Botrytis fragariae, a New Species Causing Gray Mold on Strawberries, Shows High Frequencies of Specific and Efflux-Based Fungicide Resistance

Multidrug resistance of Botrytis cinerea associated with its adaptation to plant secondary metabolites

Fungicides are an effective way to control gray mold of grapes, but the pathogen Botrytis cinerea can develop resistance, overcoming the effectiveness of a fungicide that is repeatedly applied. More importantly, the emergence of multidrug resistance (MDR) in the field, where multiple fungicides with different modes of action simultaneously lose their efficacies, is a significant concern. MDR is associated with ATP-binding cassette (ABC) transporters of the pathogen, and certain plant secondary metabolites (PSMs) stimulate the upregulation of ABC transporters, we hypothesized that the pathogen's preadaptation to PSMs might contribute to MDR development. To test this in B. cinerea, ten PSMs, namely, resveratrol, reserpine, chalcone, flavanone, eugenol, farnesol, anethene, camptothecin, salicylic acid, and psoralen, were selected based on their association with ABC transporters involved in fungicide resistance. B. cinerea strain B05.10 was continuously transferred for 15 generations on potato dextrose agar amended with a PSM (PDAP), and sensitivities to PSMs and fungicides were examined on the 5th, 10th, and 15th generations. RNA was extracted from B. cinerea from the selected generations. After 15 generations of culture transfers, an up-regulation was observed in the expression of ABC transporter-encoding genes BcatrB, BcatrD, and BcatrK using quantitative polymerase chain reaction (qPCR). This upregulation was found to contribute to MDR of B. cinerea against two or more fungicides, among azoxystrobin, boscalid, fludioxonil, difenoconazole, prochloraz, and pyrimethanil. This finding was confirmed through genetic transformation. The decreased sensitivity of B. cinerea to fungicides was confirmed as a subsequent MDR phenotype after exposure to camptothecin, flavanone, and resveratrol. Besides, transcriptome analysis also revealed the upregulation of transcription factors related to ABC expression following resveratrol exposure. This suggests that PSMs contributed to inducing preadaptation of B. cinerea, leading to subsequent MDR.IMPORTANCEThe emergence of MDR in plant pathogens is a threat to plant disease management and leads to the use of excessive fungicides. Botrytis cinerea is of particular concern because its MDR has widely emerged in the field. Understanding its genesis is the first step for controlling MDR. In this study, the contribution of PSMs to MDR has been examined. Effective management of this pathogen in agroecosystems relies on a better understanding of how it copes with phytochemicals or fungicides.

A growing threat: Investigating the high incidence of benzimidazole fungicides resistance in Iranian Botrytis cinerea isolates

Effective management of fungicide application programs requires monitoring the profile of resistant populations of Botrytis cinerea, given its high-risk nature. This research aimed to examine the sensitivity of 200 B. cinerea isolates collected from different plant species and regions across Iran towards thiophanate-methyl and carbendazim fungicides. To distinguish between susceptible and resistant isolates, the discriminatory dose assay was employed, followed by the selection of representative isolates from each group for EC50 analysis. To identify potential modifications in codon 198 of the β-tubulin gene in B. cinerea resistant isolates, the researchers employed the PCR-RFLP diagnostic method. More than two-thirds of the isolates exhibited a varying degree of resistance to MBC fungicides, even in farms where the application of these fungicides had not taken place in recent years. After treatment with the BsaI enzyme, the PCR product of sensitive isolates displayed two bands measuring 98 and 371 bp, while only one band of 469 bp was identified in resistant isolates. The study also evaluated whether resistance to fungicides could affect the pathogenicity and mycelial growth of the isolates. The findings showed no significant difference between the resistant and sensitive groups in terms of these factors, indicating that resistance does not come at a cost to the pathogen's fitness. Considering the high incidence of resistance and the absence of negative consequences on fitness, it is recommended to exercise caution in the employment of benzimidazole fungicides as part of B. cinerea management strategies.

Fungicide Resistance in Botrytis spp. and Regional Strategies for Its Management in Northern European Strawberry Production

Grey mould, caused by Botrytis cinerea and other Botrytis spp., is a major cause of fruit rot in strawberries and other fruit crops worldwide. Repeated fungicide applications are essential in order to secure harvests. However, resistance to all currently registered single-site fungicides is widespread. The rising importance of strains with multiple resistance to most or all fungicides is of particular concern. These strains may be introduced into fields via contaminated nursery plants and/or by immigration from adjacent plots. On the basis of research conducted in northern German and Danish strawberry production, a concept to manage fungicide resistance under northern European conditions has been developed and put into regional strawberry production practice. This principally includes the testing of nursery plants for fungicide-resistant Botrytis strains prior to planting; the restricted and specific use of fungicides at flowering in the production fields, taking account of the resistance spectrum within the local Botrytis population; and crop sanitation measures such as the removal of rotting fruits at the beginning of harvest. Further options such as protected cultivation, reduced fertilisation and biological control are also discussed. The practical implementation of such a strategy in northern Germany and Denmark has been shown to reduce the occurrence of multi-resistant strains to a tolerable steady-state level.

A Loop-Mediated Isothermal Amplification Assay for the Identification of Botrytis fragariae in Strawberry

Gray mold in strawberry is caused by multiple species of Botrytis, including Botrytis cinerea, B. pseudocinerea, B. fragariae, and B. mali. The species B. cinerea and B. fragariae are widespread in production regions of the eastern United States and Germany, and their distinction is important for disease management strategies. Currently, the only way to differentiate these species in field samples is by PCR, which is time consuming, labor intensive, and costly. In this study, a loop-mediated isothermal amplification (LAMP) technique was developed based on species-specific NEP2 gene nucleotide sequences. The designed primer set specifically amplified B. fragariae DNA and no other Botrytis spp. (B. cinerea, B. mali, and B. pseudocinerea) or plant pathogens. The LAMP assay was able to amplify fragments from DNA extracted from infected fruit using a rapid DNA extraction protocol, confirming its ability to detect low amounts of B. fragaria DNA from field-infected fruit. In addition, a blind test was performed to identify B. fragariae in 51 samples collected from strawberry fields in the eastern United States using the LAMP technique. The B. fragariae samples were identified with a reliability of 93.5% (29 of 32), and none of the B. cinerea, B. pseudocinerea, or B. mali samples included in the test were amplified in 10 min. Our results show that the LAMP technique is a specific and reliable method for the detection of B. fragariae from infected fruit tissue and can help to control this important disease in the field.

DORN1 and GORK regulate stomatal closure in Arabidopsis mediated by volatile organic compound ethyl vinyl ketone

Evk (ethyl vinyl ketone) is a signal substance for plant defense, but little is known about how evk mediates stomatal closure. Through stomatal biology experiments, we found that evk can mediate stomatal closure, and stomatal closure is weakened when DORN1 (DOES NOT RESPOND TO NUCLEOTIDES 1) and GORK (GATED OUTWARDLY-RECTIFYING K+ CHANNEL) are mutated. In addition, it was found by non-invasive micro-test technology (NMT) that the K⁺ efflux mediated by evk was significantly weakened when DORN and GORK were mutated. Yeast two-hybrid (Y2H), firefly luciferase complementation imaging (LCI), and in vitro pull-down assays demonstrated that DORN1 and GORK could interact in vitro and in vivo. It was found by molecular docking that evk could combine with MRP (Multidrug Resistance-associated Protein), thus affecting ATP transport, promoting eATP (extracellular ATP) concentration increase and realizing downstream signal transduction. Through inoculation of botrytis cinerea, it was found that evk improved the antibacterial activity of Arabidopsis thaliana. As revealed by reverse transcription quantitative PCR (RT-qPCR), the expression of defense related genes was enhanced by evk treatment. Evk is a potential green antibacterial drug.

The Antifungal Effect of Pyroligneous Acid on the Phytopathogenic Fungus Botrytis cinerea

In recent years, climate change has intensified harsh periods of rain alternating with periods of drought, leading to an increase in the presence of phytopathogenic fungi. In this study, we want to analyse the antifungal properties of pyroligneous acid against the fungal phytopathogen Botrytis cinerea. Through the inhibition test, we observed that the application of different dilutions of pyroligneous acid rarefied the growth of the fungal mycelium. Furthermore, we have seen through the metabolic profile that B. cinerea is not able to use pyroligneous acid as a resource or even grow in close contact with this resource. Moreover, we observed that the pre-incubation of the fungus in pyroligneous acid leads to a reduction in biomass production. These results give us hope for the possible use of this natural substance as a possible substance to protect plantations from pathogen attacks.

Fungicide Resistance and Host Influence on Population Structure in Botrytis spp. from Specialty Crops in California

Botrytis is an important genus of plant pathogens causing pre- and postharvest disease on diverse crops worldwide. This study evaluated Botrytis isolates collected from strawberry, blueberry, and table grape berries in California. Isolates were evaluated for resistance to eight different fungicides, and 60 amplicon markers were sequenced (neutral, species identification, and fungicide resistance associated) distributed across 15 of the 18 B. cinerea chromosomes. Fungicide resistance was common among the populations, with resistance to pyraclostrobin and boscalid being most frequent. Isolates from blueberry had resistance to the least number of fungicides, whereas isolates from strawberry had resistance to the highest number. Host and fungicide resistance-specific population structure explained 12 and 7 to 26%, respectively, of the population variability observed. Fungicide resistance was the major driver for population structure, with select fungicides explaining up to 26% and multiple fungicide resistance explaining 17% of the variability observed. Shared and unique significant single-nucleotide polymorphisms (SNPs) associated with host and fungicide (fluopyram, thiabendazole, pyraclostrobin, and fenhexamid) resistance-associated population structures were identified. Although overlap between host and fungicide resistance SNPs were detected, unique SNPs suggest that both host and fungicide resistance play an important role in Botrytis population structure.

Under Pressure: A Comparative Study of Botrytis cinerea Populations from Conventional and Organic Farms in Cyprus and Greece

The highly heterogeneous nature of Botrytis cinerea provides adaptive benefits to variable environmental regimes. Disentangling pathogen population structure in anthropogenic agroecosystems is crucial to designing more effective management schemes. Herein, we studied how evolutionary forces exerted in different farming systems, in terms of agrochemicals-input, shape B. cinerea populations. In total, 360 B. cinerea isolates were collected from conventional and organic, strawberry and tomato farms in Cyprus and Greece. The occurrence and frequency of sensitivities to seven botryticides were estimated. Results highlighted widespread fungicide resistance in conventional farms since only 15.5% of the isolates were sensitive. A considerable frequency of fungicide-resistant isolates was also detected in the organic farms (14.9%). High resistance frequencies were observed for boscalid (67.7%), pyraclostrobin (67.3%), cyprodinil (65.9%), and thiophanate-methyl (61.4%) in conventional farms, while high levels of multiple fungicide resistance were also evident. Furthermore, B. cinerea isolates were genotyped using a set of seven microsatellite markers (simple sequence repeat [SSR] markers). Index of association analyses (Ia and rBarD) suggest asexual reproduction of the populations, even though the mating-type idiomorphs were equally distributed, indicating frequency-dependent selection. Fungicide resistance was correlated with farming systems across countries and crops, while SSRs were able to detect population structure associated with resistance to thiophanate-methyl, pyraclostrobin, boscalid, and cyprodinil. The expected heterozygosity in organic farms was significantly higher than in conventional, suggesting the absence of selective pressure that may change the allelic abundance in organic farms. However, genetic variance among strawberry and tomato populations was high, ranking host specificity higher than other selection forces studied.

Validation of the Strawberry Advisory System in the Mid-Atlantic Region

Anthracnose fruit rot (AFR) and Botrytis fruit rot (BFR) are primary diseases affecting strawberry (Fragaria × ananassa), which typically drive fungicide applications throughout the growing season. The Strawberry Advisory System (StAS), a disease forecasting tool, was originally developed in Florida to better time the fungicide sprays by monitoring AFR and BFR infection risk based on leaf wetness and temperature input in real-time. Thirteen field trials were conducted in Maryland and Virginia between 2017 and 2019 to evaluate the StAS performance in the Mid-Atlantic region. As a result, 55, 18, and 31% fewer sprays were recorded on average in the model-based StAS treatment compared with the grower standard treatment in 2017, 2018, and 2019, respectively. Marketable yield, as well as AFR and BFR incidence, were largely comparable between the two treatments. However, poor disease control occurred during the StAS treatment in four trials in 2017, presumably because of a missed fungicide spray during a high-risk infection event and attributable to heavy rainfall that led to impassable fields. The implementation of the StAS may be further challenged by the employment of floating row covers that are essential for growing strawberries in plasticulture systems in open fields in the Mid-Atlantic region. Preliminary results indicated that row covers can alter canopy-level microclimatic conditions, possibly increasing the risk for disease occurrence. Overall, the StAS can be a valuable tool for Mid-Atlantic growers to control AFR and BFR, but sprays may need to be promptly applied when consecutive or heavy rainfalls are predicted, especially for highly susceptible cultivars. Complications in disease forecasting and management arising from the use of row covers need to be further addressed in this region because of its highly diverse climate.

Discovery of new vascular disrupting agents based on evolutionarily conserved drug action, pesticide resistance mutations, and humanized yeast

Thiabendazole (TBZ) is an FDA-approved benzimidazole widely used for its antifungal and antihelminthic properties. We showed previously that TBZ is also a potent vascular disrupting agent and inhibits angiogenesis at the tissue level by dissociating vascular endothelial cells in newly formed blood vessels. Here, we uncover TBZ's molecular target and mechanism of action. Using human cell culture, molecular modeling, and humanized yeast, we find that TBZ selectively targets only 1 of 9 human β-tubulin isotypes (TUBB8) to specifically disrupt endothelial cell microtubules. By leveraging epidemiological pesticide resistance data and mining chemical features of commercially used benzimidazoles, we discover that a broader class of benzimidazole compounds, in extensive use for 50 years, also potently disrupt immature blood vessels and inhibit angiogenesis. Thus, besides identifying the molecular mechanism of benzimidazole-mediated vascular disruption, this study presents evidence relevant to the widespread use of these compounds while offering potential new clinical applications.

Characterization of Botrytis cinerea and B. prunorum From Healthy Floral Structures and Decayed 'Hayward' Kiwifruit During Post-Harvest Storage

Gray mold is the primary postharvest disease of 'Hayward' kiwifruit (Actinidia deliciosa) in Chile, with a prevalence of 33.1% in 2016 and 7.1% in 2017. Gray mold develops during postharvest storage, which is characterized by a soft, light to brown watery decay that is caused by Botrytis cinerea and B. prunorum. However, there is no information on the role of B. prunorum during the development and storage of kiwifruit in Chile. For this purpose, asymptomatic flowers and receptacles were collected throughout fruit development and harvest from five orchards over two seasons in the Central Valley of Chile. Additionally, diseased kiwifruits were selected after storage for 100 days at 0°C and 2 days at 20°C. Colonies of Botrytis sp. with high and low conidial production were consistently obtained from apparently healthy petals, sepals, receptacles, and styles and diseased kiwifruit. Morphological and phylogenetic analysis of three partial gene sequences encoding glyceraldehyde-3-phosphate dehydrogenase, heat shock protein 60, and DNA-dependent RNA polymerase subunit II were able to identify and separate B. cinerea and B. prunorum species. Consistently, B. cinerea was predominantly isolated from all floral parts and fruit in apparently healthy tissue and diseased kiwifruit. During full bloom, the highest colonization by B. cinerea and B. prunorum was obtained from petals, followed by sepals. In storage, both Botrytis species were isolated from the diseased fruit (n = 644), of which 6.8% (n = 44) were identified as B. prunorum. All Botrytis isolates grew from 0°C to 30°C in vitro and were pathogenic on kiwifruit leaves and fruit. Notably, B. cinerea isolates were always more virulent than B. prunorum isolates. This study confirms the presence of B. cinerea and B. prunorum colonizing apparently healthy flowers and floral parts in fruit and causing gray mold during kiwifruit storage in Chile. Therefore, B. prunorum plays a secondary role in the epidemiology of gray mold developing in kiwifruit during cold storage.

Characterization of the Populations of Botrytis cinerea Infecting Plastic Tunnel-Grown Strawberry and Tomato in the Hubei Province of China

A total of 707 isolates of Botrytis were collected from plastic tunnel-grown strawberry and tomato in the Hubei province of China. They were identified based on the specific molecular markers. Diversity of the B. cinerea (Bc) isolates was evaluated by typing the transposable elements (Boty, Flipper) and the mating types (MAT1-1, MAT1-2), as well as by determining virulence on tobacco (Nicotiana benthamiana) and fenhexamid sensitivity in agar medium. The results showed that 706 isolates (99.9%) were Bc and 1 isolate (0.1%) was B. pseudocinerea. The Bc isolates (n = 706) were classified into four transposable element types, Vacuma (3.1%), Boty (9.6%), Flipper (18.4%), and Transposa (68.8%). The strawberry and tomato subpopulations of Bc had significantly different (P < 0.05) compositions of the four transposable element types. The overall ratio of MAT1-1 to MAT1-2 deviated from 1:1 (n = 706; P = 0.0002), and MAT1-2 (56.9%) predominated over MAT1-1 (43.1%). In 7 of 12 geographic subpopulations, the ratio of MAT1-1 to MAT1-2 matched 1:1; however, in the remaining five geographic subpopulations, the ratio of MAT1-1 to MAT1-2 did not match 1:1. Results of the biological characterizations showed that most Bc isolates were highly sensitive or sensitive to fenhexamid, and the majority of Bc isolates were highly virulent or virulent on tobacco. Moreover, the relationship between genetic diversity and biological characteristics was analyzed. The results achieved during this study are helpful for understanding of the populations of B. cinerea.

Population Genetic Analyses of Botrytis cinerea Isolates From Michigan Vineyards Using a High-Throughput Marker System Approach

As sequencing costs continue to decrease, new tools are being developed for assessing pathogen diversity and population structure. Traditional marker types, such as microsatellites, are often more cost effective than single-nucleotide polymorphism (SNP) panels when working with small numbers of individuals, but may not allow for fine scale evaluation of low or moderate structure in populations. Botrytis cinerea is a necrotrophic plant pathogen with high genetic variability that can infect more than 200 plant species worldwide. A panel of 52 amplicons were sequenced for 82 isolates collected from four Michigan vineyards representing 2 years of collection and varying fungicide resistance. A panel of nine microsatellite markers previously described was also tested across 74 isolates from the same population. A microsatellite and SNP marker analysis of B. cinerea populations was performed to assess the genetic diversity and population structure of Michigan vineyards, and the results from both marker types were compared. Both methods were able to detect population structure associated with resistance to the individual fungicides thiabendazole and boscalid, and multiple fungicide resistance (MFR). Microsatellites were also able to differentiate population structure associated with another fungicide, fluopyram, while SNPs were able to additionally differentiate structure based on year. For both methods, AMOVA results were similar, with microsatellite results explaining a smaller portion of the variation compared with the SNP results. The SNP-based markers presented here were able to successfully differentiate population structure similar to microsatellite results. These SNP markers represent new tools to discriminate B. cinerea isolates within closely related populations using multiple targeted sequences.

Development of Boscalid Resistance in Botrytis cinerea and an Efficient Strategy for Resistance Management

Among succinate dehydrogenase inhibitors, only boscalid has been registered in China for controlling gray mold. In Shandong Province of China, it has been more than a decade since the first use of boscalid to control gray mold. In the current study, we monitored the resistance development process of Botrytis cinerea to boscalid, identified the mutation types that occurred in boscalid-resistant isolates, and proposed an original application technique to delay resistance development. A total of 720 B. cinerea isolates collected from tomato and cucumber in Shandong Province from 2014 to 2019 were determined to be sensitive to boscalid. The results showed that the sensitivity of the B. cinerea isolates to boscalid declined gradually over time, with a mean half maximal effective concentration of 0.3 ± 0.02 mg/liter in 2014 and 6.39 ± 1.66 mg/liter in 2019. The proportion of resistant isolates quickly increased from 0.81% in 2014 to 28.97% in 2019. Mutations of P225F, N230I, H272Y, and H272R in the SdhB subunit were responsible for boscalid resistance. Four concurrent mutations (G85A, I93V, M158V, and V168I) in the SdhC subunit were first discovered in Shandong Province, but they did not affect the level of boscalid resistance. Interestingly, this study found that the fruit dipping application, a precise topical application technique, could delay the development of boscalid resistance. Therefore, this application technique provides a new method for resistance management of B. cinerea.

Identification and Characterization of Fungicide Resistance in Botrytis Populations from Small Fruit Fields in the Mid-Atlantic United States

From 2014 to 2019, 249 isolates of Botrytis sp. were collected from blackberry, black raspberry, grape, red raspberry, and strawberry showing gray mold symptoms. All isolates were phylogenetically characterized as Botrytis cinerea. A mycelial growth assay determined the following overall frequencies of resistance to fungicides: 92% to pyraclostrobin, 86% to cyprodinil, 71% to thiophanate-methyl, 48% to fenhexamid, 47% to iprodione, 26% to boscalid, 11% to fludioxonil, 8% to penthiopyrad, 7% to benzovindiflupyr, 4% to pydiflumetofen , and 4% to isofetamid. Isolates collected from blackberry, red raspberry, and strawberry had a higher median chemical class resistance value compared to isolates from black raspberry and grape. Resistance conferring mutations were found in a selection of isolates characterized as resistant to thiophanate-methyl, iprodione, pyraclostrobin, fenhexamid, and boscalid including E198A in β-tubulin; I365N/S, Q369P, and N373S in bos1; G143A in cytb; P238S, N369D, and F412I/S in erg27; and P225F and H272R/Y in sdhB, respectively. Also, multiple drug resistance phenotypes MDR1 and MDR1h were identified by analyzing fludioxonil sensitivity and mrr1 sequences. MDR1 and MDR1h isolates had multiple amino acid variations and two insertions in mrr1 that resembled the group S genotype . A detached grape assay confirmed that the aforementioned mutations in isolates from different small fruit crops resulted in field-relevant resistance. An additional in-vitro assay found that EC50 values of B. cinerea isolates to pydiflumetofen and inpyrfluxam averaged 0.4 and 1.0, 0.8 and 0.7, 149.8 and 23.2, 0.9 and 0.9, and 38.8 and 48.8 µg/ml for the wild-type, H272R, H272Y, N230I, and P225F genotypes, respectively. These results revealed widespread fungicide resistance in B. cinerea from Mid-Atlantic small fruit fields, highlighting the need for resistance management alternatives.

The History of Botrytis Taxonomy, the Rise of Phylogenetics, and Implications for Species Recognition

Botrytis is one of the oldest, most well studied, and most economically important fungal taxa. Nonetheless, many species in this genus have remained obscured for nearly 300 years because of the difficulty in distinguishing these species by conventional mycological methods. Aided by the use of phylogenetic tools, the genus is currently undergoing a taxonomic revolution. The number of putative species in the genus has nearly doubled over the last 10 years and more species are likely to be discovered in the future. The implementation of phylogenetic species recognition concepts in Botrytis is providing for more resolution on the relatedness among species than ever before, and this has helped to overcome issues in historical species recognition using morphology, sexual crosses, and pathogenicity tests. Meanwhile, the use of genetic tools is helping to reveal surprising insight into this archetypal necrotroph's behavior, making these approaches increasingly important in species recognition and identification. As Botrytis taxonomy continues to evolve at a rapid pace, researchers should be encouraged to continue to employ the powerful tool of phylogenetics while considering how it fits into a larger framework of classical Botrytis species recognition. Starting points for discussion on how to move forward with Botrytis species recognition are included herein, with an emphasis on the implications and utility of new species descriptions.

Botrytis polygoni, a new species of the genus Botrytis infecting Polygonaceae in Gansu, China

A new species, Botrytis polygoni, was isolated from several species of Polygonaceae in 2011 and 2012 in Tongwei County, Gansu Province, China. The species infects Fagopyrum esculentum, F. tataricum, and Fallopia convolvulus, causing brown leaf spots and large blotches with concentric rings in the field. Botrytis polygoni is morphologically characterized by conidia spherical, unicellular, hyaline to pale brown or brown, (10.2-)14.3-21.4(-23.5) μm; and sclerotia black, spherical to subspherical, allantoid, or irregular-shaped, 0.2-4.1 × 0.1-3.0 mm. Comparison of the nuc rDNA internal transcribed spacer region (ITS1-5.8S-ITS2) sequences confirmed its placement in the genus Botrytis. Phylogenetic analysis based on the protein-coding genes glyceraldehyde 3-phosphate dehydrogenase (G3PDH), heat shock protein 60 (HSP60), and DNA-dependent RNA polymerase subunit II (RPB2) showed that the new species is clustered close but separate from Botrytis pyriformis, which was distant from 37 other Botrytis species and 17 undescribed species. Pathogenicity tests showed that the new species has aggressive pathogenicity to four species of Polygonaceae, specifically Fag. tataricum, Fal. convolvulus, Polygonum sibiricum, and Pol. aviculare, weak pathogenicity to Vicia faba in the Fabaceae, and no pathogenicity to eight other tested plants: Amaranthus retroflexus, Cirsium arvense, Convolvulus arvensis, Kalanchoe blossfeldiana, Lagopsis supine, Mentha canadensis, Plantago asiatica, and Raphanus sativus.

Botrytis prunorum Associated to Vitis vinifera Blossom Blight in Chile

Table grapes are highly susceptible to Botrytis cinerea infections during the bloom period. After reaching the flower development stage, B. cinerea remains quiescent until berry ripening or gives rise to blossom blight under specific climate conditions. A research study was conducted on the Chilean Central Valley during the 2018-2019 growing season. Flowers of Vitis vinifera cv. Thompson Seedless were collected and B. cinerea was isolated together to a second and morphologically different species, characterized by white mycelium and low to no sporulation (11.4% of total isolates). Three randomly selected isolates within this population were genetically examined and identified as Botrytis prunorum based on a phylogenetic multilocus approach using partial regions of genes RPB2, HSP60, and G3PDH or NEP1 and NEP2. Pathogenicity tests showed that B. prunorum infects and causes wilting in healthy table grape flowers. B. prunorum isolates were able to infect Thompson Seedless berries, inducing lesions between 13.11 and 41.53% with respect to the lesion diameter generated by B. cinerea B05.10. The fungicide sensitivity was evaluated. The three genetically characterized isolates were sensitive to boscalid and to cyprodinil/fludioxonil mixture with a mean EC₅₀ value of 5.5 µg/ml and 0.065 µg/ml, respectively. However, loss of sensitivity to fenhexamid was determined, with a mean EC₅₀ value of 5.13 µg/ml. Our understanding about blossom blight in V. vinifera has been limited to B. cinerea. Here we associated B. prunorum as a second causal agent of this disease in Chile. This data represents a first approach to the epidemiological characteristics of B. prunorum associated with blossom blight in table grapes.

Diversity, prevalence and phylogenetic positioning of Botrytis species in Brazil

Botrytis is a necrotrophic fungal genus of great economic importance worldwide. Together, the Botrytis species are able to infect over one thousand host plant species, including dicotyledons and monocotyledons. As the identification of Botrytis species in Brazil has mostly been based only on morphological characterization and comparisons of the rDNA ITS region, which is not informative in the genus, its diversity remains unknown. Thus, in this study we determined the diversity and prevalence of Botrytis spp. in Brazil by multilocus phylogeny. Phylogenetic reconstruction of the genus was performed using the nuclear genes glyceraldehyde-3-phosphate dehydrogenase (G3PDH), heat-shock protein 60 (HSP60) and RNA polymerase II second largest subunit (RPB2). From analyses of 56 Botrytis isolates obtained from different hosts and geographical regions in Brazil, we found that Botrytis cinerea is the most prevalent species with considerable intraspecific genetic diversity detected by nuclear genes. Two new hosts to B. cinerea and eight host never previously reported in Brazil were found. We also reported for the first time the occurrence of Botrytispseudocinerea associated with Accasellowiana (Myrtaceae). Due to the new phylogenetic positioning of Botrytispelargonii and Botrytiseucalypti, a taxonomic review of these species was suggested.

Population Genetics and Fungicide Resistance of Botrytis cinerea on Vitis and Prunus spp. in California

Botrytis cinerea, the causal agent of gray mold, has high genetic diversity and a broad host range. In Vitis sp. and Prunus spp., B. cinerea causes pre- and postharvest diseases, and fungicides are routinely applied to prevent yield loss. In total, 535 isolates of B. cinerea collected from Vitis sp. and Prunus spp. in 2012, 2016, and 2017 were genotyped using 18 microsatellite markers and the transposable elements (TEs) Boty and Flipper. Only nine of the polymorphic markers and the two TEs were considered informative and retained for the final analyses. Of the 532 isolates, 297 were tested for resistance to seven fungicides representing six Fungicide Resistance Action Committee classes. After clone correction, 295 multilocus genotype groups were retained across the 3 years in 326 individuals, and four genetic subpopulations were detected. High levels of clonality were observed across the dataset. Significant pairwise differentiation was detected among years, locations, and TE composition. However, most of the diversity observed was within a subpopulation and not among subpopulations. No genetic differentiation was detected among resistant and sensitive isolates for individual fungicide classes. When resistance to the total number of fungicides was compared, regardless of the fungicide class, significant differentiation was detected among isolates that are resistant to two fungicide classes and those resistant to three or four fungicide groups. Fungicide resistance frequencies were stable for most chemistries evaluated with the exception of fluopyram, which increased from 2012 to 2016/2017.

Botrytis polyphyllae: A New Botrytis Species Causing Gray Mold on Paris polyphylla

Paris polyphylla is an important perennial medicinal plant in China. A disease similar to gray mold on P. polyphylla occurred at the seedling stage in March 2016 and 2017 in Tengchong city, Yunnan Province of China. The disease resulted in up to 50% mortality in serious cases. Isolates from diseased plants grew 10.6 mm/day at 20°C on PDA. After 21 days, sclerotia were spherical to elliptical (0.4-2.5 × 0.3-1.8 mm). Conidia from diseased tissues were hyaline to pale brown, long, ovoid, unicellular, and measured 15.1-24.5 × 8.8-13.4 μm; conidiophores were 526-1,064 ×12-15 μm. Isolates did not form conidiophores or conidia on PDA or MYA. A phylogenetic analysis based on G3PDH, RPB2, and HSP60 sequence data supported assignment of three representative isolates as a new species of Botrytis. Based on morphological, phylogenetic characteristics and Koch's Postulates, the causal agent of gray mold on P. polyphylla was identified as a novel species, Botrytis polyphyllae.

Polyphenols from Rheum Roots Inhibit Growth of Fungal and Oomycete Phytopathogens and Induce Plant Disease Resistance

A growing world population requires an increase in the quality and quantity of food production. However, field losses due to biotic stresses are currently estimated to be between 10 and 20% worldwide. The risk of resistance and strict pesticide legislation necessitate innovative agronomical practices to adequately protect crops in the future, such as the identification of new substances with novel modes of action. In the present study, liquid chromatography mass spectrometry was used to characterize Rheum rhabarbarum root extracts that were primarily composed of the stilbenes rhaponticin, desoxyrhaponticin, and resveratrol. Minor components were the flavonoids catechin, epicatechin gallate, and procyanidin B1. Specific polyphenolic mixtures inhibited mycelial growth of several phytopathogenic fungi and oomycetes. Foliar spray applications with fractions containing stilbenes and flavonoids inhibited spore germination of powdery mildew in Hordeum vulgare with indications of synergistic interactions. Formulated extracts led to a significant reduction in the incidence of brown rust in Triticum aestivum under field conditions. Arabidopsis thaliana mutant and quantitative reverse-transcription polymerase chain reaction studies suggested that the stilbenes induce salicylic acid-mediated resistance. Thus, the identified substances of Rheum roots represent an excellent source of antifungal agents that can be used in horticulture and agriculture.

atrB-Associated Fludioxonil Resistance in Botrytis fragariae Not Linked to Mutations in Transcription Factor mrr1

Resistance to fludioxonil in Botrytis cinerea and B. fragariae was previously found to be linked to either overexpression of the drug efflux pump atrB activated by mutations in transcription factor mrr1 or to mutations in the osmoregulation gene os1. In the present study, isolates of B. cinerea, Botrytis group S, or B. fragariae collected from strawberry fields in the United States were resistant to fludioxonil with half-maximal effective concentration values ranging from 0.04 to 0.43 µg/ml for B. cinerea, 0.03 to 1.03 µg/ml for Botrytis group S, and 0.28 to 3.48 µg/ml for B. fragariae. Analyses of mrr1 sequences revealed various mutations linked to fludioxonil resistance in B. cinerea and Botrytis group S isolates. However, no mutations in mrr1 correlated with atrB overexpression-mediated resistance in B. fragariae isolates. Neither nucleotide variations in the 1,370-bp upstream region of atrB nor increased atrB copy numbers could explain the atrB overexpression in these B. fragariae isolates. Mutations in os1 conferred resistance to iprodione in B. cinerea and Botrytis group S isolates; none correlated with resistance to fludioxonil in B. fragariae. In contrast to European isolates, U.S. B. fragariae isolates contained a 3-bp insertion in the coding region of os1. These isolates were more sensitive to osmotic stress but it is unclear whether the insertion is responsible for this phenotype. Our findings suggest that atrB overexpression-associated fludioxonil resistance is an across-species mechanism of resistance to fludioxonil that can be induced by mutations in mrr1 and other, still-unknown mechanisms.

Genetic analysis reveals unprecedented diversity of a globally-important plant pathogenic genus

Genus Botrytis contains approximately 35 species, many of which are economically-important and globally-distributed plant pathogens which collectively infect over 1,400 plant species. Recent efforts to genetically characterize genus Botrytis have revealed new species on diverse host crops around the world. In this study, surveys and subsequent genetic analysis of the glyceraldehyde-3-phosate dehydrogenase (G3PDH), heat-shock protein 60 (HSP60), DNA-dependent RNA polymerase subunit II (RPB2), and necrosis and ethylene-inducing proteins 1 and 2 (NEP1 and NEP2) genes indicated that Botrytis isolates collected from peony fields in the United States contained more species diversity than ever before reported on a single host, including up to 10 potentially novel species. Together, up to 16 different phylogenetic species were found in association with peonies in the Pacific Northwest, which is over a third of the total number of species that are currently named. Furthermore, species were found on peonies in Alaska that have been described on other host plants in different parts of the world, indicating a wider geographic and host distribution than previously thought. Lastly, some isolates found on peony share sequence similarity with unnamed species found living as endophytes in weedy hosts, suggesting that the isolates found on peony have flexible lifestyles as recently discovered in the genus. Selected pathogenicity, growth, and morphological characteristics of the putatively new Botrytis species were also assessed to provide a basis for future formal description of the isolates as new species.

Fungicide Resistance in Botrytis fragariae and Species Prevalence in the Mid-Atlantic United States

Botrytis fragariae was recently described causing gray mold of strawberry in Germany and the United States. The goal of the present study was to determine its prevalence, distribution, and sensitivity to fungicides in strawberry fields of five states. In total, 188 Botrytis isolates were obtained from flowers and fruit collected from the states of Maryland (n = 35), Virginia (n = 38), North Carolina (n = 46), South Carolina (n = 41), and Georgia (n = 28). Only 13 of these were fruit samples and came from South Carolina (n = 5) and Georgia (n = 8). B. fragariae made up 35.1% of the entire collection, and composed close to half of the Botrytis population in North Carolina (43.4%), South Carolina (61.0%), and Georgia (42.9%). One isolate of B. mali was also found, and the rest of the isolates were B. cinerea (sensu lato). B. fragariae and B. cinerea were found coexisting in 11 fields, while other field samples consisted of only B. fragariae (n = 3) or only B. cinerea (n = 10) isolates. B. fragariae isolates with resistance to one or more fungicides were found, and resistance profiles differed from those of B. cinerea, in that no resistance to cyprodinil (FRAC 8) or boscalid and other FRAC 7 botryticides was detected. We detected B. fragariae resistance to the active ingredients thiophanate-methyl, iprodione, fludioxonil, and fenhexamid. We also detected B. fragariae isolates with resistance to up to four chemical classes of fungicides, though most isolates were resistant to one or two chemical classes. In conclusion, isolates of the newly detected species B. fragariae were commonly found on strawberry flowers in the Mid-Atlantic United States, and have developed resistance to many of the most commonly used botryticides. Though the relevance of this species to pre- and postharvest fruit infections is unknown, fludioxonil applications may give this species a competitive advantage over B. cinerea. Controlling this fungus with FRAC 7 fungicides may be an effective way of limiting its spread in strawberry fields.

Prevalence of Botrytis Cryptic Species in Strawberry Nursery Transplants and Strawberry and Blueberry Commercial Fields in the Eastern United States

Botrytis isolates from strawberry transplants originating from Canada and the northern United States as well as isolates collected from strawberry and blueberry commercial fields in the southeastern United States were investigated for the frequency of Botrytis cinerea, other cryptic Botrytis spp. reported recently, and the transposable elements (TE) using six genetic markers. B. cinerea sensu stricto was predominant (94%) in strawberry and blueberry in all surveyed regions. Botrytis group S, a newly reported clade on strawberry from Germany, was found at low frequencies (6%) in strawberry in the United States and Canada and on blueberry isolates from Florida. Neither B. caroliniana nor B. pseudocinerea were detected in the U.S. or Canadian populations. Transposa isolates containing the TE boty and flipper accounted for 74% of 410 isolates studied herein. Isolates containing boty only or flipper only elements were found at 21 and 2%, respectively. However, boty isolates were predominant in the blueberry population with more than 50%. The TE were found in B. cinerea and Botrytis group S at similar frequencies, except that flipper was more frequent (10.7%) in Botrytis group S, compared with 1.6% in B. cinerea. The sensitivity of 256 Botrytis isolates from the different genetic groups described above was evaluated to seven fungicides registered to control gray mold in commercial fields. Results indicate that B. cinerea and transposa isolates have higher resistance frequencies to almost all fungicides tested compared with the other Botrytis genotypes or species, whereas the TE flipper may be related to resistance to fludioxonil. Similarities observed between nursery and commercial field populations and their impact on gray mold development and management are discussed.

Genotypic and Phenotypic Variations in Botrytis spp. Isolates from Single Strawberry Flowers

Gray mold, caused by Botrytis spp., is among the most devastating diseases affecting strawberry worldwide. The great diversity present in the pathogen enhances its ability to survive and adapt in the field. In this study, we explored the genotypic and phenotypic diversity present in single strawberry flowers. In total, 192 isolates were collected from 19 flowers and four farms, and 9 to 12 isolates were collected from each flower. Forty-two haplotypes were found using microsatellite fragment analysis. Multiple haplotypes of two different Botrytis spp. (Botrytis cinerea and B. fragariae) were found in 12 flowers. In the remaining seven flowers, the single-spore isolates examined were of identical haplotypes. In three flowers, the two Botrytis spp. were found to coexist. Isolates were either sensitive (zero chemical class resistance) or resistant to one, two, three, four, or five chemical classes of fungicides. Resistance to multiple fungicides was commonly observed in both species but resistance to boscalid and penthiopyrad was only found in B. cinerea isolates. Resistance to cyprodinil was found in B. fragariae for the first time in the United States. Each haplotype was generally linked to a single resistance profile; however, a single resistance profile often was represented by multiple haplotypes. Isolates from the same flower of multiple haplotypes were largely identical in resistance profiles. This study is a first detailed investigation of genotypic diversity combined with phenotypic analysis of Botrytis spp. at the single-tissue level. It demonstrates that high genotypic and phenotypic diversity is present not only within fields but also in individual blossoms as well. This information is important for understanding the epidemiology of Botrytis and also has implications for fungicide resistance management, particularly related to resistance monitoring practices.

Identification and Characterization of Botrytis fragariae Isolates on Strawberry in the United States

Gray mold is a devastating disease on strawberry, and may be caused by several species of Botrytis. The goal of this study was to better understand and characterize the species of Botrytis with reduced sensitivity to the fungicide Polyoxin D, particularly Botrytis fragariae. In total, 78 Botrytis isolates of unknown species that were sensitive (28 isolates; S), moderately sensitive (22 isolates; MS), or reduced sensitive (28 isolates; RS) to Polyoxin-D were collected from commercial strawberry fields of five states in the United States, identified to the species level, and characterized. The majority (75%) of S isolates were Botrytis cinerea and the majority (79%) of RS isolates were the recently described species B. fragariae, indicating an innate ability of B. fragariae to tolerate Polyoxin-D. B. fragariae produced fluffy, white mycelium and was less likely to sporulate on potato dextrose agar than B. cinerea. Isolates from a commercial field recovered from blossoms in early spring were all B. fragariae, those from leaves of the same plants in late spring were a mixture of B. fragariae and B. cinerea, and those from fruit in early summer were all B. cinerea, indicating that B. fragariae may preferentially colonize blossom tissue. A polymerase chain reaction-based assay was developed based on NEP2 sequence variability to distinguish B. fragariae from other Botrytis spp. that have been reported on strawberry, including B. cinerea, B. mali, B. caroliniana, and B. ricini. None of the isolates collected from Canada, California, or North Carolina nurseries were B. fragariae, indicating that the newly described species may not exist or not be widely distributed in planting stock.

Botrytis euroamericana, a new species from peony and grape in North America and Europe

A novel species of Botrytis isolated from peony in Alaska, USA, and grape in Trento District, Italy, was identified based on morphology, pathogenicity, and sequence data. The grape and peony isolates share sequence homology in the glyceraldehyde-3-phosphate dehydrogenase (G3PDH), heat shock protein 60 (HSP60), DNA-dependent RNA polymerase subunit II (RPB2), and necrosis- and ethylene-inducing protein 1 and 2 (NEP1 and NEP2) genes that place them in a distinct group closely related to B. aclada, a globally distributed pathogen of onions. Genetic results were corroborated with morphological and pathogenicity trials that included two isolates of B. cinerea and two isolates of B. paeoniae from peony in Alaska and one isolate of B. aclada. The authors observed differences in colony and conidia morphology and ability to cause lesions on different host tissues that suggest that the grape and peony isolates represent a distinct species. Most notably, the grape and peony isolates did not colonize onion bulbs, whereas B. aclada readily produced lesions and prolific sporulation on onion tissue. The new species Botrytis euroamericana is described herein.