First specific detection and validation of tomato wilt caused by Fusarium brachygibbosum using a PCR assay

Tomato wilt is a widespread soilborne disease of tomato that has caused significant yield losses in many tomato growing regions of the world. Previously, it was reported that tomato wilt can be caused by many pathogens, such as Fusarium oxysporum, Ralstonia solanacearum, Ralstonia pseudosolanacearum, Fusarium acuminatum, and Plectosphaerella cucumerina. In addition, we have already reported that Fusarium brachygibbosum caused symptomatic disease of tomato wilt for the first time in China. The symptoms of tomato wilt caused by these pathogens are similar, making it difficult to distinguish them in the field. However, F. brachygibbosum specific identification method has not been reported. Therefore, it is of great importance to develop a rapid and reliable diagnostic method for Fusarium brachygibbosum to establish a more effective plan to control the disease. In this study, we designed F. brachygibbosum-specific forward primers and reverse primers with a fragment size of 283bp located in the gene encoding carbamoyl phosphate synthase arginine-specific large chain by whole genome sequence comparison analysis of the genomes of eight Fusarium spp.. We then tested different dNTP, Mg2+ concentrations, and annealing temperatures to determine the optimal parameters for the PCR system. We evaluated the specificity, sensitivity and stability of the PCR system based on the optimized reaction system and conditions. The PCR system can specifically identify the target pathogens from different fungal pathogens, and the lower detection limit of the target pathogens is at concentrations of 10 pg/uL. In addition, we can accurately identify F. brachygibbosum in tomato samples using the optimized PCR method. These results prove that the PCR method developed in this study can accurately identify and diagnose F. brachygibbosum.

Development of a multiplex PCR assay for the detection of tomato wilt caused by co-infection of Fusarium brachygibbosum, Fusarium oxysporum, and Ralstonia solanacearum based on comparative genomics

Tomato is widely consumed worldwide as fresh or processed food products. However, soil-borne diseases of tomato plants caused by co-infection of various pathogens result in great economic losses to the tomato industry. It is difficult to accurately identify and diagnose soil-borne diseases of tomato plants caused by pathogen complexes. In this study, we investigated field diseases of tomato plants by pathogen isolation and molecular identification and found that tomato wilt was caused by co-infection of Fusarium brachygibbosum, Fusarium oxysporum, and Ralstonia solanacearum. Therefore, the development of a method for simultaneous detection of DNA from Fusarium brachygibbosum, Fusarium oxysporum, and Ralstonia solanacearum can efficiently and accurately monitor disease development at different growth stages of tomato plants. In this study, we performed a comparative genomic analysis of Fusarium brachygibbosum, Fusarium oxysporum, and Ralstonia solanacearum, and determined the primer sets for simultaneous detection of DNA from these target pathogens. Then, we tested the reagent and condition parameters of multiplex PCR, including primers, dNTP and Mg2+ concentrations, and the annealing temperatures, to determine the optimal parameters of a multiplex PCR system. We evaluated the specificity, sensitivity and stability of the multiplex PCR system based on the optimized reaction conditions. The multiplex PCR system can specifically identify 13 target pathogens from 57 different fungal and bacterial pathogens, at the lower detection limit of the three target pathogens at concentrations of 100pg/ul. In addition, we can accurately identify the three pathogens in tomato plants using the optimized multiplex PCR method. These results demonstrated that the multiplex PCR method developed in this study can simultaneously detect DNA from Fusarium brachygibbosum, Fusarium oxysporum, and Ralstonia solanacearum in a single PCR to accurately identify and diagnose the pathogen causing tomato wilt.

Mutation introduced in DDTFR10/A gene of ethylene response element-binding protein (EREBP) family through CRISPR/Cas9 genome editing confers increased Fusarium wilt tolerance in tomato

We investigated the role of the DDTFR10/A gene of the ethylene response element-binding protein (EREBP) family through the CRISPR/Cas9 genome editing approach. The associated role of this gene in tomato fruit ripening was known. The involvement of ripening-regulatory proteins in plant defense has been documented; therefore, to find the involvement of the DDTFR10/A gene in host susceptibility, we introduced the mutation in DDTFR10/A gene through CRISPR/cas9 in the genome of the tomato plant. The 50% biallelic and 50% homozygous mutations were observed in the T0 generation. The CRISPR/Cas9 edited plants showed 40% reduced symptoms of Fusarium wilt compared to control plants (non-edited). The DDTFR10/A gene expression in tomato plants was evaluated against biotic (Fusarium wilt) and abiotic (salinity) stresses, and the upregulated expression of this gene was found under both challenges. However, a comparative increase in DDTFR10/A gene expression was observed in tomato plants upon inoculation with Fusarium oxysporum f. sp. lycopersici. The phenotypic assay performed on edited tomato plants demonstrated the role of the DDTFR10/A gene in contributing toward susceptibility against Fusarium wilt.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-022-01273-6.

lycopersici induced tomato wilt

Wilt disease, caused by Fusarium oxysporum. f. sp. lycopersici, is a global threat to tomato production that needs to be addressed seriously. The current research envisages the use of two self-compatible Bacillus strains, Bacillus tequilensis PKDN31 and Bacillus licheniformis PKDL10, in a combinatorial approach. The spent supernatant of liquid cultures from strains PKDN31 and PKDL10 showed in vitro antifungal activity against Fusarium sp. attaining an inhibition percentage of 95.33% and 96.54%, respectively. The bacterial isolates lytic activity against Fusarium oxysporum was evaluated by scanning electron microscopic analysis and lytic enzyme production of amylase, lipase, protease and β-1,3 glucanase. Furthermore, PKDN31 and PKDL10 produced siderophores and had root colonizing ability that enhanced the biocontrol efficiency. Combined in vivo inoculation of Bacillus tequilensis PKDN31 and Bacillus licheniformis PKDL10 on tomato seeds revealed that the strains could induce systemic resistance in tomato against Fusarium oxysporum. f. sp. lycopersici by increasing defence enzymes such as β-1,3 glucanase, polyphenol oxidase, peroxidase, phenylalanine ammonia-lyase, chitinase, and total phenol accumulations. Pot culture experiments also proved the biocontrol efficacy of the above dual culture supplementation as this treatment displayed a better growth as well as defense against Fusarium challenge compared to the controls. The obtained results suggest that rhizobacterial isolates could be employed as systemic resistance inducers and biocontrol agents in tomato plants to protect against Fusarium wilt disease.