Genetic Diversity Among Alternaria solani Isolates from Potatoes in South Africa

Genotyping-by-Sequencing Reveals Population Differentiation and Linkage Disequilibrium in Alternaria linariae from Tomato

Alternaria linariae is an economically important foliar pathogen that causes early blight disease in tomatoes. Understanding genetic diversity, population genetic structure, and evolutionary potential is crucial to contemplating effective disease management strategies. We leveraged genotyping-by-sequencing (GBS) technology to compare genome-wide variation in 124 isolates of Alternaria spp. (A. alternata, A. linariae, and A. solani) for comparative genome analysis and to test the hypotheses of genetic differentiation and linkage disequilibrium (LD) in A. linariae collected from tomatoes in western North Carolina. We performed a pangenome-aware variant calling and filtering with GBSapp and identified 53,238 variants conserved across the reference genomes of three Alternaria spp. The highest marker density was observed on chromosome 1 (7 Mb). Both discriminant analysis of principal components and Bayesian model-based STRUCTURE analysis of A. linariae isolates revealed three subpopulations with minimal admixture. The genetic differentiation coefficients (FST) within A. linariae subpopulations were similar and high (0.86), indicating that alleles in the subpopulations are fixed and the genetic structure is likely due to restricted recombination. Analysis of molecular variance indicated higher variation among populations (89%) than within the population (11%). We found long-range LD between pairs of loci in A. linariae, supporting the hypothesis of low recombination expected for a fungal pathogen with limited sexual reproduction. Our findings provide evidence of a high level of population genetic differentiation in A. linariae, which reinforces the importance of developing tomato varieties with broad-spectrum resistance to various isolates of A. linariae.

Alternaria diseases on potato and tomato

Alternaria spp. cause different diseases in potato and tomato crops. Early blight caused by Alternaria solani and brown spot caused by Alternaria alternata are most common, but the disease complex is far more diverse. We first provide an overview of the Alternaria species infecting the two host plants to alleviate some of the confusion that arises from the taxonomic rearrangements in this fungal genus. Highlighting the diversity of Alternaria fungi on both solanaceous hosts, we review studies investigating the genetic diversity and genomes, before we present recent advances from studies elucidating host-pathogen interactions and fungicide resistances.

TAXONOMY

Kingdom Fungi, Phylum Ascomycota, Class Dothideomycetes, Order Pleosporales, Family Pleosporaceae, Genus Alternaria.

BIOLOGY AND HOST RANGE

Alternaria spp. adopt diverse lifestyles. We specifically review Alternaria spp. that cause disease in the two solanaceous crops potato (Solanum tuberosum) and tomato (Solanum lycopersicum). They are necrotrophic pathogens with no known sexual stage, despite some signatures of recombination.

DISEASE SYMPTOMS

Symptoms of the early blight/brown spot disease complex include foliar lesions that first present as brown spots, depending on the species with characteristic concentric rings, which eventually lead to severe defoliation and considerable yield loss.

CONTROL

Good field hygiene can keep the disease pressure low. Some potato and tomato cultivars show differences in susceptibility, but there are no fully resistant varieties known. Therefore, the main control mechanism is treatment with fungicides.

Isolation and Identification of Alternaria alternata from Potato Plants Affected by Leaf Spot Disease in Korea: Selection of Effective Fungicides

Brown leaf spot disease caused by Alternaria spp. is among the most common diseases of potato crops. Typical brown spot symptoms were observed in commercial potato-cultivation areas of northern Korea from June to August 2020-2021. In total, 68 isolates were collected, and based on sequence analysis of the internal transcribed spacer (ITS) region, the collected isolates were identified as Alternaria spp. (80.9%). Phylogenetic analysis revealed that a majority of these isolates clustered within a clade that included A. alternata. Additionally, the ITS region and rpb2 yielded the most informative sequences for the identification of A. alternata. Pathogenicity tests confirmed that the collected pathogens elicited symptoms identical to those observed in the field. In pathogenicity tests performed on seven commercial cultivars, the pathogens exhibited strong virulence in both wound and non-wound inoculations. Among the cultivars tested, Arirang-1ho, Arirang-2ho, and Golden Ball were resistant to the pathogens. Furthermore, among the fungicides tested in vitro, mancozeb and difenoconazole were found to be effective for inhibiting mycelial growth. In summary, our findings suggest that A. alternata plays a critical role in leaf disease in potato-growing regions and emphasise the necessity of continuous monitoring and management to protect against this disease in Korea.

Random amplified microsatellites (RAMS) analysis ascertains genetic variation of Alternaria alternata causing black spot disease on Carya illinoinensis in South Africa

Limited information regarding the occurrence of black spot disease of pecan (Carya illinoinensis), caused by A. alternata, in South Africa is known. The pecan industry is growing rapidly, so it is essential to understand the impact of the fungal pathogen to pecan health. In this study, the genetic variation of 364 A. alternata isolates was investigated by two RAMS primers (CCA5 and CGA5). In total, 6,525 alleles were produced, with a minimum of 3,182 alleles on the CGA5 primer and maximum of 3,343 alleles for CCA5 primer. Further analysis of the primers showed relatively low genetic diversity of A. alternata isolate populations, with mean values; (H = 0.12) and Shannon's information index (I = 0.20). The analysis of molecular variance (AMOVA) revealed significant differences between populations, with 88% of the genetic variation was found within populations (Nm = 3.59, PhiPT = 0.12), and were not significantly different (p > 0.001). While 12% variation was observed among populations (Nm = 2.89, PhiPT = 0.08) and the estimates were statistically significant (p < 0.001). STRUCTURE HARVESTER output showed that K value is K = 8, where ΔK cannot find the true number of populations because of less variation. The dendrogram cluster tree generated by Ward's analysis unveiled two main distinct clades and 10 sub-clades, revealing similar findings as those of PCoA analysis clusters. Therefore, it was evident that these analyses depicted no distinct relationship between the A. alternata isolates and their geographic locations or the prevalence of distribution among the populations.

Morphological and Molecular Variability of Alternaria solani and Phytophthora infestans Causing Tomato Blights

Alternaria solani and Phytophthora infestans cause early and late blight diseases in tomato and potato, respectively. A. solani can survive for more than a decade in the soil, seed, or in plant residues at optimum temperature. The pathogen exhibits high molecular and genetic variation between isolates from potato and tomato plants, in different countries. Morphological studies reveal separate conidia borne singly on simple conidiophores. Spores are elongated, muriform, beaked, septate, and dark coloured. The mycelia are branched and septate. A. solani demonstrated a high genetic variability among isolates originating from the United States, Greece, Cuba, Canada, Russia, Turkey, South Africa, Brazil, and China based on vegetative compatibility groups and molecular markers (random amplified polymorphic DNA markers, random amplified microsatellite markers, and amplified fragment length polymorphisms). Different morphological and molecular variations indicate the presence of variability among the isolates. On the other hand, P. infestans is a diploid, obligate, heterothallic, and biotrophic oomycete, whose asexual lifecycle is characterized by alternating phases of sporangia germination, hyphal growth, and sporulation. The mycelia of P. infestans is coenocytic, multinucleate, and aseptate although the cross walls do not form in old cultures. Sporangia are borne singly on the branch tips of the alternately branched sporangiophore. Sporangium is hyaline and lemon shaped with a papilla at the distal end. Mating types A1 and A2 with different clonal lineages have been discovered in various parts of the world indicating variation in the species.

New Insight in the Occurrence of Early Blight Disease on Potato Reveals High Distribution of Alternaria solani and Alternaria protenta in Serbia

Early blight is an economically important disease of potato worldwide. Understanding which fungal pathogens are the causal agents of early blight and their distribution on the same host is essential to finding the best strategy for the control of this disease. Previous studies have shown that Alternaria solani is the main early blight pathogen parasitizing potato. Here, we analyzed genetic and phenotypic diversity in isolates of Alternaria spp. covering all potato production areas in Serbia. We showed that the four species of Alternaria were found in areas with different distributions of the species. The occurrence of Alternaria spp. was studied by analyzing isolates from symptomatic potato leaves during multiyear sampling. In addition to Alternaria solani, we detected three more large-spored species identified as A. linariae (syn. A. tomatophila), A. protenta, and A. grandis that were involved in early blight disease on naturally infected potato leaves in Serbia. Differentiation of species was supported by phylogeny obtained from the DNA sequences of the GAPDH, calmodulin and Rpb2 genes. Our findings present a new perspective into the population structure of large-spored Alternaria species associated with early blight disease. Within the groups of large-spored Alternaria present in Serbia, evidence of A. protenta at high frequency reveals new insight into the contribution of Alternaria species in early blight disease. This work opens new perspectives for early blight management, while the distribution of different species on the same host suggests that the etiology of disease could depend on crop organization and the presence of other Alternaria hosts in close proximity to potato plants.

Whole genome sequencing elucidates the species‐wide diversity and evolution of fungicide resistance in the early blight pathogen Alternaria solani

Early blight of potato is caused by the fungal pathogen Alternaria solani and is an increasing problem worldwide. The primary strategy to control the disease is applying fungicides such as succinate dehydrogenase inhibitors (SDHI). SDHI‐resistant strains, showing reduced sensitivity to treatments, appeared in Germany in 2013, shortly after the introduction of SDHIs. Two primary mutations in the SDH complex (SdhB‐H278Y and SdhC‐H134R) have been frequently found throughout Europe. How these resistances arose and spread, and whether they are linked to other genomic features, remains unknown. For this project, we performed whole‐genome sequencing for 48 A. solani isolates from potato fields across Europe to better characterize the pathogen's genetic diversity in general and understand the development and spread of the genetic mutations that lead to SDHI resistance. The isolates can be grouped into seven genotypes. These genotypes do not show a geographical pattern but appear spread throughout Europe. We found clear evidence for recombination on the genome, and the observed admixtures might indicate a higher adaptive potential of the fungus than previously thought. Yet, we cannot link the observed recombination events to different Sdh mutations. The same Sdh mutations appear in different, non‐admixed genetic backgrounds; therefore, we conclude they arose independently. Our research gives insights into the genetic diversity of A. solani on a genome level. The mixed occurrence of different genotypes, apparent admixture in the populations, and evidence for recombination indicate higher genomic complexity than anticipated. The conclusion that SDHI tolerance arose multiple times independently has important implications for future fungicide resistance management strategies. These should not solely focus on preventing the spread of isolates between locations but also on limiting population size and the selective pressure posed by fungicides in a given field to avoid the rise of new mutations in other genetic backgrounds.

Green Synthesis of Silver Nanoparticles Using Pomegranate and Orange Peel Extracts and Their Antifungal Activity against Alternaria solani, the Causal Agent of Early Blight Disease of Tomato

This study aimed to synthesize silver nanoparticles (AgNPs) by pomegranate and orange peel extracts using a low concentration of AgNO₃ solution to controlearly blight of tomato caused by Alternaria solani. The pathogen was isolated from infected tomato plants growing in different areas of Saudi Arabia. The isolates of this pathogen were morphologically and molecularly identified. Extracts from peels of pomegranate and orange fruits effectively developed a simple, quick, eco-friendly and economical method through a synthesis of AgNPs as antifungal agents against A. solani. Phenolic content in the pomegranate peel extract was greater than orange peel extract. Phenolic compounds showed a variation of both peel extracts as identified and quantified by High-Performance Liquid Chromatography. The phenolic composition displayed variability as the pomegranate peel extract exhibited an exorbitant amount of Quercitrin (23.62 mg/g DW), while orange peel extract recorded a high amount of Chlorogenic acid (5.92 mg/g DW). Biosynthesized AgNPs were characterized using UV- visible spectroscopy which recorded an average wavelength of 437 nm and 450 nm for pomegranate and orange peels, respectively. Fourier-transform infrared spectroscopy exhibited 32x73.24, 2223.71, 2047.29 and 1972.46 cm^-1, and 3260.70, 1634.62, 1376.62 and 1243.76 cm^-1 for pomegranate and orange peels, respectively. Transmission electron microscopy showed spherical shape of nanoparticles. Zetasizer analysis presented negative charge values; -16.9 and -19.5 mV with average particle sizes 8 and 14 nm fin case of pomegranate and orange peels, respectively. In vitro, antifungal assay was done to estimate the possibility of biosynthesized AgNPs and crude extracts of fruit peels to reduce the mycelial growth of A. solani. AgNPs displayed more fungal mycelial inhibition than crude extracts of two peels and AgNO₃. We recommend the use of AgNPs synthesized from fruit peels for controlling fungal plant pathogens and may be applied broadly and safely in place by using the chemical fungicides, which display high toxicity for humans.

Impact of SDH Mutations in Alternaria solani on Recently Developed SDHI Fungicides Adepidyn and Solatenol

Early blight, caused by Alternaria solani, is observed annually in all midwestern potato production areas. The use of foliar fungicides remains a primary management strategy. However, A. solani has developed reduced sensitivity or resistance to many single-site fungicides such as quinone outside inhibitor (QoI, FRAC group 11), succinate dehydrogenase inhibitor (SDHI, FRAC group 7), demethylation inhibitor (DMI, FRAC group 3), and anilinopyrimidine (AP, FRAC group 9) fungicides. Boscalid, fluopyram, solatenol, and adepidyn are EPA-registered SDHI fungicides used commercially on a variety of crops, including potato. Five SDH mutations have been characterized previously in A. solani that affect the efficacy of boscalid while only one of these mutations has been demonstrated to negatively affect fluopyram efficacy. Conidial germination assays were used to determine if a shift in sensitivity has occurred in these SDHI fungicides. A. solani isolates collected prior to the commercial application of SDHI fungicides (baseline) were compared with recently collected isolates (nonbaseline). Greenhouse evaluations were conducted also to evaluate the efficacy of boscalid, fluopyram, solatenol, and adepidyn on A. solani isolates possessing individual SDH mutations. Additionally, field trials were conducted to determine the effects of application of these SDHI fungicides on the frequency of SDH mutations. Fluopyram, solatenol, and adepidyn had high intrinsic activity against A. solani when compared with boscalid, based on in vitro assays. The application of adepidyn and solatenol resulted in greater early blight control than the application of boscalid and fluopyram in greenhouse experiments. Molecular characterization of A. solani isolates collected from the field trials determined that the frequency of the H134R-mutation can increase in response to more recently developed SDHI fungicides. In contrast, the H278R/Y- and H133R-mutations decreased to the point of being nearly absent in these field experiments.

Genetic diversity and population structure of Alternaria species from tomato and potato in North Carolina and Wisconsin

Early blight (EB) caused by Alternaria linariae or Alternaria solani and leaf blight (LB) caused by A. alternata are economically important diseases of tomato and potato. Little is known about the genetic diversity and population structure of these pathogens in the United States. A total of 214 isolates of A. alternata (n = 61), A. linariae (n = 96), and A. solani (n = 57) were collected from tomato and potato in North Carolina and Wisconsin and grouped into populations based on geographic locations and tomato varieties. We exploited 220 single nucleotide polymorphisms derived from DNA sequences of 10 microsatellite loci to analyse the population genetic structure between species and between populations within species and infer the mode of reproduction. High genetic variation and genotypic diversity were observed in all the populations analysed. The null hypothesis of the clonality test based on the index of association \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\left( {\overline{r}_{d} } \right)$$\end{document}r¯d was rejected, and equal frequencies of mating types under random mating were detected in some studied populations of Alternaria spp., suggesting that recombination can play an important role in the evolution of these pathogens. Most genetic differences were found between species, and the results showed three distinct genetic clusters corresponding to the three Alternaria spp. We found no evidence for clustering of geographic location populations or tomato variety populations. Analyses of molecular variance revealed high (> 85%) genetic variation within individuals in a population, confirming a lack of population subdivision within species. Alternaria linariae populations harboured more multilocus genotypes (MLGs) than A. alternata and A. solani populations and shared the same MLG between populations within a species, which was suggestive of gene flow and population expansion. Although both A. linariae and A. solani can cause EB on tomatoes and potatoes, these two species are genetically differentiated. Our results provide new insights into the evolution and structure of Alternaria spp. and can lead to new directions in optimizing management strategies to mitigate the impact of these pathogens on tomato and potato production in North Carolina and Wisconsin.

Parasexual reproduction in Alternaria solani: Simple sequence repeat molecular evidence for haploidization

Multiple alleles were constantly detected in Alternaria solani isolates by simple sequence repeat (SSR) analysis, and sectors were also observed in their subcultures. These preliminary results and observations point to a possible parasexual cycle in A. solani. In this study, codominant SSR markers were used as molecular markers on the chromosomes of A. solani and single-conidium subculture was used to simulate the mitosis process of A. solani in nature. The number of alleles at locus As-95236 changed from 2 to 1 as a molecular marker for haploidy of parasexuality of A. solani. Fifty monosporic F1 strains were tested. The results showed that two parent strains lost allele with a haploid probability of 38%. For F2 strains, the results showed that all four F1 strains lost allele with a haploid probability of 75%. Since sexual recombination of A. solani has not been found so far, the allele lost in the subcultures of A. solani isolates provides molecular evidence for the existence of parasexual reproduction in A. solani.

Species diversity, novel interactions and absence of well-supported host-guided phylogenetic groupings of Neotropical Alternaria isolates causing foliar lesions in Solanaceae

AIM

To report the characterization of 120 Alternaria isolates inducing early blight-like foliar lesions in nine species of five Solanaceae genera collected across all macrogeographical Brazilian regions.

MATERIAL AND RESULTS

Phylogenetic relationships were assessed via analyses of the Alternaria alternata allergenic protein-coding, glyceraldehyde-3-phosphate dehydrogenase and the calmodulin gene sequences. Most of the tomato isolates were placed into the Alternaria linariae cluster, whereas most of the potato isolates were grouped with Alternaria grandis. Novel host-pathogen interactions were also reported. Seventeen isolates were selected for morphometrical characterization, and a subsample of 13 isolates was employed in pathogenicity assays on tomato, potato, eggplant, scarlet eggplant, Capsicum annuum, Datura stramonium, Physalis angulata and Nicotiana tabacum. Eleven isolates were able to induce foliar lesions in tomatoes but none in C. annuum. Potato was susceptible to a subgroup of isolates but displayed a subset of isolate-specific interactions. Morphological traits were in overall agreement with molecular and host range data.

CONCLUSION

Alternaria linariae and A. grandis were confirmed as the major causal agents of tomato and potato early blight, respectively. However other Alternaria species are also involved with early blight in solanaceous hosts in Brazil.

SIGNIFICANCE AND IMPACT OF THE STUDY

The diversity and host-specific patterns of the Alternaria isolates from Solanaceae may have practical implications in establishing effective early blight genetic resistance and cultural management strategies especially for tomato and potato crops.

Diversity and Virulence of Alternaria spp. Causing Potato Early Blight and Brown Spot in Wisconsin

Early blight, caused by Alternaria solani, along with brown spot, caused by A. alternata, have the potential to reduce quality and yield in potato production globally. Prior to this study, the incidence, disease impact, and fungicide resistance attributes of A. alternata in Wisconsin were poorly understood. Potato pathogens were isolated from foliar lesions at three commercial locations in Wisconsin in 2012 and 2017 and were initially morphologically identified as A. solani (n = 33) and A. alternata (n = 40). Identifications were further corroborated with the phylogenetic analysis of the internal transcribed spacer (ITS), translation elongation factor 1 (TEF1), gapdh, Alt a 1, and OPA10-2. A multigene phylogeny of ITS, TEF1, gapdh, and Alt a 1 showed five genotypes of A. alternata and one single genotype of A. solani. We demonstrated that the A. alternata isolates were virulent on potato cultivars Russet Burbank (P < 0.013) and Atlantic (P < 0.0073), though they caused less disease than A. solani (P < 0.0001 and P < 0.0001, respectively). A. alternata caused little disease on the breeding line 24-24-12 (P = 0.9929), and A. solani caused fewer disease symptoms on 24-24-12 than on Russet Burbank (P < 0.0001) or Atlantic (P < 0.0001). Breeding line 24-24-12 may be a promising source of potential resistance for the two diseases. There was no significant difference in virulence of different A. alternata genotypes, and no significant difference in virulence or genotype clustering among isolates from the three locations. Isolates of A. alternata that induced chlorosis caused larger lesion areas than isolates that did not in Russet Burbank (P < 0.0001), Atlantic (P < 0.0001), and 24-24-12 (P = 0.0365). There was no significant difference in virulence between quinone outside inhibitor (QoI)-sensitive and QoI-resistant isolates of A. alternata. This study enhanced our understanding of potato early blight and brown spot in Wisconsin, and suggested that A. alternata in addition to A. solani should be carefully monitored and possibly uniquely managed in order to achieve overall disease control.

The Population Genetics of Alternaria tenuissima in Four Regions of China as Determined by Microsatellite Markers Obtained by Transcriptome Sequencing

A total of 32,284 unigenes were obtained from the transcriptome of Alternaria tenuissima, a pathogenic fungus causing foliar disease in tomato, using next-generation sequencing (NGS) technology. In total, 24,670 unigenes were annotated using five databases, including NCBI non-redundant protein, Swiss-Prot, euKaryotic Orthologous Groups, Kyoto Encyclopedia of Genes and Genomes, and the Gene Ontology. A total of 1,140 simple sequence repeats were also identified for use as molecular markers. Sixteen of the simple sequence repeat loci were selected to study the population structure of A. tenuissima. A population genetic analysis of 191 A. tenuissima isolates, sampled from four geographic regions in China, indicated that A. tenuissima had a high level of genetic diversity, and that the selected simple sequence repeat markers could reliably capture the genetic variation. The null hypothesis of random mating was rejected for all four geographic regions in China. Isolation by distance was observed for the entire data set, but not within clusters, which is indicative of barriers to gene flow among geographic regions. The analyses of Bayesian and principal coordinates, however, did not separate four geographic regions into four separate genetic clusters. The different levels of historical migration rates suggest that isolation by distance did not represent a major biological obstacle to the spread of A. tenuissima. The potential epidemic spread of A. tenuissima in China may occur through the transport of plant products or other factors. The presented results provide a basis for a comprehensive understanding of the population genetics of A. tenuissima in China.

Genome sequence of the potato pathogenic fungus Alternaria solani HWC-168 reveals clues for its conidiation and virulence

BACKGROUND

Alternaria solani is a known air-born deuteromycete fungus with a polycyclic life cycle and is the causal agent of early blight that causes significant yield losses of potato worldwide. However, the molecular mechanisms underlying the conidiation and pathogenicity remain largely unknown.

RESULTS

We produced a high-quality genome assembly of A. solani HWC-168 that was isolated from a major potato-producing region of Northern China, which facilitated a comprehensive gene annotation, the accurate prediction of genes encoding secreted proteins and identification of conidiation-related genes. The assembled genome of A. solani HWC-168 has a genome size 32.8 Mb and encodes 10,358 predicted genes that are highly similar with related Alternaria species including Alternaria arborescens and Alternaria brassicicola. We identified conidiation-related genes in the genome of A. solani HWC-168 by searching for sporulation-related homologues identified from Aspergillus nidulans. A total of 975 secreted protein-encoding genes, which might act as virulence factors, were identified in the genome of A. solani HWC-168. The predicted secretome of A. solani HWC-168 possesses 261 carbohydrate-active enzymes (CAZy), 119 proteins containing RxLx[EDQ] motif and 27 secreted proteins unique to A. solani.

CONCLUSIONS

Our findings will facilitate the identification of conidiation- and virulence-related genes in the genome of A. solani. This will permit new insights into understanding the molecular mechanisms underlying the A. solani-potato pathosystem and will add value to the global fungal genome database.

Identification and Characterization of Alternaria Species Associated with Moldy Core of Apple in Chile

Moldy core (MC) of apple is an important disease in Chile, with prevalence observed between 4 and 46% in Fuji, Oregon Spur Red Chief, and Scarlet apple in the 2014-15 and 2015-16 growing seasons. However, there is no information on the identity of the causal agents associated with MC in Chile. The analysis of 653 MC fruit revealed the presence of several genera of filamentous fungi. However, species of Alternaria (67.7%) were by far the most frequently fungi isolated. In total, 41 Alternaria isolates were characterized morphologically and molecularly using Alternaria major allergen Alt a1, calmodulin, and plasma membrane ATPase gene regions. Six small-spored Alternaria spp. were identified; namely, in order of importance, Alternaria tenuissima, A. arborescens, A. alternata, and A. dumosa in sect. Alternaria; A. frumenti in sect. Infectoriae; and A. kordkuyana in sect. Pseudoalternaria. MC symptoms were reproducible and consisted of a light gray to dark olive-green mycelium over the carpel and seed of immature and mature fruit, confirming that the isolates of these Alternaria spp. were pathogenic. These isolates caused brown necrotic lesions with concentric rings on wounded detached apple leaves. This study demonstrated that at least six Alternaria spp. are the cause of MC of apple in Chile. These Alternaria spp. were isolated alone, or with two or more species coexisting in the same fruit. This is the first report of A. tenuissima, A. arborescens, A. frumenti, A. dumosa, and A. kordkuyana associated with MC of apple in Chile and the first report of A. frumenti, A. kordkuyana, and A. dumosa causing MC of apple worldwide.

Population structure and virulence analysis of Alternaria carthami isolates of India using ISSR and SSR markers

Alternaria leaf spot caused by Alternaria carthami is one of the most devastating diseases of safflower. Diversity among 95 isolates of A. carthami was determined using virulence assays, enzyme assays, dominant (ISSR) and co-dominant (SSR) markers. Collections and isolations were made from three major safflower producing states of India. The virulence assays categorised the population into four groups based on level of virulence. Estimation of activities of cell wall degrading enzymes (CWDE) yielded concurrent results to virulence assays with maximum CWDE activities in most virulent group. Eighteen ISSR primers were used and 23 polymorphic microsatellite markers were developed to assess the genetic diversity and determine the population structure of A. carthami. Analysis of ISSR profiles revealed high genetic diversity (Nei's Genetic diversity index; h = 0.36). Microsatellite markers produced a total of 56 alleles with an average of 2.43 alleles per microsatellite marker and Nei's genetic diversity index as h = 0.43. Unweighted Neighbor-joining and population structure analysis using both the marker systems differently arranged the isolates into three clusters. Distance analysis of the marker profiles provided no evidence for geographical clustering of isolates, indicating that isolates are randomly spread across India, signifying high potential of the fungus to adapt to diverse regions. Microsatellite markers clustered the isolates in consonance to the virulence groups in the dendrogram. This implies that the fungus has a high potential to adapt to resistant cultivars or fungicides. The information can aid in the breeding and deployment of A. carthami resistant varieties, and in early blight disease management in all safflower growing regions of the world.

Discovering Novel Alternaria solani Succinate Dehydrogenase Inhibitors by in Silico Modeling and Virtual Screening Strategies to Combat Early Blight

Alternaria blight is an important foliage disease caused by Alternaria solani. The enzyme Succinate dehydrogenase (SDH) is a potential drug target because of its role in tricarboxylic acid cycle. Hence targeting Alternaria solani SDH enzyme could be efficient tool to design novel fungicides against A. solani. We employed computational methodologies to design new SDH inhibitors using homology modeling; pharmacophore modeling and structure based virtual screening. The three dimensional SDH model showed good stereo-chemical and structural properties. Based on virtual screening results twelve commercially available compounds were purchased and tested in vitro and in vivo. The compounds were found to inhibit mycelial growth of A. solani. Moreover in vitro trials showed that inhibitory effects were enhanced with increase in concentrations. Similarly increased disease control was observed in pre-treated potato tubers. Hence the applied in silico strategy led us to identify novel fungicides.

Population Diversity and Sensitivity to Azoxystrobin of Alternaria brassicicola in New York State

Alternaria brassicicola is the causal agent of Alternaria leaf spot, a common disease of brassica crops in New York State. New York isolates of A. brassicicola were collected from a variety of brassica crops and locations to evaluate the population diversity and screen for fungicide sensitivity. Isolates were genotyped for 10 microsatellite loci and assayed for sensitivity to azoxystrobin, a quinone outside inhibitor fungicide. The New York State population of A. brassicicola was found to have high levels of genotypic diversity and the population was found to be in linkage disequilibrium. Based on in vitro assays, the effective concentrations of azoxystrobin reducing spore germination by 50% ranged from 0.22 to 14.12 μg/ml. In order to confirm the sensitivity of 47 isolates to azoxystrobin, the cytb gene was characterized and sequenced to determine whether any of the mutations known to confer resistance to azoxystrobin were present. The mutations F129L, G137R, and G143A were not detected in the isolates studied.

Natural Occurrence of Alternaria Toxins in the 2015 Wheat from Anhui Province, China

The exposure to Alternaria toxins from grain and grain-based products has been reported to be related to human esophageal cancer in China. In this study, a total of 370 freshly harvested wheat kernel samples collected from Anhui province of China in 2015 were analyzed for the four Alternaria toxins tenuazonic acid (TeA), tentoxin (TEN), alternariol (AOH) and alternariol monomethyl ether (AME) by high performance liquid chromatography-tandem mass spectrometry method (HPLC-MS/MS). TeA was the predominant toxin detected followed by TEN, AOH and AME. The concentrations of the four Alternaria toxins varied geographically. The samples from Fuyang district showed higher TEN concentration levels than the other regions studied (p < 0.05). Furthermore, 95% (352/370) of the wheat samples were positive for more than one type of Alternaria toxins. Positive correlation was observed between concentration levels of TeA and TEN, AOH and AME, TeA and AOH, and the total dibenzopyrone derivatives (AOH + AME) and TeA. Results indicate that there is a need to set the tolerance limit for Alternaria toxins in China, and more data on the contamination of these toxins in agro-products is required.

Genetic diversity and occurrence of the F129L substitutions among isolates of Alternaria solani in south-eastern Sweden

BACKGROUND

Early blight, caused by the fungus Alternaria solani, occurs on potato mainly in the south-eastern part of Sweden, but also in other parts of the country. The aim of this study was to investigate the genetic diversity of A. solani populations from different potato growing regions in south-eastern Sweden using AFLP marker analysis. In addition, the cultured isolates were examined for substitutions in the gene encoding cytochrome b, associated with loss of sensitivity against QoI fungicides.

RESULTS

Nei's gene diversity index for the Swedish populations of A. solani revealed a gene diversity of up to 0.20. Also genetic differentiation was observed among populations of A. solani from different locations in south-eastern Sweden. The mitochondrial genotype of the isolates of A. solani was determined and both known genotypes, GI (genotype 1) and GII (genotype 2), were found among the isolates. The occurrence of the F129L substitution associated with a loss of sensitivity to strobilurins was confirmed among the GII isolates. In vitro conidial germination tests verified that isolates containing the F129L substitution had reduced sensitivity to azoxystrobin and, at a lower extent, to pyraclostrobin.

CONCLUSIONS

Genetic diversity was relatively high among isolates of A. solani in south-eastern part of Sweden. F129L substitutions, leading to reduced sensitivity to strobilurins, have been established in field populations, which may have implications for the future efficacy of QoI fungicides.

Spatial and Temporal Sensitivity of Alternaria Species Associated With Potato Foliar Diseases to Demethylation Inhibiting and Anilino-Pyrimidine Fungicides

Early blight and brown spot, caused by Alternaria solani and Alternaria alternata, respectively, are important foliar diseases of potato, affecting both tuber yield and quality. Most of the commercial cultivars lack resistance; therefore, the application of foliar fungicides remains a primary disease management strategy. Baseline sensitivities of A. solani to difenoconazole and metconazole (demethylation inhibitors) using mycelial growth assay exhibited similar intrinsic activity against the pathogen with mean EC₅₀ (the effective concentration at which the fungal growth is inhibited by 50%) values of 0.09 μg/ml. However, the sensitivity of individual baseline A. solani isolates to each fungicide varied substantially, resulting in very low and nonsignificant correlation coefficients among fungicides. Mean EC₅₀ values for baseline A. alternata isolates in response to difenoconazole and metconazole were 0.14 and 0.26 μg/ml, respectively. The sensitivity of the majority of A. solani and A. alternata isolates collected from 2010 to 2014 from various potato production states was consistent with baseline isolates, therefore, these potato pathogens remain sensitive to the two demethylation inhibitor chemistries used to manage it. Baseline sensitivity assays of pyrimethanil (anilino-pyrimidine) also indicated great intrinsic activity against both foliar pathogens with mean EC₅₀ values of 0.44 and 0.35 μg/ml for A. solani and A. alternata, respectively. Although A. alternata remains largely sensitive to pyrimethanil, 6 out of 245 A. solani isolates collected from 2010 to 2014 exhibited reduced-sensitivity to the fungicide in in vitro assays. Reduced-sensitive isolates were not controlled at most pyrimethanil doses except at 100 μg/ml in greenhouse in vivo efficacy tests. These chemistries remain valuable options for fungicide rotation programs in areas of high disease pressure.

Survey of Alternaria toxin contamination in food from the German market, using a rapid HPLC-MS/MS approach

A HPLC-MS/MS-based method for the quantification of nine mycotoxins produced by fungi of the genus Alternaria in various food matrices was developed. The method relies on a single-step extraction, followed by dilution of the raw extract and direct analysis. In combination with an analysis time per sample of 12 min, the sample preparation is cost-effective and easy to handle. The method covers alternariol (AOH), alternariol monomethyl ether (AME), tenuazonic acid (TeA), altenuene (ALT), iso-altenuene (isoALT), tentoxin (TEN), altertoxin-I (ATX-I), and the AAL toxins TA1 and TA2. Some Alternaria toxins which are either not commercially available or very expensive, namely AOH, AME, ALT, isoALT, and ATX-I, were isolated as reference compounds from fungal cultures. The method was extensively validated for tomato products, bakery products, sunflower seeds, fruit juices, and vegetable oils. AOH, AME, TeA, and TEN were found in quantifiable amounts and 92.1% of all analyzed samples (n = 96) showed low level contamination with one or more Alternaria toxins. Based on the obtained results, the average daily exposure to Alternaria toxins in Germany was calculated.

Large-spored Alternaria pathogens in section Porri disentangled

The omnipresent fungal genus Alternaria was recently divided into 24 sections based on molecular and morphological data. Alternaria sect. Porri is the largest section, containing almost all Alternaria species with medium to large conidia and long beaks, some of which are important plant pathogens (e.g. Alternaria porri, A. solani and A. tomatophila). We constructed a multi-gene phylogeny on parts of the ITS, GAPDH, RPB2, TEF1 and Alt a 1 gene regions, which, supplemented with morphological and cultural studies, forms the basis for species recognition in sect. Porri. Our data reveal 63 species, of which 10 are newly described in sect. Porri, and 27 species names are synonymised. The three known Alternaria pathogens causing early blight on tomato all cluster in one clade, and are synonymised under the older name, A. linariae. Alternaria protenta, a species formerly only known as pathogen on Helianthus annuus, is also reported to cause early blight of potato, together with A. solani and A. grandis. Two clades with isolates causing purple blotch of onion are confirmed as A. allii and A. porri, but the two species cannot adequately be distinguished based on the number of beaks and branches as suggested previously. This is also found among the pathogens of Passifloraceae, which are reduced from four to three species. In addition to the known pathogen of sweet potato, A. bataticola, three more species are delineated of which two are newly described. A new Alternaria section is also described, comprising two large-spored Alternaria species with concatenate conidia.

Gomes A. Unravelling the diversity of grapevine microbiome

Vitis vinifera is one of the most widely cultivated fruit crops with a great economic impact on the global industry. As a plant, it is naturally colonised by a wide variety of both prokaryotic and eukaryotic microorganisms that interact with grapevine, having either beneficial or phytopathogenic effects, who play a major role in fruit yield, grape quality and, ultimately, in the evolution of grape fermentation and wine production. Therefore, the objective of this study was to extensively characterize the natural microbiome of grapevine. Considering that the majority of microorganisms are uncultivable, we have deeply studied the microflora of grapevine leaves using massive parallel rDNA sequencing, along its vegetative cycle. Among eukaryotic population the most abundant microorganisms belonged to the early diverging fungi lineages and Ascomycota phylum, whereas the Basidiomycota were the least abundant. Regarding prokaryotes, a high diversity of Proteobacteria, Firmicutes and Actinobacteria was unveiled. Indeed, the microbial communities present in the vineyard during its vegetative cycle were shown to be highly structured and dynamic. In all cases, the major abundant microorganisms were the yeast-like fungus Aureobasidium and the prokaryotic Enterobacteriaceae. Herein, we report the first complete microbiome landscape of the vineyard, through a metagenomic approach, and highlight the analysis of the microbial interactions within the vineyard and its importance for the equilibrium of the microecosystem of grapevines.

Biochemical evaluation of resistance responses of potato to different isolates of Alternaria solani

The resistance phenotypes of nine potato cultivars to five isolates of Alternaria solani, causal agent of early blight, were studied after inoculation and growth under greenhouse conditions. We identified potato cultivars with both susceptible and resistant phenotypes as well as A. solani isolates with varying degrees of aggressiveness. Two potato cultivars and two pathogen isolates were selected for biochemical analysis of phenol production and peroxidase activity after inoculation. Phenol compounds were evaluated 2, 4, 6, and 8 days after inoculation, while peroxidase activities were monitored daily for 10 days. Native polyacrylamide electrophoresis was used to identify one protein with peroxidase activity in extracts taken 6 days after inoculation. Significantly higher peroxidase activity as well as total phenol content in potato was correlated with resistance in the Iranian potato cultivar Diamond. Variability of responses within the same cultivar to different isolates of A. solani suggests genotypic diversity between isolates that results in phenotypic diversity for pathogen aggressiveness.

Aggressiveness and Fungicide Sensitivity of Alternaria dauci from Cultivated Carrot

Isolates of Alternaria dauci causing Alternaria leaf blight (ALB) were collected from commercial carrot (Daucus carota var. sativus) fields in northeastern North America during 2004. Twenty-two isolates representing a range of genetic diversity were analyzed for their aggressiveness on three commercial carrot varieties (Bolero, Enterprise, and Heritage) varying in disease susceptibility as well as their in vitro response to three fungicides (azoxystrobin, chlorothalonil, and boscalid) commonly used for ALB control. Severity of leaf and petiole blight and leaf chlorosis varied among isolates and carrot varieties in each of three experiments. Visible differences in disease severity, which ranged from 10.9 to 45.1% of the leaf area affected, were apparent 16 days after inoculation. Intensity of chlorosis correlated strongly with blight severity among all isolates. Significant differences were noted among carrot varieties in response to ALB. These varieties may prove useful as differentials capable of distinguishing isolates because variety by isolate interactions were detected. Inhibition of conidial germination ranged from 0.01 to 0.37 μg/ml for azoxystrobin, 0.009 to 0.08 μg/ml for chlorothalonil, and 0.09 to 0.59 μg/ml for boscalid. On average, isolates were more sensitive to chlorothalonil than to azoxystrobin and boscalid. No significant correlation was noted between fungicide sensitivity and aggressiveness. These data provide evidence for phenotypic diversity among A. dauci isolates collected from areas of commercial carrot production.

Molecular diversity and evolutionary processes of Alternaria solani in Brazil inferred using genealogical and coalescent approaches

Alternaria spp. form a heterogeneous group of saprophytic and plant-pathogenic fungi widespread in temperate and tropical regions. However, the relationship between evolutionary processes and genetic diversity with epidemics is unknown for several plant-pathogenic Alternaria spp. The interaction of Alternaria solani populations with potato and tomato plants is an interesting case study for addressing questions related to molecular evolution of an asexual fungus. Gene genealogies based on the coalescent process were used to infer evolutionary processes that shape the A. solani population. Sequences of the rDNA internal transcribed spacer (ITS) region and the genes which encode the allergenic protein alt a 1 (Alt a 1) and glyceraldehyde-3-phosphate dehydrogenase (Gpd) were used to estimate haplotype and nucleotide diversity as well as for the coalescent analyses. The highest number of parsimony informative sites (n = 14), nucleotide diversity (0.007), and the average number of nucleotide differences (3.20) were obtained for Alt a 1. Although the highest number of haplotypes (n = 7) was generated for ITS, haplotype diversity was the lowest (0.148) for this region. Recombination was not detected. Subdivision was inferred from populations associated with hosts but there was no evidence of geographic subdivision, and gene flow is occurring among subpopulations. In the analysis of the Alt a 1, balancing selection and population expansion or purifying selection could have occurred in A. solani subpopulations associated with potato and tomato plants, respectively. There is strong evidence that the subpopulation of A. solani that causes early blight in potato is genetically distinct from the subpopulation that causes early blight in tomato. The population of A. solani is clonal, and gene flow and mutation are the main evolutionary processes shaping its genetic structure.