Biocontrol of wilt disease complex of pea using Pseudomonas fluorescens and Rhizobium sp.

Biocontrol of wilt disease complex of pea caused by the root-knot nematode Meloidogyne incognita and Fusarium oxysporum f. sp. pisi was studied on pea (Pisum sativum L.) using plant growth-promoting rhizobacterium Pseudomonas fluorescens and root nodule bacterium Rhizobium sp. Inoculation of M. incognita and F.oxysporum alone caused significant reductions in plant growth over un-inoculated control. Reduction in plant growth caused by M. incognita was statistically equal to that caused by F. oxysporum. Inoculation of M. incognita plus F. oxysporum together caused a greater reduction in plant growth than the sum of damage caused by these pathogens singly. Inoculation of P. fluorescens and Rhizobium sp. individually or both together increased plant growth in pathogen inoculated and un-inoculated plants. Inoculation of P. fluorescens to pathogen-inoculated plants caused a greater increase in plant growth than caused by Rhizobium sp. Application of Rhizobium plus P. fluorescens caused a greater increase in plant growth than caused by each of them singly. Inoculation of P.fluorescens caused higher reduction in galling and nematode multiplication than caused by Rhizobium sp. Use of Rhizobium plus P. fluorescens caused higher reduction in galling and nematode multiplication than their individual inoculation. Plants inoculated with both pathogens plus Rhizobium showed less nodulation than plants inoculated with single pathogen plus Rhizobium. Inoculation of Rhizobium plus P. fluorescens resulted in higher root-nodulation than inoculated only with Rhizobium. Wilting indices were 4 and 5, respectively, when plants were inoculated with F. oxysporum and F. oxysporum plus M. incognita. Wilting indices were reduced maximum to 1 and 2, respectively, when plants inoculated with F.oxysporum and plants with both pathogens were treated with P. fluorescens plus Rhizobium.     

Evaluation of an enzyme-linked immunosorbent assay for detection of Mycosphaerella pinodes in pea seeds

A polyclonal antiserum was raised against soluble mycelial extracts of Mycosphaerella pinodes aiming at pathogen detection in infected pea seeds by ELISA. When tested against the homologous antigen, it allowed the detection of 5 ng fungal soluble protein ml^-1 buffer, by double-antibody sandwich ELISA (DAS-ELISA). Positive reactions were obtained with isolates of M. pinodes of wide geographical origins but also with all tested isolates of Ascochyta pisi and Phoma medicaginis var. pinodella, two closely related pathogens forming with the target organism the Ascochyta complex. Out of the 11 other genera of pea seed-borne fungi tested, only two (Alternaria sp. and Stemphylium sp.) cross-reacted strongly by both antigen-coated plate (ACP-ELISA) and DAS-ELISA. Cross-absorption of the crude antiserum could not lead to a species-specific antiserum; however, a combination of P. medicaginis var. pinodella and Stemphylium sp. antigens resulted in an antiserum preferentially recognising A. pisi and M. pinodes. The cross-absorbed antiserum detected 50 and 500 ng of fungal protein ml^-1 buffer and healthy seed extracts respectively. DAS-ELISA proved suitable for the detection and quantification of M. pinodes in infected pea seeds tested singly.     

Origin of pisatin demethylase (PDA) in the genus Fusarium

Host specificity of plant pathogens can be dictated by genes that enable pathogens to circumvent host defenses. Upon recognition of a pathogen, plants initiate defense responses that can include the production of antimicrobial compounds such as phytoalexins. The pea pathogen Nectria haematococca mating population VI (MPVI) is a filamentous ascomycete that contains a cluster of genes known as the pea pathogenicity (PEP) cluster in which the pisatin demethylase (PDA) gene resides. The PDA gene product is responsible for the detoxification of the phytoalexin pisatin, which is produced by the pea plant (Pisum sativum L.). This detoxification activity allows the pathogen to evade the phytoalexin defense mechanism. It has been proposed that the evolution of PDA and the PEP cluster reflects horizontal gene transfer (HGT). Previous observations consistent with this hypothesis include the location of the PEP cluster and PDA gene on a dispensable portion of the genome (a supernumerary chromosome), a phylogenetically discontinuous distribution of the cluster among closely related species, and a bias in G + C content and codon usage compared to other regions of the genome. In this study we compared the phylogenetic history of PDA, beta-tubulin, and translation elongation factor 1-alpha in three closely related fungi (Nectria haematococca, Fusarium oxysporum, and Neocosmospora species) to formally evaluate hypotheses regarding the origin and evolution of PDA. Our results, coupled with previous work, robustly demonstrate discordance between the gene genealogy of PDA and the organismal phylogeny of these species, and illustrate how HGT of pathogenicity genes can contribute to the expansion of host specificity in plant-pathogenic fungi.     

Influence of pea-root exudates on germination of conidia and chlamydospores of physiologic races of Fusarium oxysporum f. pisi

Sterile root exudates from wilt susceptible and wilt resistant pea cultivars showed no differential effects on spore germination of Fusarium oxysporum Schl. f.pisi (Linf.) Snyd. & Hans, races 1 and 2 which could be correlated with the pathogenicity of a particular isolate to a given cultivar. Uniformly high percentages of germination were obtained with conidia of the two races in aseptic shake culture with exudates collected from resistant or susceptible plants of various ages. Chlamydospores of the two races incubated with exudates under sterile conditions germinated to uniformly high levels irrespective of exudate origin. Conidia and chlamydospores of Fusarium solani (Mart.) Sacc. f. pisi (Jones) Snyd. & Hans., used for comparative purposes, also germinated to high levels in the presence of exudate solutions of all cultivars. Non-specific germination of the two races of F. oxysporum f. pisi occurred in soil when the exudates were supplied to populations of chlamydospores via diffusion units. Germination was lower than that recorded under sterile conditions and was rapidly followed by germling lysis.     

Effect of Mannich bases on some plant pathogenic fungi

3-(2-Pyridyl)-3-iminoisatin, 1-piperidinomethyl-3-(2-pyridyl)-3-iminoisatin, and 1-acetyl-3-(2-pyridyl)-3-iminoisatin affect spore germination ofAlternaria alternata, A. carthemi, Curvularia lunata, Fusarium oxysporum f.sp.cieri andF. udum and influence the development of powdery mildew (Erysiphe pisi) on pea under glasshouse condition as well as conidial germination ofE. pisi on excised pea leaves. Spore germination was inhibited in the sequence 1-acetyl-3-(2-pyridyl)-3-iminoisatin > 1-piperidinomethyl-3-(2-pyridyl)-3-iminoisatin > 3-(2-pyridyl)-3-iminoisatin followed the order accordingly. The powdery mildew development and conidial germination ofE. pisi 1-piperidinomethyl-3-(2-pyridyl)-3-iminoisatin > 1-acetyl-3-(2-pyridyl)-3-iminoisatin > 3-(2-pyridyl)-3-iminoisatin. The chemicals were compared with commonly used antifungal fungicides.     

Common Antigen(s) in Cotton to Fusarium oxysporum f. sp. vasinfectum

Antigen-antibody reactions in agar gel, as demonstrated by the double diffusion technique, between cotton seed globulins and the antisera specific to each of the tested Fusarium oxysporum f. sp. vasinfectum isolates as well as the antiserum of F. moniliforme revealed that all the tested antisera of F. oxysporum f. sp. vasinfectum reacted with seed globulins except the Menoufi cultivar globulins. No precipitin lines were detected in the reaction between the antigenof the cotton cultivar Acala SJ2 versus the antiserum of P10 isolate. The 5 cultivars behaved differently with each fungal antiserum to the extent that they could be distinguished accordingly. When the seed globulins of the susceptible cultivars (Giza 74, and Bahtim 110) reacted with antiserum of the tested F. oxysporum f. sp. vasinfectum isolates, more precipitin lines were formed than the resistant cultivars. On the other hand, no obvious reaction was detected in case of F. moniliforme antiserum.     

Effect of the saprophytic fungus Fusarium oxysporum on arbuscular mycorrhizal colonization and growth of plants in greenhouse and field trials

Effects of the saprophytic fungus Fusarium oxysporum on arbuscular mycorrhizal (AM) colonization and plant dry matter were studied in greenhouse and field experiments. Host plants: maize (Zea mays L.), sorghum (Sorghum vulgare L.), lettuce (Lactuca sativa L.), tomato (Lycopersicum esculentum L.), wheat (Triticum vulgare L), lentil (Ervum lens L.) and pea (Pisum sativum L.), the AM fungi: Glomus mosseae, G. fasciculatum, G. intraradices, G. clarum, and G. deserticola and the carriers for F. oxysporum inoculum: aqueous solution, thin agar slices, and pellets of agar and alginate were tested under greenhouse conditions. Greatest plant growth and AM colonization responses in sterilized and unsterilized soils were observed with pea, Glomus deserticola and sodium alginate pellets as the carrier for F. oxysporum inoculum. Under field conditions, adding F. oxysporum increased the survival of transplanted pea, possibly through a beneficial effect on AM fungi. Application of F. oxysporum increased shoot dry matter, N and P concentrations of pea and sorghum plants, and the level of AM colonization attained by indigenous or introduced AM fungi. These parameters were similar in plants inoculated with either G. deserticola or with the indigenous AM fungi. Application of the saprophytic fungus increased the number of propagules of AM fungi in field plots in which pea was grown, but this increase was not sufficient to increase AM colonization of sorghum after the pea crop. This revised version was published online in June 2006 with corrections to the Cover Date.     

Optimization of RAPD-PCR Fingerprinting to Analyse Genetic Variation Within Populations of Fusarium oxysporum f.sp. cubense

Genetic variation among 11 isolates of Fusarium oxysporum f.sp. cubense (FOC) was analysed by random amplification of polymorphic DNA using the polymerase chain reaction (RAPD-PCR). The isolates represented three of the four FOC races and the seven vegetative compatibility groups (VCGs) known to occur in Australia. Isolates of F. oxysporum f.sp. cubense were also compared to isolates of F. oxysporum f.sp. gladioli, F. oxysporum f.sp. zingiberi, F. oxysporum f.sp. lycopersici, F. moniliforme, Aspergillus niger and Colletotrichum gloeosporioides. DNA was extracted from fungal mycelium and amplified by RAPD-PCR using one of two single random 10-mer primers; the primer sequences were chosen arbitrarily. The RAPD-PCR products were separated by polyacrylamide gel electrophoresis producing a characteristic banding pattern for each isolate. The genetic relatedness of the F. oxysporum f.sp. cubense isolates was determined by comparing the banding patterns generated by RAPD-PCR. This RAPD-PCR analysis revealed variation at all five levels of possible genetic relatedness examined. F. oxysporum f.sp. cubense could very easily be distinguished from the other fungi, and the three races and five VCGs of F. oxysporum f.sp. cubense could also be differentiated. Within F. oxysporum f.sp. cubense, each isolate was scored for the presence or absence of each band (50 different bands were produced for primer SS01 and 59 different bands for primer RC09) and these data were clustered using the UPGMA method (unweighted pair-group method, arithmetic average). UPGMA cluster analysis of the data generated by primer SS01 revealed two distinct clusters. One cluster contained race 4 isolates (VCGs 0120, 0129 and 01211) and the other cluster contained both race 1 (VCGs 0124, 0124/5 and 0125) and race 2 isolates (VCG 0128). Similar results were obtained with primer RC09. The banding patterns for each isolate were reproducible between experiments. These results indicated that RAPD-PCR was a useful method for analysing genetic variation within F. oxysporum f.sp. cubense. Some of the advantages of this technique were that it was rapid, no sequence data were required to design the primers and no radioisotopes were required.     

Molecular cloning and characterization of a pea chitinase gene expressed in response to wounding,fungal infection and the elicitor chitosan

The fungicidal class I endochitinases (E.C.3.3.1.14, chitinase) are associated with the biochemical defense of plants against potential pathogens. We isolated and sequenced a genomic clone, DAH53, corresponding to a class I basic endochitinase gene in pea, Chil. The predicted amino acid sequence of this chitinase contains a hydrophobic C-terminal domain similar to the vacuole targeting sequences of class I chitinases isolated from other plants. The pea genome contains one gene corresponding to the chitinase DAH53 probe. Chitinase RNA accumulation was observed in pea pods within 2 to 4 h after inoculation with the incompatible fungal strain Fusarium solani f. sp. phaseoli, the compatible strain F. solani f.sp. pisi, or the elicitor chitosan. The RNA accumulation was high in the basal region (lower stem and root) of both fungus challenged and wounded pea seedlings. The sustained high levels of chitinase mRNA expression may contribute to later stages of pea's non-host resistance.     

The synthetic strigolactone GR24 influences the growth pattern of phytopathogenic fungi

Strigolactones that are released by plant roots to the rhizosphere are involved in both plant symbiosis with arbuscular mycorrhizal fungi and in plant infection by root parasitic plants. In this paper, we describe the response of various phytopathogenic fungi to the synthetic strigolactone GR24. When GR24 was embedded in the growth medium, it inhibited the growth of the root pathogens Fusarium oxysporum f. sp. melonis, Fusarium solani f. sp. mango, Sclerotinia sclerotiorum and Macrophomina phaseolina, and of the foliar pathogens Alternaria alternata, Colletotrichum acutatum and Botrytis cinerea. In the presence of this synthetic strigolactone, intense branching activity was exhibited by S. sclerotiorum, C. acutatum and F. oxysporum f. sp. melonis. Slightly increased hyphal branching was observed for A. alternata, F. solani f. sp. mango and B. cinerea, whereas suppression of hyphal branching by GR24 was observed in M. phaseolina. These results suggest that strigolactones not only affect mycorrhizal fungi and parasitic plants, but they also have a more general effect on phytopathogenic fungi.     

Biological Control Activity of Three Trichoderma Isolates Against Fusarium Wilts of Cotton and Muskmelon and Lack of Correlation with their Lytic Enzymes

The enzymatic activity and the biocontrol ability of two new isolates of Trichoderma spp. (T-68 and Gh-2) were compared in laboratory and glasshouse experiments with a previously studied T. harzianum strain (T-35). In dual culture tests with Fusarium oxysporum f. sp. melonis and F. oxysporum f. sp. vasinfectum, isolates T-68 and Gh-2 overgrew the colonies of Fusarium, whereas T-35 failed to parasitize both wilt pathogens. Under glasshouse conditions, the three isolates of Trichoderma were effective in controlling Fusarium wilt of cotton but only T-35 was effective against F. oxysporum f. sp. melonis on muskmelon. When the three Trichoderma isolates were grown on liquid media containing laminarin, colloidal chitin or F. oxysporum f. sp. melonis cell walls as sole carbon sources, maximum β-1,3-glucanase and chitinase specific activity in the culture filtrates of all fungi was reached after 72h of incubation. When culture filtrates of the three Trichoderma isolates were incubated with freeze-dried mycelium of F. oxysporum f. sp. melonis or F. oxysporum f. sp. vasinfectum, different concentrations of glucose and N-acetyl-D-glucosamine were released. Overall no correlation was found between enzymatic activity and the biocontrol capability against Fusarium wilt on muskmelon and cotton.     

Location of pathogenicity genes on dispensable chromosomes inNectria haematococca MPVI

Nectria haematococca MPVI can be found in many different biological habitats but has been most studied as a pathogen of pea (Pisum sativum). Genetic analyses of isolates obtained from a variety of biological sources has indicated that a number of genes control pathogenicity on pea but that one important PEa Pathogenicity (PEP) gene isPDA, which confers the ability to detoxify the pea phytoalexin pisatin. In these studies, all naturally occurring isolates that lackedPDA (i.e. Pda^– isolates) and all Pda^– progeny were essentially non-pathogenic on pea. However, we have demonstrated recently that Pda^– mutants created by transformation-mediated gene disruptions, while having a modest reduction in virulence, and more virulent than any naturally occurring Pda^– isolates. In addition we know thatPDA genes are on dispensable (DS) chromosomes in this fungus. We believed that the gene disruption mutants have allowed the detection of otherPEP genes that are present on the DS chomosomes along withPDA and that naturally occuring Pda^– isolates usually lack this DS chromosome. This would explain why naturally occurring Pda^– isolates are always low in virulence. We propose that the DS chromosomes in fungi are analogous to bacterial plasmids which allow those microorganisms to colonise different habitats, i.e. the DS chromosomes ofNectria haematococca contain genes that allow individual isolates of this broad host range pathogen to occupy different biological niches.     

Detection of pea wilt pathogen <Emphasis Type="Italic">Fusarium oxysporum</Emphasis> f. sp. <Emphasis Type="Italic">pisi</Emphasis> using DNA-based markers

Identification of the fungus Fusarium oxysporum f. sp. pisi (Fop), the causal organism of wilt disease of pea, is a time consuming and arduous task. Diagnosis of Fop by traditional means requires more than 2 months and involves two steps, identification of species using morphological characters and formae specialis ‘pisi’ using pathogenicity assays. The ambiguous morphological differences between F. solani and F. oxysporum further complicate the diagnosis of F. oxysporum. A polymerase chain reaction–restriction fragment length polymorphism (PCR–RFLP) based method was developed to detect Fop from India. A PCR–RFLP marker, HPACAPS1₃₈₀, generated after restriction of 28S rDNA region with enzyme MvaI, detected accurately the Fop among several other fungi with detection sensitivity of 5 fg of Fop genomic DNA. In a mixture of Fop and pea DNA, the sensitivity was 500 pg of Fop DNA in 50 ng of pea DNA. The assay was further refined to detect the Fop from infected tissues and infested soil. The current assay can detect Fop from culture, plant tissues and soil in a considerably shorter period of time compared to traditional methods.     

Myrothins A–F from Endophytic Fungus Myrothecium sp. BS-31 Harbored in Panax notoginseng

Endophytic fungi play important roles for host's stress tolerance including invasion by pathogenic microbes. Small molecules are common weapons in the microbe–microbe interactions. Panax notoginseng is a widely used traditional Chinese medicinal plant and harbors many endophytes, some exert functions against pathogens. Here, we report six new compounds named myrothins A–F ( 1 – 6 ) produced by Myrothecium sp. BS-31, an endophyte isolated from P. notoginseng, and their antifungal activities against pathogenic fungi causing host root-rot disease. Their structures were elucidated with analysis of spectroscopic data including 1D and 2D NMR, HR-ESI-MS. Myrothins B ( 2 ) and E ( 5 ) showed the weak activity against Fusarium oxysporum and Phoma herbarum, and myrothins F ( 6 ) showed weak activity against F. oxysporum.     

Effects of treatment with phenylthiosemicarbazide and 4'-chlorophenylthiosemicarbazide on Fusarium wilt of pea and tomato plants

Effects of treatment with phenylthiosemicarbazide (PTS) and its 4′-chloro-derivative (4′-chloro-PTS) on Fusarium wilt of pea and tomato plants were investigated. Depending on pH and availability of oxygen, PTS and 4′-chloro-PTS are converted to their corresponding phenylazothioformamides and phenylazothioformamide-S-oxides, which are the actual fungitoxic compounds. PTS and 4′-chloro-PTS were shown to inhibit growth of Fusarium oxysporum f. pisi and F. oxysporum f. lycopersici in liquid media as well as on agar plates at concentrations of 50–100 mg/1. Inhibition was greater at pH 7 than at pH 5. When administered to pea and tomato plants, both compounds caused severe phytotoxic effects, especially at temperatures favouring Fusarium wilt, thus almost entirely obscuring any protective activity against the diseases. All compounds were strongly adsorbed to loam, but readily released from sand. Neither in pea nor in tomato plants were PTS and 4′-chloro-PTS converted to any fungitoxic substance, not already present in the aqueous solutions administered.     

An improved test for evaluating the pathogenicity of isolates of Fusarium solani f.sp. pisi on pea

An improved in vitro test is described for determining the pathogenicity of Fusarium solani f.sp. pisi isolates on pea. This technique involves the use of polypropylene fibre Milcap plugs to suspend peas in boiling tubes containing spore suspensions in 0.1% water agar. Results were available after 14 days of incubation at 25°C. Four levels of pathogenicity were detected on pea cultivars Little Marvel and Dark Skinned Perfection using a total of eight isolates and strains of F. solani f.sp. pisi.     

Interactions of the tomato with two formae speciales of Fusarium oxysporum

Tomato cuttings were inoculated with Fusarium oxysporum f.sp. lycopersici (FL) and F. oxysporum f.sp. pisi (FP) by standing the cuttings in suspensions of bud-cells of the fungi. FP never induced external symptoms although the fungus persisted in the lower parts of the cutting. FL at concentrations from 10³ to 10⁶ spores per ml induced typical wilt symptoms but there was subsequent recovery of some cuttings with the production of uninvaded side shoots. When the cuttings were inoculated with mixed suspensions of bud cells of the two fungi there was marked reduction of symptoms. The extent of this reduction was related to the proportion of FP/FL bud cells for a fixed inoculum of FL in the mixture and was moderate at a rate of 1/3 and complete at ratios from 4/1 to 9/1. Mixed suspensions of heat-killed bud cells of FP with live bud cells of FL in the ratio of 4/1 induced normal symptoms and it was concluded that the symptom mitigation induced by FP was related to the presence of living cells of the fungus. Root inoculations with mixed suspensions also gave less wilt than with FL alone. Symptom mitigation was apparently associated with a reduction of the extent of invasion of the cuttings but in vitro tests failed to demonstrate that exudates or extracts from normal or invaded tomato tissue induced any reduction of growth of the tomato pathogen.     

Molecular markers reflect differentiation of Fusarium oxysporum forma speciales on tomato and forma on eggplant

Selective pressure induces pathogens to change their method of infection and, sometimes, causes species to become infectious. Pathogenic fungi must differentiate different morphological and physiological properties during the process of host specialization in their life cycle. In the present study, we conducted a genetic investigation and compared similarities within a generation of Fusarium oxysporum forma speciales (f. sp.) infecting tomato and forma (f.) infecting eggplants using selected ISSR and RAPD markers, two horticultural commodities belonging to the same taxon of the Solanaceae. Interestingly, genetic data showed that fungi belonging to F. oxysporum f. sp. infecting tomato have a close genetic relationship with the fungi f. infecting eggplant. Furthermore, F. oxysporum f. sp. infecting tomato showed less genetic variation than F. oxysporum f. melongenae, suggesting that it could be developed more recently during host adaptation. On the other hand, the gene sequence of inter-simple sequence repeat (ISSR) markers resulting in high polymorphism showed matches with gene sequences encoding specific proteins related to pathogenicity of F. oxysporum species. These findings support the notion that selected ISSR markers can be used to follow host-associated divergence of F. oxysporum species infecting tomato and eggplant and that differentiation of their specific genes can also be related to pathogenicity and development as predictive studies before initiating detailed sequencing analysis.     

Detection of cross-reactive antigens shared byFusarium oxysporum andGlycine max by indirect ELISA and their cellular location in root tissues

Pathogenicity test ofFusarium oxysporum on ten cultivars of soybean revealed Soymax and Punjab-1 to be most resistant while JS-2 and UPSM-19 were most susceptible. Antigens were prepared from the roots of all the ten varieties of soybean and the mycelium ofF. oxysporum. Polyclonal antisera were raised against the mycelial suspension ofF. oxysporum and the root antigen of the susceptible cultivar UPSM-19. Cross reactive antigens shared by the host and the pathogen were detected first by immunodiffusion. The immunoglobulin fraction of the antiserum was purified by ammonium sulfate precipitation and DEAE-Sephadex column chromatography. The immunoglobulin fractions were used for detection of cross-reactive antigens by enzyme-linked immunosorbent assay. In enzyme-linked immunosorbent assay, antigens of susceptible cultivars showed higher absorbance values when tested against the purified anti-F. oxysporum antiserum. Antiserum produced against UPSM-19 showed cross-reactivity with the antigens of other cultivars. Indirect staining of antibodies using fluorescein isothiocyanate indicated that in cross-sections of roots of susceptible cultivar (UPSM-19) cross-reactive antigens were concentrated around xylem elements, endodermis and epidermal cells, while in the resistant variety, fluorescence was concentrated mainly around epidermal cells and distributed in the cortical tissues. CRAs were also present in microconidia, macroconidia and chlamydospores of the fungus.     

Population structure and linkage disequilibrium in a large collection of Fusarium oxysporum strains analysed through iPBS markers

In the current study, 160 pathogenic strains of Fusarium oxysporum collected from tomato, eggplant and pepper were studied. Eighteen inter‐primer binding site (iPBS)‐retrotransposon primers were used, and these primers generated 205 scorable polymorphic bands. The number of polymorphic bands per primer varied between 9 and 19, with a mean of 11 bands per primer. The highest polymorphism information content (PIC) value was determined as 0.27, and the lowest was 0.05. The unweighted pair‐group method with arithmetic averages (UPGMA) dendrogram including a heat map revealed that the 160 pathogenic strains of F. oxysporum were divided into two main clusters. The first cluster mainly included F. oxysporum f. sp. capsici (FOC) and F. oxysporum f. sp. melongenae (FOMG) isolates. The second cluster mainly comprised F. oxysporum f. sp. lycopersici (FOL) and F. oxysporum f. sp. radicis lycopersici (FORL) isolates. The highest percentage of loci in significant linkage disequilibrium (LD) was detected for FOL, whereas the lowest level of LD was found for FOC, and 95.2%, 99.4%, 99.1% and 97.4% of the relative kinship estimates were less than 0.4 for FOL, FOMG, FORL and FOC, respectively. LD differences were detected among formae speciales, and LD was higher in FOL as compare to FOC species. The findings of this study confirm that iPBS‐retrotransposon markers are highly polymorphic at the intraspecific level in Fusarium spp.