Population structure and migration of the witches’ broom pathogen Moniliophthora perniciosa from cacao and cultivated and wild solanaceous hosts in southeastern Brazil

Moniliophthora perniciosa, causal agent of witches’ broom disease in cacao plantations in South America and the Caribbean Islands, has co‐evolved with its host cacao, but the pathogen has also emerged in many solanaceous hosts in Brazil, including economically important food crops and wild species. This study was carried out to: (i) determine the existence of host subpopulations of M. perniciosa in Brazil; (ii) estimate gene and genotypic diversity of M. perniciosa host subpopulations infecting solanaceous hosts in southeastern Bahia and Minas Gerais states, Brazil; and (iii) estimate the amount and directionality of historical migration of M. perniciosa subpopulations. Up to 203 M. perniciosa isolates collected from solanaceous hosts with symptoms from Bahia and Minas Gerais states in Brazil and from Theobroma spp. (cacao) and Herrania spp. were characterized with 11 microsatellite markers. Factorial correspondence analyses, minimum‐spanning network and Bayesian clustering revealed genetic clusters associated with their host of origin. Significant subpopulation differentiation was evident (Φ_ST = 0.30, P ≤ 0.05) among M. perniciosa host subpopulations. Most of the multilocus microsatellite genotypes (MLMGs) were host‐specific, with few MLMGs shared among subpopulations. Pairwise comparisons among M. perniciosa host subpopulations were significant, except between jurubeba (Solanum paniculatum) and cultivated solanaceous subpopulations. The combined analyses rejected the null hypothesis that M. perniciosa in Brazil is a single genetic population not structured by host. These findings support a scenario of introduction and subsequent adaptation to solanaceous hosts that should be taken into consideration to improve mitigation and management of M. perniciosa.     

Population structure of the ash dieback pathogen,Hymenoscyphus fraxineus,in relation to its mode of arrival in the UK

The ash dieback fungus, Hymenoscyphus fraxineus, a destructive, alien pathogen of common ash (Fraxinus excelsior), has spread across Europe over the past 25 years and was first observed in the UK in 2012. To investigate the relationship of the pathogen's population structure to its mode of arrival, isolates were obtained from locations in England and Wales, either where established natural populations of ash had been infected by wind‐dispersed ascospores or where the fungus had been introduced on imported planting stock. Population structure was determined by tests for vegetative compatibility (VC), mating type and single‐nucleotide polymorphisms (SNPs). VC heterogeneity was high at all locations, with 96% of isolate pairings being incompatible. Frequencies of the MAT1‐1‐1 and MAT1‐2‐1 idiomorphs were approximately equal, consistent with H. fraxineus being an obligate outbreeder. Most SNP variation occurred within study location and there was little genetic differentiation between the two types of location in the UK, or between pathogen populations in the UK and continental Europe. There was modest differentiation between UK subpopulations, consistent with genetic variation between source populations in continental Europe. However, there was no evidence of strong founder effects, indicating that numerous individuals of H. fraxineus initiated infection at each location, regardless of the route of pathogen transmission. The ssRNA virus HfMV1 was present at moderate to high frequencies in all UK subpopulations. The results imply that management of an introduced plant pathogen requires action against its spread at the continental level involving coordinated efforts by European countries.     

Microsatellite and mating type markers reveal unexpected patterns of genetic diversity in the pine root‐infecting fungus Grosmannia alacris

Grosmannia alacris is a fungus commonly associated with root‐infesting bark beetles occurring on Pinus spp. The fungus has been recorded in South Africa, the USA, France, Portugal and Spain and importantly, has been associated with pine root diseases in South Africa and the USA. Nothing is known regarding the population genetics or origin of G. alacris, although its association with root‐infesting beetles native to Europe suggests that it is an invasive alien in South Africa. In this study, microsatellite markers together with newly developed mating type markers were used to characterize a total of 170 isolates of G. alacris from South Africa and the USA. The results showed that the genotypic diversity of the South African population of G. alacris was very high when compared to the USA populations. Two mating types were also present in South African isolates and the MAT1‐1/MAT1‐2 ratio did not differ from 1:1 (χ² = 1·39, P = 0·24). This suggests that sexual reproduction most probably occurs in the fungus in South Africa, although a sexual state has never been seen in nature. In contrast, the large collection of USA isolates harboured only a single mating type. The results suggest that multiple introductions, followed by random mating, have influenced the population structure in South Africa. In contrast, limited introductions of probably a single mating type (MAT1‐2) may best explain the clonality of USA populations.     

Population structure,genetic diversity,and sexual state of the rice brown spot pathogen Bipolaris oryzae from three Asian countries

Bipolaris oryzae causes brown spot in rice (Oryza sativa) inflicting substantial grain yield losses worldwide. Knowledge of the population structure, genetic diversity and sexual recombination of the fungal pathogen can help to implement effective disease management strategies. In this study, B. oryzae isolates sampled from Iran, the Philippines and Japan were analysed with 12 simple‐sequence repeat (SSR) markers, newly developed from the genome sequence of the fungus. Among the 288 B. oryzae isolates genotyped, 278 unique haplotypes were identified. High genotype numbers (richness) with even distribution (evenness) were found within the collection sites. Both mating types, MAT1‐1 and MAT1‐2, were present in each collection area, and the sexual state was induced under controlled conditions with production of viable ascospores. However, the tests of linkage disequilibrium rejected of the hypothesis of random mating. Discriminant analysis of principal components (DAPC) revealed that the B. oryzae collection formed three clusters, each consisting of isolates from different collection sites. Analysis of molecular variance (amova ) showed that genetic variation among clusters was 18.7%, with the rest of the variation distributed within clusters (R_ST = 0.187, P < 0.001). Statistically significant pairwise genetic differentiation was found between the clusters. These results show that Asian B. oryzae isolates are genetically diverse, and, overall, distributed in three groups. These findings will be helpful in managing the disease and guide the use of representative isolates needed for selection of resistant rice varieties.     

Comparative analysis of genetic structures and aggressiveness of Fusarium pseudograminearum populations from two surveys undertaken in 2008 and 2015 at two sites in the wheat belt of Western Australia

Fusarium crown rot (FCR), caused predominantly by Fusarium pseudograminearum (Fp) in Australia, is an important fungal disease of wheat and barley. FCR causes significant yield losses and reduced grain quality worldwide. This study investigated the population dynamics of FCR-causing F. pseudograminearum isolates from Western Australia (WA), a major wheat-growing region. Wheat samples were collected from a total of seven different sites in 2008 and 2015. Two sites, Tammin and Karlgarin, with moderate to high FCR incidence, were intensively sampled in both years. The results revealed significant increase in Fp isolation frequency between 2008 and 2015. Over 86% of 1100 Fusarium isolates were Fp in 2015 compared with 59% of 639 isolates from 2008. Mating type idiomorphs, toxin chemotypes and population genetic structures were determined for a subset of 279 Fp isolates (132 isolates from 2008 and 165 from 2015). Mating type analysis revealed differences in MAT1-1 and MAT1-2 distributions between Tammin and Karlgarin for both years. Results also showed that 97.6% of Fp isolates analysed had the 3-ADON trichothecene chemotype. Additionally, for the first time in Australia, the 15-ADON chemotype was identified in 2.3% and 2.4% of Fp isolates from 2008 and 2015, respectively. The genetic structure of Fp population determined using 21 cleaved amplified polymorphic sequence (CAPS) markers revealed a high level of genetic variation within and between populations. In addition, 2015 isolates from Tammin and Karlgarin were significantly more aggressive (P < 0.0001) than 2008 isolates. This finding may have implications in managing this significant fungal disease.     

Pathotypic and genetic diversity in the population of Rhizoctonia solani AG1‐IA causing rice sheath blight in China

Sheath blight, caused by Rhizoctonia solani AG1‐IA, is one of the most serious diseases of rice. In this study, a total of 175 isolates of R. solani AG1‐IA were collected from five rice‐growing regions in China. Pathogenicity tests revealed that all isolates were virulent to five cultivars with different levels of resistance at the rice seedling stage in the greenhouse. There was considerable variation in aggressiveness, and the isolates were classified into three pathotypes based on disease severity, with moderately virulent isolates prevalent in the population. Forty‐three haplotypes were identified based on ITS sequencing, and 39 haplotypes were distinct among isolates. There were high levels of haplotype diversity and nucleotide diversity within the populations of R. solani AG1‐IA. High gene flow (Nm = 1·63–5·22) was detected, consistent with relatively low differentiation between pairs of populations. Five populations were divided into two distinct clusters by the unweighted pair group method with arithmetic mean (UPGMA), and no spatial population differentiation was discernible. The majority (97·8%) of genetic diversity was distributed among isolates within populations, with only 2·2% of the genetic diversity attributed to differences among populations. The star‐like shape of the haplotype network provided evidence of signatures of population expansion in recent history. No significant relationships were found between the genetic diversity and aggressiveness or geographic origin among populations of R. solani AG1‐IA. These results highlight that the population characteristics of R. solani AG1‐IA should be taken into account in evaluating the germplasm resistance of rice cultivars to sheath blight.     

Comparative analysis of pathogenic and nonpathogenic Fusarium oxysporum populations associated with banana on a farm in Minas Gerais,Brazil

Fusarium wilt is one of the most devastating diseases on banana. The causal agent, Fusarium oxysporum f. sp. cubense (Foc) is genetically diverse and its origin and virulence are poorly understood. In this study, pathogenic Foc isolates and nonpathogenic F. oxysporum isolates from Minas Gerais in Brazil were compared using EF‐1α and IGS sequences. This allowed the examination of the origin and evolutionary potential of Foc in a country outside the region of origin of the banana plant. Two different sequence types were found among Foc isolates. One appeared to be of local origin because it was identical to the sequence type of the largest group of nonpathogenic isolates. To explore if the ‘local’ Foc isolates had acquired pathogenicity either independently through coevolution with the host, or through horizontal gene transfer (HGT) of pathogenicity genes from other, probably introduced, Foc isolates, the presence and sequence of putative SIX effector genes were analysed. Homologues of SIX1, SIX3 and SIX8 were found. SIX1 sequences were identical and exclusively found in all pathogenic isolates, while variable ratios of sequences of multicopy gene SIX8 were found among nonpathogenic and different pathogenic isolates. This observation supports the HGT hypothesis. Horizontal transfer of genes between isolates of F. oxysporum has important implications for the development of reliable diagnostic tools and effective control measures. Full genome sequencing is required to confirm HGT and to further unravel the virulence mechanisms of forma specialis cubense.     

Genetic variability of Pseudocercospora fijiensis,the black Sigatoka pathogen of banana (Musa spp.) in Mexico

Pseudocercospora (previously known as Mycosphaerella) fijiensis causes black Sigatoka disease in banana (Musa spp.) and is considered to be the most devastating pathogen of this crop worldwide. To improve knowledge of its evolutionary patterns, this study determined the genetic variability of populations from two regions of Mexico: Central Pacific (Colima and Michoacan) and Southern (Chiapas, Tabasco and Oaxaca), using 10 simple sequence repeat (SSR) loci and the MAT-specific PCR assay. Both mating types were present in all regions under study, with frequencies of 63% MAT1-1 and 37% MAT1-2. The SSR markers showed an average of three alleles per locus, resulting in 34 alleles in total. The genetic diversity (H_T) was 0.3308, but at the local level (H_S) ranged from 0.0976 (Colima) to 0.2228 (Oaxaca). However, the genotypic diversity was usually high (H′ > 2.4, S > 0.89). Cluster analysis grouped the isolates into five clusters with high statistical support (au > 80%), suggesting a geographic organization of the genetic variability of P. fijiensis; AMOVA, the minimum spanning tree and the population structure analysis supported this result, and all data indicated that the major genetic differences were between the different populations under analysis. Thus, the high level of genetic variability in P. fijiensis is attributed partly to a high rate of sexual reproduction, and also to a strong evolutionary capacity coupled with isolation due to limited genetic flow between distant populations. Both possibilities could be playing a relevant role in population differentiation of the pathogen.     

Low genetic variability in Sclerotinia sclerotiorum populations from common bean fields in Minas Gerais State,Brazil, at regional,local and micro‐scales

Sclerotinia sclerotiorum, causal agent of white mould, is the most destructive and widely distributed soilborne pathogen of common bean during the autumn–winter season in Brazil. Nevertheless, little is known about the genetic structure of the pathogen population. Microsatellite (SSR) markers and mycelial compatibility groups (MCGs) were used to characterize 118 isolates collected from 20 bean fields located in the most important growing regions of Minas Gerais State (MG). Additionally, the genetic variability among 10 isolates obtained from a single sclerotium was investigated in 10 different sclerotia. Seventy SSR haplotypes and 14 MCGs were identified among the 118 isolates. The genetic differences within bean growing areas accounted for most of the genetic variation (72%). Despite the relatively high genotypic diversity, the SSR loci were at linkage disequilibrium. Moreover, 70% of the isolates were assigned to only two MCGs, and haplotypes of a given MCG were closely related. The discriminant analysis of principal components revealed five groups. There was strong genetic differentiation between isolates collected in one municipality in southern MG when compared to other regions. Common bean resistance to white mould should be assessed with representative isolates of the five genetic groups and, if possible, of the different MCGs detected in the present study. One to five haplotypes were detected among the 10 isolates obtained from a single sclerotium. Therefore, in order to ensure genetic identity of an isolate, hyphal tip or monoascosporic isolates should be used.     

Genetic diversity and structure of Hemileia vastatrix populations on Coffea spp.

Coffee leaf rust is the most limiting disease for coffee cultivation in Brazil. Despite its importance, relatively little is known about the genetic diversity of Hemileia vastatrix, the rust causal agent. In this work, the DNA from 112 monopustule isolates from different geographic locations and coffee genotypes were analysed by amplified fragment length polymorphisms (AFLP). The objectives were to assess the influence of the host and geographic origin on the diversity and population differentiation in H. vastatrix. The fungal population showed a low level of genotypic diversity. Gene diversity (h) was 0·027 and the hypothesis of random mating in the total population was rejected, but evidence for recombination was found for two subpopulations (São Paulo and Paraná). The analysis of molecular variance revealed that 90% of the genetic distribution of the pathogen occurs among isolates within the subpopulation (states or host of origin). There was no correlation between geographic and genetic distance (r = ?0·024, P = 0·74), which together with the high number of migrants and the low degree of differentiation in populations of H. vastatrix, is consistent with the fact that the inoculum is probably easily dispersed by wind over long distances, allowing dispersal of the pathogen among coffee growing areas in Brazil. Therefore, it is difficult to predict the durability of resistant sources to coffee rust. The recommendation for the breeding programmes is thus to incorporate multigenic resistance as a control strategy.     

Genetic diversity of Phytophthora pluvialis,a pathogen of conifers,in New Zealand and the west coast of the United States of America

Phytophthora pluvialis is the causal agent of red needle cast on Pinus radiata in New Zealand. It was first isolated in 2008 but had previously been recovered from tanoak (Notholithocarpus densiflorus) and Douglas‐fir (Pseudotsuga menziesii) trees in Oregon, USA in 2002. Phytophthora pluvialis was subsequently described as a new species in 2013 and classified as a clade III Phytophthora species. The aim of this study was to gain a better understanding of the genetic diversity, population structure and origin of this pathogen. A total of 360 P. pluvialis isolates were collected from the USA and New Zealand. The genome sequences of two P. pluvialis isolates were used to identify 27 single nucleotide polymorphism (SNP) markers that were then used to genotype the two populations. The genotypic data showed that the USA population of P. pluvialis had twice the genetic diversity and a greater number of multilocus genotypes (MLGs) compared to the New Zealand population, with 126 and 24 MLGs, respectively. The majority of the subpopulations within the USA and New Zealand showed linkage disequilibrium. All subpopulations had a negative fixation index, indicating that clonal reproduction is prevalent in both countries. A minimum spanning network (MSN) showed two unique clusters of isolates in the New Zealand population, suggesting two potential introductions of P. pluvialis into New Zealand from the USA. There was no significant structure within the New Zealand or USA populations. This study provides novel insight into the genetic structure of P. pluvialis in New Zealand and the USA.     

Development,characterization and application of genomic SSR markers for the oat stem rust pathogen Puccinia graminis f. sp. avenae

Oat stem rust, caused by Puccinia graminis f. sp. avenae (Pga), is one of the most severe diseases of oats worldwide. Population studies are scarce for this pathogen, mainly due to the lack of polymorphic molecular markers suitable for genetic analysis. In this study, an Australian Pga isolate was sequenced, the abundance of simple sequence repeats (SSRs) was determined and PCR‐based polymorphic markers suitable for genetic diversity analysis were developed. The amplification of 194 primer pairs was initially assessed using a set of 12 isolates of different cereal rust species and their formae speciales. A high frequency of cross‐species amplification was observed for most markers; however, 36 SSRs were diagnostic for P. graminis only. A subset of 19 genome‐derived SSRs were deemed useful for genetic diversity analysis of Pga and were assessed on 66 Pga isolates from Australia, Brazil and Sweden. Brazilian and Australian isolates were characterized by one and two predominant clonal lineages, respectively. In contrast, the Swedish isolates, previously shown to undergo sexual recombination, were highly diverse (nine distinct genotypes out of 10 isolates) and divided into two subpopulations. The genome‐derived SSR markers developed in this study were well suited to the population studies undertaken, and have diagnostic capabilities that should aid in the identification of unknown rust pathogen species.     

Molecular and biological characterization of Cowpea mild mottle virus isolates infecting soybean in Brazil and evidence of recombination

The biological and molecular characterization of six isolates of a new Cowpea mild mottle virus strain (CPMMV; Carlavirus, Betaflexiviridae) are reported. Soybean plants with mosaic and stem necrosis were collected in Bahia, Goiás, Mato Grosso and Minas Gerais states, Brazil. Complete genomes of the CPMMV isolates are 8180–8198 nucleotides (nt) long, excluding the 3′‐polyadenylated tail, and have 67–68% nt sequence identity with a Ghana isolate of CPMMV, the only CPMMV isolate for which the genome has previously been sequenced. The replicase has only 60–61% nt sequence identity with the Ghana CPMMV isolate, and the coat protein (CP) is highly conserved (79% nt sequence identity and 95–96% amino acid sequence identity). The high CP identity and the phylogenetic analyses supported the classification of the Brazilian isolates as CPMMV. Biological and molecular differences with the Ghana CPMMV isolate were found and indicated that the six isolates represent a distinct CPMMV strain denominated as CPMMV‐BR. Furthermore, it is shown that recombination occurred mainly in the polymerase gene, and may occur less frequently in other regions of the CPMMV genome.     

Genotypic diversity and migration of clonal lineages of Botrytis cinerea from chickpea fields of Bangladesh inferred by microsatellite markers

An analysis of allelic diversity at nine microsatellite loci provided an insight into the population structure of Botrytis cinerea from four fields (sampled in 2003 and 2004) that represented important regional locations for chickpea production in Bangladesh. Although three populations were limited by sample size after clone‐correction, a total of 51 alleles were amplified among 146 B. cinerea isolates from Bangladesh, which revealed a high amount of within‐population and overall genetic diversity (H_S = 0·48 and H_T = 0·54, respectively). The percentage of maximal genotypic diversity (G) ranged between populations (G = 23–40), with a total of 69 haplotypes detected (G = 25). Bayesian cluster analysis depicted two major clusters distributed among the four Bangladesh populations, indicating population admixture from two origins that have spread throughout these regions. Genotype flow between regions was detected and indicated the spread of clonal lineages, consistent with relatively low differentiation among the four populations (mean G_ST = 0·1, P < 0·05). These results highlighted the potential threat of host resistance breakdown as a result of considerable genetic diversity, genotype flow and the evolutionary potential of B. cinerea.     

Genetic diversity and population structure of Lasiodiplodia theobromae from different hosts in northeastern Brazil and Mexico

Lasiodiplodia theobromae is one of the most frequent fungal pathogens associated with dieback, gummosis, leaf spot, stem-end rot and fruit rot symptoms in cashew, mango, papaya and grapevine. In this study, the variation in the genetic diversity of 117 L. theobromae isolates from northeastern Brazil (n = 100) and Mexico (n = 17), which were collected from these four crops, was analysed using microsatellite markers. The results revealed low genetic diversity among L. theobromae populations and the existence of two genetic groups. All Mexican isolates were grouped with Brazilian isolates, suggesting a low level of differentiation between these populations. Furthermore, no evident host or climate-based population differentiation was observed for L. theobromae in Brazil. The populations studied were mostly clonal, but additional studies are needed to better understand the mode of reproduction of the pathogen. The low genetic diversity of L. theobromae populations in northeastern Brazil suggests that resistant cultivars could be used as a durable management strategy to reduce the impact of the diseases caused by this pathogen.     

Genetic diversity of the root‐knot nematode Meloidogyne ethiopica and development of a species‐specific SCAR marker for its diagnosis

Meloidogyne ethiopica is an important nematode pathogen causing serious economic damage to grapevine in Chile. In Brazil, M. ethiopica has been detected with low frequency in kiwifruit and other crops. The objectives of this study were to evaluate the intraspecific genetic variability of M. ethiopica isolates from Brazil and Chile using AFLP and RAPD markers and to develop a species‐specific SCAR‐PCR assay for its diagnosis. Fourteen isolates were obtained from different geographic regions or host plants. Three isolates of an undescribed Meloidogyne species and one isolate of M. ethiopica from Kenya were included in the analysis. The results showed a low level of diversity among the M. ethiopica isolates, regardless of their geographical distribution or host plant origin. The three isolates of Meloidogyne sp. showed a high homogeneity and clustered separately from M. ethiopica (100% bootstrap). RAPD screenings of M. ethiopica allowed the identification of a differential DNA fragment that was converted into a SCAR marker. Using genomic DNA from pooled nematodes as a template, PCR amplification with primers designed from this species‐specific SCAR produced a fragment of 350 bp in all 14 isolates of M. ethiopica tested, in contrast with other species tested. This primer pair also allowed successful amplification of DNA from single nematodes, either juveniles or females and when used in multiplex PCR reactions containing mixtures of other root‐knot nematode species, thus showing the sensitivity of the assay. Therefore, the method developed here has potential for application in routine diagnostic procedures.     

Genetic variability of Cercospora coffeicola from organic and conventional coffee plantings, characterized by vegetative compatibility

Cercospora leaf spot is a destructive fungal disease that has become a threat to the coffee industry in Brazil. Nevertheless, little is known about populations of its causal agent, Cercospora coffeicola. We evaluated the potential of using nitrogen-nonutilizing (nit) mutants and vegetative compatibility groups (VCGs) to characterize the genetic variability of the C. coffeicola population associated with coffee plantings in Minas Gerais state (MG), Brazil. A total of 90 monosporic isolates were obtained from samples collected according to a hierarchical sampling scheme: (i) state geographical regions (Sul, Mata, and Triangulo), and (ii) production systems (conventional and organic). Nit mutants were obtained and 28 VCGs were identified. The 10 largest VCGs included 72.31% of all isolates, whereas each of the remaining 18 VCGs included 1.54% of the isolates. Isolates of the largest VCGs were found in the three regions sampled. Based on the frequencies of VCGs at each sampled level, we estimated the Shannon diversity index, as well as its richness and evenness components. Genetic variability was high at all hierarchical levels, and a high number of VCGs was found in populations of C. coffeicola associated with both conventional and organic coffee plantings.     

Phylotype and sequevar variability of Ralstonia solanacearum in Brazil,an ancient centre of diversity of the pathogen

The β‐proteobacterium Ralstonia solanacearum causes bacterial wilt of many plant species. Knowledge of phylotype and sequevar variability in populations of this microorganism is useful for implementing control measures, particularly host resistance. To this end, 301 isolates of R. solanacearum were collected from different geographic regions and hosts in Brazil. Their phylotype and sequevar characterization was used to determine the amount and distribution of phenetic and phylogenetic variability. Isolates were classified into phylotypes I (n = 48), clade 1; and phylotype II, clades 2–5. Phylotype II was divided into subclusters IIA (n = 112) and IIB (n = 141). Phylotype II was widely distributed, whereas phylotype I isolates were found in Central, Northern, and Northeastern regions of Brazil. There were 108 haplotypes identified among endoglucanase (egl) gene sequences from 301 isolates and 32 haplotypes among DNA repair (mutS) gene regions from 176 isolates. The egl and mutS sequence analyses identified eight known (1, 4, 7, 18, 27, 28, 41 and 50) and four new (54, 55, 56 and 57) sequevars. Phylotype IIB showed high diversity in sequevars and host range. Multiplex PCR, using primers specific to the Moko ecotype, characterized banana and long pepper isolates as sequevar 4 and 4/NPB, respectively. This constitutes the first report of the emergent ecotype IIB/4NPB in a new host, long pepper. The majority of sequevars were associated with geographic regions. This high variability of R. solanacearum in Brazil suggests use of host resistance to control bacterial wilt should be mainly focused by region.     

Genetic variation in Fusarium avenaceum causing root rot on field pea

Isolates of Fusarium spp. were recovered from the roots of field pea (Pisum sativum) collected from 15 commercial fields in Alberta, Canada. Most of the isolates (75 out of 96) were identified as F. avenaceum, based on morphology, phylogeny and species‐specific PCR amplification. Molecular differences in the F. avenaceum isolates were detected based on putative mating type, and on ITS and CPN60 sequences. MAT‐1 and MAT‐2 were equally distributed among the isolates. Phylogenetic analysis based on ITS and CPN60 sequences clustered most of the F. avenaceum isolates into a single group. In some cases, isolates with low aggressiveness clustered together in additional groups. There was no correlation between phylogenetic profile and either mating type or geographic origin. This population of F. avenaceum has a low level of genetic variation and consists of isolates derived from the two mating types. Isolates with low aggressiveness are also retained in the population.