

Potato (Solanum tuberosum L.), an important food crop in the world, is susceptible to many fungal pathogens including Alternaria solani and Fusarium oxysporum causing Fusarium wilt and early blight diseases. Mycoparasitic fungi like Trichoderma encode chitinases, cell wall degrading enzymes, with high antifungal activity against a wide range of phytopathogenic fungi. In this study, a binary vector harboring endochitinase gene of ~1,000 bp was constructed and used to transform potato nodes through Agrobacterium-mediated transformation. Out of several primary transformants, two transgenic potato lines were verified for transgene insertion and integration by Southern blot. In a pot experiment for Fusarium resistance, the transgenic potato lines didn’t show any symptoms of disease, instead they remained healthy post infection. The transgenic potato lines exhibited 1.5 fold higher mRNA expression of endochitinase at 7 days as compared to 0 day post fungus inoculation. It was evident that the mRNA expression decreased over days of inoculation but was still higher than at 0 day and remained stable upto 30 days post inoculation. Similarly, for A. solani infection assay, the mRNA expression of the endochitinase gene was 3 fold higher 7 days post inoculation compared to expression at 0 day. Although the expression decreased by1.2 fold during subsequent days post infection, it remained stable for 30 days, suggesting that protection in transgenic potato plants against fungal pathogens was achieved through an increase in endochitinase transcript.

Early blight caused by Alternaria solani (Ell. and Mart.) is one of the most important economic diseases, which caused considerable loss in their yield and quality under Egyptian conditions. Aim the research was to study the relationship between climate change and disease severity for prediction in future seasons. Disease severity was recorded for three growing periods i.e. summer (May. to Aug), autumn (Jul. to Oct) and winter (Nov. to Mar.), at three governorates (Behira, Ismailia, and Assuit) during growing seasons 2016/2017-2017/2018. Severity of early blight disease on tomato has been predicted by regression estimated accumulative disease severity values during 2007/2008 to 2015/2016 season and average max and min temperature and humidity through these seasons. Prediction of disease has been formed as Y= b0+b1x1+b2x2+.......... bqxq. Three models were created to describe the severity disease by multiple regressions (MINITAB® program). The highest value of early blight disease was recorded through season 2017/2018, while the lowest value was recorded during season 2016/2017. Also, highly disease severity was estimated during summer period compared with autumn and winter growing periods, but through winter growing period was the least severity and moderately severity estimated in the autumn growing period. Influence of environmental conditions on the severity of early blight disease during seasons from 2007/2008 to 2015/2016, in Behira governorate, the highest disease severity was showed in season 2010-2011, and the lowest disease was in season 2012-2013, but in Ismailia governorate, highest disease severity was estimated in season 2010-2011and lowest disease was recorded in season 2013-2014 and in Assuit governorate, the highest value of disease was in season 2010-2011, and the lowest value was in season 2013-2014. For Forecasting, significantly differences noticed between disease severity through 2020/2030, 2030/2040 and 2040/ 2050s seasons compared with 2008/2018s seasons and thier relation with climate change in tested governorates, where severity of tomato early blight disease was icreased from 11.8% during 2008/2018s seasons to 2040/ 2050s seasons 15.4% during at Behira governorate, from 18.8% during 2008/2018s seasons to 2040/ 2050s seasons 36.3% during at Ismailia governorate and from 18.8% during 2008/2018s seasons to 2040/ 2050s seasons 40.4% during at Assuit governorate with slight change in maximum or minimum temperatures and percentage of relative humidity.

Tomato (Solanum lycopersicum L.) is among the most important vegetable crops worldwide. Early blight disease, caused by Alternaria solani, is a destructive foliar disease of tomato and other Solanaceae species. Herein, we investigated the in vitro antifungal properties of gallic acid and two of its derivatives (syringic and pyrogallic acids) against A. solani during 2019 and 2020 seasons. The physiological and biochemical effects of these compounds on infected tomato plants were also investigated using the whole plant bioassay. The in vitro investigation showed that all tested compounds showed fungistatic action and inhibited the mycelial radial growth of A. solani in a dose-dependent manner. In two separate pot-experiments, those compounds efficiently suppressed the development of the disease symptoms and area under disease progress curve (AUDPC), without any phytotoxic effects on the treated tomato plants. Additionally, all tested compounds positively enhanced the biochemical traits of treated plants including the chlorophyll content, the total soluble phenolics, the total soluble flavonoids, and the enzymatic activities of catalase, peroxidase, and polyphenol oxidase during 2019 and 2020 seasons. Moreover, the treatment with gallic acid and its derivatives significantly increased all yield components of A. solani-infected tomato plants such as the total number of flowers and fruits, and the fruit yield for each tomato plant in both experiments. Considering the fungitoxicity of phenolic acids against A. solani with no phytotoxicity on treated tomato plants, we believe that gallic acid and its derivatives might be a sustainable eco-friendly control strategy to reduce the usage of chemical fungicides partially or entirely against A. solani particularly, and fungal diseases in general.

The reaction of 21 tomato varieties and genotypes to alternaria blight were evaluated in greenhouse and field conditions. Genotypes and varieties were inoculated with of this pathogen artificially in both experiments. After inoculation, disease characteristics such as disease index, area under disease progress curve (AUDPC), percent of dried flower and yield in the field and disease index, percent of infected leaves and surfaces of blight on leaves in greenhouse were recorded. Results of greenhouse experiment showed that varieties and genotypes including Super 2270 King stone, Kallgi and 8403 had the least infection to disease. On the other hand, Imperial variety and 8406 genotype exhibited the highest amount of infection. Varieties in the field experiment, including Super 2270, King stone, Early urbano VF, and 8402 genotype, showed the least infection and genotypes like 8405, 8406, 8407 and Peto early ch variety had the highest amount of infection. In both experiments Super 2270, King stone and Early urbano VF varieties were found resistant to be this pathogen, but 8402 genotype was resistant only in the field and 8403 genotype and Kallgi variety were resistant only under greenhouse condition. Soria variety showed a considerable disease spot in both experiment but could produce the highest means of yield about 91.64 ton/ha. in the field, compared to other varieties and genotypes. Hence it is assumed to be the tolerant variety.

This study investigated both spectrum and texture features for detecting early blight disease on eggplant leaves. Hyperspectral images for healthy and diseased samples were acquired covering the wavelengths from 380 to 1023 nm. Four gray images were identified according to the effective wavelengths (408, 535, 624 and 703 nm). Hyperspectral images were then converted into RGB, HSV and HLS images. Finally, eight texture features (mean, variance, homogeneity, contrast, dissimilarity, entropy, second moment and correlation) based on gray level co-occurrence matrix (GLCM) were extracted from gray images, RGB, HSV and HLS images, respectively. The dependent variables for healthy and diseased samples were set as 0 and 1. K-Nearest Neighbor (KNN) and AdaBoost classification models were established for detecting healthy and infected samples. All models obtained good results with the classification rates (CRs) over 88.46% in the testing sets. The results demonstrated that spectrum and texture features were effective for early blight disease detection on eggplant leaves.