Assessment of Diversity in Claviceps africana and Other Claviceps Species by RAM and AFLP Analyses

Population Genetic Structure of Claviceps purpurea in Cool-Season Grass Seed Crops of Oregon

Ergot, caused by Claviceps purpurea, is a primary disease concern in irrigated cool-season grass seed production systems of Oregon. In order to better understand the genetic diversity, population structure, and the epidemiology of C. purpurea in grasses grown for seed, 226 isolates were obtained using a hierarchical sampling strategy from two fields each of Kentucky bluegrass (n = 102) and perennial ryegrass (n = 124) and characterized using 12 microsatellite markers. A total of 194 unique multilocus genotypes (MLGs) were identified in this study. There were moderate levels of genotypic diversity (H = 3.43 to 4.23) and gene diversity (H_exp = 0.45 to 0.57) within fields. After clone correction, analysis of molecular variance revealed that 66% of the genetic variation occurred between the two C. purpurea isolates collected from the same seed head of individual plants, indicating that many of the seed heads bearing multiple sclerotia were infected by ascospores rather than conidia. However, the majority of the clonal isolates obtained in this study were collected from the same seed head (i.e., the two isolates were identical MLGs), indicating a role of conidia (honeydew) in secondary infections within seed heads. Genetic differentiation was observed between populations from different hosts (22%) but was confounded by geography. The standardized index of association ranged from 0.007 to 0.122 among the four populations, suggesting potential outcrossing and differences in the relative contribution of ascospores and conidia to ergot among the fields. The results from this study provide insights into the epidemiology of ergot in cool-season grass seed crops of Oregon.

Intraspecific functional and genetic diversity of Petriella setifera

The aim of the study was an analysis of the intraspecific genetic and functional diversity of the new isolated fungal strains of P. setifera. This is the first report concerning the genetic and metabolic diversity of Petriella setifera strains isolated from industrial compost and the first description of a protocol for AFLP fingerprinting analysis optimised for these fungal species. The results showed a significant degree of variability among the isolates, which was demonstrated by the clearly subdivision of all the isolates into two clusters with 51% and 62% similarity, respectively. For the metabolic diversity, the BIOLOG system was used and this analysis revealed clearly different patterns of carbon substrates utilization between the isolates resulting in a clear separation of the five isolates into three clusters with 0%, 42% and 54% of similarity, respectively. These results suggest that genetic diversity does not always match the level of functional diversity, which may be useful in discovering the importance of this fungus to ecosystem functioning. The results indicated that P. setifera strains were able to degrade substrates produced in the degradation of hemicellulose (D-Arabinose, L-Arabinose, D-Glucuronic Acid, Xylitol, γ-Amino-Butyric Acid, D-Mannose, D-Xylose and L-Rhamnose), cellulose (α-D-Glucose and D-Cellobiose) and the synthesis of lignin (Quinic Acid) at a high level, showing their importance in ecosystem services as a decomposer of carbon compounds and as organisms, which make a significant contribution to carbon cycling in the ecosystem.The results showed for the first time that the use of molecular biology techniques (such as AFLP and BIOLOG analyses) may allow for the identification of intraspecific diversity of as yet poorly investigated fungal species with favourable consequences for our understanding their ecosystem function.

Alteration of Genetic Make-up in Karnal Bunt Pathogen (Tilletia indica) of Wheat in Presence of Host Determinants

Alteration of genetic make-up of the isolates and monosporidial strains of Tilletia indica causing Karnal bunt (KB) disease in wheat was analyzed using DNA markers and SDS-PAGE. The generation of new variation with different growth characteristics is not a generalized feature and is not only dependant on the original genetic make up of the base isolate/monosporidial strains but also on interaction with host. Host determinant(s) plays a significant role in the generation of variability and the effect is much pronounced in monosporidial strains with narrow genetic base as compared to broad genetic base. The most plausible explanation of genetic variation in presence of host determinant(s) are the recombination of genetic material from two different mycelial/sporidia through sexual mating as well as through para-sexual means. The morphological and development dependent variability further suggests that the variation in T. indica strains predominantly derived through the genetic rearrangements.

Molecular identification and characterization of Fusarium spp. associated with sorghum seeds

BACKGROUND

Fusarium spp. are not only pathogenic to plants but are also known as toxin producers that negatively affect animal and human health. The identification of Fusarium spp. remains one of the most critical issues in fungal taxonomy. In this study, different strains of Fusarium spp. were isolated from sorghum seed samples and identified at the molecular level by tef-1α gene amplification. A multiplex polymerase chain reaction (mPCR) assay was developed to differentiate toxigenic and non-toxigenic Fusarium spp. by designing a primer for the Fum21 gene along with the Fum1 and Fum8 genes. A competitive direct enzyme-linked immunosorbent assay (CD-ELISA) was employed to assess the fumonisin-producing ability of Fusarium spp. Phylogenetic analyses were performed using partial sequences of tef-1α and inter-simple sequence repeat (ISSR) markers of different Fusarium spp.

RESULTS

All 27 isolates of Fusarium spp. were positive for the tef-1α gene and revealed the presence of F. verticillioides, F. thapsina and F. cf. incarnatum-equiseti complex. The standardized mPCR assay distinguished toxigenic and non-toxigenic F. verticillioides. Further, mPCR fumonisin-positive F. verticillioides isolates were also positive by CD-ELISA. The tef-1α gene sequence was found to be useful in revealing intraspecific polymorphism to some extent. ISSR markers revealed a high level of polymorphism among different isolates of Fusarium spp., and the dendrogram of ISSR analyses grouped the 27 isolates into two major clusters.

CONCLUSION

The present method provided rapid and reliable detection of fumonisin-producing Fusarium spp. The mPCR assay could be an alternative strategy to current conventional mycotoxin analytical techniques and a reliable tool for high-throughput monitoring of major mycotoxin-producing fungi during the processing steps of food and feed commodities.

Analysis of genetic and virulence diversity of Cylindrocarpon liriodendri and C. macrodidymum associated with black foot disease of grapevine

Inter-simple sequence repeat (ISSR) analysis was used to investigate the genetic diversity of 87 Cylindrocarpon liriodendri and C. macrodidymum isolates, the causal agents of black foot disease of grapevine. The four ISSR primers (GT)7, (CCA)5, (CGA)5 and (TCG)5, were able to provide reproducible and polymorphic DNA fingerprint patterns and detected relevant genetic diversity in C. macrodidymum. The cluster analysis of ISSR data showed 21 different genotypes that were grouped in seven ISSR groups, from which two corresponded to C. liriodendri (G1 and G2) and five to C. macrodidymum (G3-G7). Nineteen isolates selected from the seven ISSR groups were inoculated in grapevine seedlings obtained from cv. 'Tempranillo'. The pathogenicity tests detected virulence diversity in C. macrodidymum. The isolates belonging to ISSR groups G6 and G7 were significantly more virulent than the other C. macrodidymum and C. liriodendri isolates.

Lima Bean Downy Mildew Epiphytotics Caused by New Physiological Races of Phytophthora phaseoli

Before 1995, race D of Phytophthora phaseoli, the causal agent of downy mildew on lima bean (Phaseolus lunatus), was the prevalent physiological race in the mid-Atlantic region of the United States. Since 1995, however, new physiological races of P. phaseoli have been responsible for downy mildew outbreaks in previously resistant cultivars in this region. Cultivar differential testing of 180 isolates of P. phaseoli collected between 1994 and 2005 from Delaware and the eastern shore of Maryland has confirmed the presence of two new physiological races. The detection of race E in 1995 and race F only 5 years later in 2000, plus the lack of resistant cultivars to manage the epiphytotics in lima bean, have led to millions of dollars of crop losses. Intra- and interspecific genetic variation of Phytophthora spp. and isolates were assessed using amplified fragment length polymorphism DNA fingerprinting. Primer groups EcoRI+AG and MseI+C distinguished P. phaseoli and P. capsici from P. infestans but did not distinguish among different races of P. phaseoli.

Analysis of Claviceps africana and C. sorghi from India using AFLPs, EF-1alpha gene intron 4, and beta-tubulin gene intron 3

Isolates of Claviceps causing ergot on sorghum in India were analysed by AFLP analysis, and by analysis of DNA sequences of the EF-1alpha gene intron 4 and beta-tubulin gene intron 3 region. Of 89 isolates assayed from six states in India, four were determined to be C. sorghi, and the rest C. africana. A relatively low level of genetic diversity was observed within the Indian C. africana population. No evidence of genetic exchange between C. africana and C. sorghi was observed in either AFLP or DNA sequence analysis. Phylogenetic analysis was conducted using DNA sequences from 14 different Claviceps species. A multigene phylogeny based on the EF-1alpha gene intron 4, the beta-tubulin gene intron 3 region, and rDNA showed that C. sorghi grouped most closely with C. gigantea and C. africana. Although the Claviceps species we analysed were closely related, they colonize hosts that are taxonomically very distinct suggesting that there is no direct coevolution of Claviceps with its hosts.

Cultural characteristics, morphology, and variation within Claviceps africana and C. sorghi from India

Sorghum ergot in India is caused by Claviceps africana and C. sorghi. The distributions of these two species in India is not known. Eighty-nine sorghum ergot isolates were cultured from young sphacelia obtained from male sterile sorghum plants artificially inoculated using inoculum collected in the field. Based on cultural characteristics, the isolates were separated into two groups which differed distinctly in the morphology of their sphacelia, conidia, and sclerotia. Marked differences also were observed in rates of secondary conidial production and disease spread between the groups. In combination with molecular evidence, our results confirm that the isolates placed in Group I represent C. africana and Group II isolates represent C. sorghi. C. africana was found to be widely distributed in all sorghum growing areas of India. The species first described as occuring in India, C. sorghi, appears to be restricted to a few locations in the states of Maharashtra, Andhra Pradesh, and Karnataka.

Alkaloid production by isolates of the sorghum ergot pathogen (Claviceps africana) from Australia and other countries

Isolates of Claviceps africana from Australia, Africa, Asia, and America were tested for the production of dihydroergosine (DHES), and its biogenic precursors dihydroelymoclavine (DHEL) and festuclavine (FEST), in culture. Several growth media were evaluated to optimise alkaloid production with little success. The best of these involved 2-stage culturing on high-sucrose substrate. Australian C. africana isolates varied widely and inconsistently in alkaloid production, with DHES concentrations in mycelium ranging from: <0.1 to 9 mg DHES/kg; <0.1 to 1.6 mg DHEL/kg; and <0.1 to 0.4 mg FEST/kg. In a separate experiment using similar culturing techniques, DHES was produced by 2 of 3 Australian isolates, 1 of 3 USA isolates, 1 of 4 Indian isolates, the sole Puerto Rican isolate, the sole Japanese isolate, but not the sole South African isolate. In this experiment, DHES concentrations detected in mycelium of Australian isolates (0.1–1.0 mg DHES/kg) were of similar magnitude to isolates from other countries (0.2–1.8 mg DHES/kg). Three C. africana isolates, including one that produced only traces of alkaloid in culture after 8 weeks, were inoculated onto panicles of sterile male sorghum plants. After 8 weeks, all 3 isolates produced 10–19 mg DHES/kg in the panicles, demonstrating that the growing plant favoured more consistent alkaloid production than culture medium.

Ochratoxin A producing Penicillium verrucosum isolates from cereals reveal large AFLP fingerprinting variability

AIMS

To examine if molecular amplified fragment length polymorphism (AFLP) fingerprinting of the only ochratoxin A-producing species in European cereals, Penicillium verrucosum, can be used as a method in hazard analysis using critical control points (HACCP).

METHODS AND RESULTS

A total of 321 isolates of P. verrucosum were isolated from ochratoxin A-contaminated cereals from Denmark (oats), UK (wheat and barley) and Sweden (wheat). Of these, 236 produced ochratoxin A as determined by thin layer chromatography; 185 ochratoxin A-producing isolates were selected for AFLP fingerprinting. A total of 138 isolates had unique AFLP patterns, whereas 52 isolates could be allocated to small groups containing from two to four isolates with similar AFLP patterns. A total of 155 clones were found among the 185 P. verrucosum isolates, thus 84% of the isolates may represent different genets of P. verrucosum. As the few isolates that were grouped often came from the same farm, and those groups that contained AFLP-identical isolates from different countries were morphotypically different. On single farms up to 35 clones were found. The few groups of ramets from the same genet indicated that a HACCP approach based on clones may require a very large number of AFLP analysis to work in practice, we recommend basing the HACCP approach on the actual species P. verrucosum. A more detailed characterization should rather be based on the profile of species present at different control points, or analysis of the mycotoxins ochratoxin A and citrinin in the isolates. Examination of 86 isolates with HPLC and diode array detection of P. verrucosum showed that 66% produced ochratoxin A, 87% produced citrinin, 92% produced verrucin and 100% produced verrucolone.

CONCLUSIONS

Among 184 ochratoxin A-producing Penicillium verrucosum, 155 clonal lineages were indicated by AFLP fingerprinting, indicating a high genetical diversity, yet the species P. verrucosum is phenotypically distinct and valid.

SIGNIFICANCE AND IMPACT OF THE STUDY

AFLP fingerprinting of Penicillium verrucosum indicates that genetic recombination takes place in this fungus.

Oligosaccharides produced by submerged cultures of Claviceps africana and Claviceps sorghi

Oligosaccharides produced by submerged cultures of C. africana and C. sorghi were isolated by semipreparative HPLC. Structure of 6-O-beta-D-fructofuranosyl-D-glucopyranose (blastose), 1,6-bis-O-(beta-D-fructofuranosyl)-alpha-D-glucopyranoside (neokestose) and two sugar alcohols, 1-O-beta-D-fructofuranosyl-D-mannitol (fructosylmannitol) and 1,6-bis-O-(beta-D-fructofuranosyl)-D-mannitol (bisfructosylmannitol) was determined by NMR spectrometry. MALDI TOF MS analysis revealed molecular ions [M+Na]+ that indicate the presence of other tetra- and pentasaccharides (m/z = 689.4 and 851.5, respectively) and corresponding sugar alcohol (m/z = 691.4). Rapid conversion of sucrose into series of oligosaccharides and corresponding sugar alcohols was observed in all tested strains.

AFLP Analysis of Phytophthora cactorum Isolates from Strawberry and Other Hosts: Implications for Identifying the Primary Source of Inoculum

Forty-seven isolates of Phytophthora cactorum from North America and Germany were subjected to amplified fragment length polymorphism (AFLP) analysis to investigate genetic diversity among isolates and geographical populations; 42 isolates were recovered from cultivated strawberry plants (Fragaria × ananassa), and five isolates had been recovered from plants in four other genera (Syringa, Abies, Malus, and Panax). From all isolates evaluated, 226 out of 264 markers (85.6%) were polymorphic and provided 42 unique AFLP profiles. The genetic diversity among isolates of P. cactorum from strawberry was greater than that among isolates from the other hosts. Isolates collected during recent crown rot epidemics in strawberry fields in South Carolina were genetically diverse and scattered among isolates from other geographical areas in an unweighted pair-group mean analysis (UPGMA) dendrogram. Isolates collected during recent crown rot epidemics in North Carolina also were genetically diverse, but most isolates clustered with isolates collected in 1997 from Florida strawberry fields. These data suggest that recent outbreaks of Phytophthora crown rot in the southeastern United States resulted from use of transplants already infected or infested with P. cactorum rather than from endemic populations of this pathogen, which would affect recommendations for disease management.

Laboratory, Greenhouse, and Field Assessment of Fourteen Fungicides for Activity Against Claviceps africana, Causal Agent of Sorghum Ergot

Commercial formulations of 14 fungicides representing seven chemical classes were assessed in vitro and in vivo for activity against Claviceps africana, causal agent of sorghum ergot. All fungicides markedly reduced spore germination in vitro on water agar, with effective concentration (EC)₅₀ values (based on active ingredient) that ranged from 0.01 μg ml^-1 for thiophanatemethyl and trifloxystrobin to 1.18 μg ml^-1 for cyprodinil. In vivo assays included applications of fungicide on full bloom panicles of a male-sterile line, ATx623, and then inoculating panicles with a conidial suspension immediately after the fungicide had dried. In greenhouse trials and in the 2000 field evaluation, a single application of propiconazole, tebuconazole, triadimefon, myclobutanil, or azoxystrobin at a rate of 25 μg ml^-1 markedly suppressed ergot severity on ATx623. In the 2001 field evaluation, tebuconazole applied at 25 μg ml^-1 was most effective in reducing levels of ergot severity. Ergot control was greater when fungicides were applied at 25 μg ml^-1 than at 5 μg ml^-1. Generally, triazole and strobilurin classes of fungicide were more effective in controlling ergot than benzimidazole, anilinopyrimidine, ethylenebisdithiocar-bamate (EBDC), pyridinamine, and organometallic classes. At the two fungicide rates used in this study, ergot severity increased between 7 and 10 days after inoculation. Results showed that in vitro fungicide screening by measuring spore germination inhibition was not a good predictor of performance in the field. Results from the field trials suggest that control, particularly under ergot-favorable environments, may require higher rates than used in this study.

AFLP Comparisons Among Claviceps africana Isolates from the United States, Mexico, Africa, Australia, India, and Japan

Eighty-seven isolates of the sorghum ergot pathogen, Claviceps africana, from diverse geographic locations were analyzed using four different amplified fragment length polymorphism (AFLP) primer combinations to determine genetic relationships among isolates. Most isolates showed unique AFLP haplotypes, indicating that substantial genetic variation is present within C. africana populations. Two major groupings of isolates were observable, with ca. 70% similarity between the two groups. One group consisted of Australian, Indian, and Japanese isolates and the other of U.S., Mexican, and African isolates. In spite of overall high levels of genetic diversity observed in C. africana, isolates within the two major groups were between 75 and 100% similar. The observed associations of C. africana isolates from worldwide sources could be the result of intercontinental trade and/or movement of seed. The data indicate that Africa was the likely source of C. africana that has become established in the Americas since 1996. Analysis of additional isolates in future studies will reveal whether these groupings are being maintained or whether population subdivision or reshuffling may occur.

The internet-based fungal pathogen database: a proposed model

ABSTRACT A better understanding of the phenotypic and genetic diversity of significant agricultural pathogens and how their populations change in the field is critical for designing successful, long-term disease management strategies. Although efforts to determine the genetic diversity of plant pathogens have substantially increased in recent years, mainly due to the availability of various molecular tools, complementary efforts to archive and integrate the resulting data have been very limited. As a consequence, it is often difficult to compare the available data from various laboratories because the data have been generated by diverse tools, often preventing any direct comparisons, and are saved in a format that is unsuitable for comparative studies. The establishment of an internet-based database that cross-links the digitized genotypic and phenotypic information of individual pathogens at both the species and population levels may allow us to effectively address these problems by coordinating the generation of data and its subsequent archiving. We discuss the needs, benefits, and potential structure of such a database.