Modified primers for the identification of nonpathogenic Fusarium oxysporum isolates that have biological control potential against Fusarium wilt of cucumber in Taiwan

Colonization of human opportunistic Fusarium oxysporum (HOFo) isolates in tomato and cucumber tissues assessed by a specific molecular marker

Fusarium oxysporum is a large complex cosmopolitan species composed of plant pathogens, human opportunistic pathogens, and nonpathogenic isolates. Many plant pathogenic strains are known based on host plant specificity and the large number of plant species attacked. F. oxysporum is an opportunistic pathogen in humans with a compromised immune system. The objectives of this study were: (1) to develop a specific marker to detect human opportunistic F. oxysporum (HOFo) isolates; (2) to determine whether or not HOFo isolates can colonize and cause disease symptoms in plants; and (3) to assess Taiwan isolates sensitivity to two agro-fungicides. The primer pair, Primer 5/ST33-R, specifically amplifying Taiwan and international reference HOFo isolates was developed and used to detect and assess the distribution of a Taiwan isolate in inoculated tomato plants and tomato and cucumber fruit. Taiwan HOFo isolate MCC2074 was shown to colonize tomato roots, hypocotyls, and cotyledons, but did not show any visible symptoms. Four days after surface inoculation of tomato and cucumber fruit with the same isolate, MCC2074 was detected in the pericarp and locular cavities of both tomato and cucumber fruit and in columella of tomato fruit. Three Taiwan HOFo isolates were found to be moderately sensitive to azoxystrobin and highly sensitive to difenconazole.

A Culture-Independent PCR-Based Assay to Detect the Root Rot Pathogen Fusarium solani Species Complex 11 from Soybean Roots and Soil

Fusarium solani species complex (FSSC) 11 is the primary phylogenetic species of FSSC causing root rot in soybean in the north-central United States. A polymerase chain reaction (PCR)-based assay was developed to identify and differentiate FSSC 11 from the less aggressive FSSC 5 and other Fusarium and Pythium spp. associated with soybean roots. The primer set FSSC11-F and FSSC11-R designed from the RNA polymerase second largest subunit gene yielded the expected amplicon of about 900 bp with DNA from all 22 FSSC 11 isolates tested in PCR. However, it did not produce an amplicon with DNA from 29 isolates of FSSC 5, seven other Fusarium spp., three Pythium spp., and soybean tested in PCR. Furthermore, the primer set successfully detected FSSC 11 from a DNA mixture containing the DNA of FSSC 11, FSSC 5, other Fusarium spp., and soybean. The primer set also detected FSSC 11 from both soil and soybean roots. Additionally, the prevalence of FSSC 11 in soybean roots was determined in five fields in North Dakota by both a culture-independent PCR approach with FSSC11-F and FSSC11-R and a culture-dependent approach. Results from both the culture-dependent and culture-independent approaches with FSSC11-F and FSSC11-R were consistent and revealed the presence of the FSSC 11 in three of five fields sampled.

Use of Comparative Genomics-Based Markers for Discrimination of Host Specificity in Fusarium oxysporum

The polyphyletic nature of many formae speciales of Fusarium oxysporum prevents molecular identification of newly encountered strains based on conserved, vertically inherited genes. Alternative molecular detection methods that could replace labor- and time-intensive disease assays are therefore highly desired. Effectors are functional elements in the pathogen-host interaction and have been found to show very limited sequence diversity between strains of the same forma specialis, which makes them potential markers for host-specific pathogenicity. We therefore compared candidate effector genes extracted from 60 existing and 22 newly generated genome assemblies, specifically targeting strains affecting cucurbit plant species. Based on these candidate effector genes, a total of 18 PCR primer pairs were designed to discriminate between each of the seven Cucurbitaceae-affecting formae speciales When tested on a collection of strains encompassing different clonal lineages of these formae speciales, nonpathogenic strains, and strains of other formae speciales, they allowed clear recognition of the host range of each evaluated strain. Within Fusarium oxysporum f. sp. melonis more genetic variability exists than anticipated, resulting in three F. oxysporum f. sp. melonis marker patterns that partially overlapped with the cucurbit-infecting Fusarium oxysporum f. sp. cucumerinum, Fusarium oxysporum f. sp. niveum, Fusarium oxysporum f. sp. momordicae, and/or Fusarium oxysporum f. sp. lagenariae For F. oxysporum f. sp. niveum, a multiplex TaqMan assay was evaluated and was shown to allow quantitative and specific detection of template DNA quantities as low as 2.5 pg. These results provide ready-to-use marker sequences for the mentioned F. oxysporum pathogens. Additionally, the method can be applied to find markers distinguishing other host-specific forms of F. oxysporumIMPORTANCE Pathogenic strains of Fusarium oxysporum are differentiated into formae speciales based on their host range, which is normally restricted to only one or a few plant species. However, horizontal gene transfer between strains in the species complex has resulted in a polyphyletic origin of host specificity in many of these formae speciales This hinders accurate and rapid pathogen detection through molecular methods. In our research, we compared the genomes of 88 strains of F. oxysporum with each other, specifically targeting virulence-related genes that are typically highly similar within each forma specialis Using this approach, we identified marker sequences that allow the discrimination of F. oxysporum strains affecting various cucurbit plant species through different PCR-based methods.

Development of a TaqMan Probe-Based Insulated Isothermal Polymerase Chain Reaction (iiPCR) Assay for Detection of Fusarium oxysporum f. sp. cubense Race 4

This study developed a novel and inexpensive detection method based on a TaqMan probe-based insulated isothermal polymerase chain reaction (iiPCR) method for the rapid detection of Panama disease caused by Fusarium oxysporum f. sp. cubense (Foc) race 4, which is currently among the most serious fungal vascular diseases worldwide. By using the portable POCKIT™ device with the novel primer set iiFoc-1/iiFoc-2, the Foc race 4 iiPCR assay (including DNA amplification and signal monitoring) could be completed within one hour. The developed Foc race 4 iiPCR assay is thus a user-friendly and efficient platform designed specifically for the detection of Foc race 4. The detection limit of this optimized Foc iiPCR system was estimated to be 1 copy of the target standard DNA as well as 1 fg of the Foc genomic DNA. This approach can serve as a rapid detection method for in planta detection of Foc race 4 in field-infected banana. It was concluded that this molecular detection procedure based on iiPCR has good potential for use as an efficient detection method.