Temporal Patterns of Sporulation Potential of Phomopsis viticola on Infected Grape Shoots, Canes, and Rachises

DEFHAZ: A Mechanistic Weather-Driven Predictive Model for Diaporthe eres Infection and Defective Hazelnut Outbreaks

The browning of the internal tissues of hazelnut kernels, which are visible when the nuts are cut in half, as well as the discolouration and brown spots on the kernel surface, are important defects that are mainly attributed to Diaporthe eres. The knowledge regarding the Diaporthe eres infection cycle and its interaction with hazelnut crops is incomplete. Nevertheless, we developed a mechanistic model called DEFHAZ. We considered georeferenced data on the occurrence of hazelnut defects from 2013 to 2020 from orchards in the Caucasus region and Turkey, supported by meteorological data, to run and validate the model. The predictive model inputs are the hourly meteorological data (air temperature, relative humidity, and rainfall), and the model output is the cumulative index (Dh-I), which we computed daily during the growing season till ripening/harvest time. We established the probability function, with a threshold of 1% of defective hazelnuts, to define the defect occurrence risk. We compared the predictions at early and full ripening with the observed data at the corresponding crop growth stages. In addition, we compared the predictions at early ripening with the defects observed at full ripening. Overall, the correct predictions were >80%, with <16% false negatives, which confirmed the model accuracy in predicting hazelnut defects, even in advance of the harvest. The DEFHAZ model could become a valuable support for hazelnut stakeholders.

The road to molecular identification and detection of fungal grapevine trunk diseases

Grapevine is regarded as a highly profitable culture, being well spread worldwide and mostly directed to the wine-producing industry. Practices to maintain the vineyard in healthy conditions are tenuous and are exacerbated due to abiotic and biotic stresses, where fungal grapevine trunk diseases (GTDs) play a major role. The abolishment of chemical treatments and the intensification of several management practices led to an uprise in GTD outbreaks. Symptomatology of GTDs is very similar among diseases, leading to underdevelopment of the vines and death in extreme scenarios. Disease progression is widely affected by biotic and abiotic factors, and the prevalence of the pathogens varies with country and region. In this review, the state-of-the-art regarding identification and detection of GTDs is vastly analyzed. Methods and protocols used for the identification of GTDs, which are currently rather limited, are highlighted. The main conclusion is the utter need for the development of new technologies to easily and precisely detect the presence of the pathogens related to GTDs, allowing to readily take phytosanitary measures and/or proceed to plant removal in order to establish better vineyard management practices. Moreover, new practices and methods of detection, identification, and quantification of infectious material would allow imposing greater control on nurseries and plant exportation, limiting the movement of infected vines and thus avoiding the propagation of fungal inoculum throughout wine regions.

Development and Validation of a Mechanistic Model That Predicts Infection by Diaporthe ampelina, the Causal Agent of Phomopsis Cane and Leaf Spot of Grapevines

Phomopsis cane and leaf spot (PCLS), known in Europe as "excoriose," is an important fungal disease of grapevines caused by Diaporthe spp., and most often by Diaporthe ampelina (synonym Phomopsis viticola). PCLS is re-emerging worldwide, likely due to climate change, changes in the management of downy mildew from calendar- to risk-based criteria that eliminate early-season (unnecessary) sprays, and the progressive reduction in the application of broad-spectrum fungicides. In this study, a mechanistic model for D. ampelina infection was developed based on published information. The model accounts for the following processes: (i) overwintering and maturation of pycnidia on affected canes; (ii) dispersal of alpha conidia to shoots and leaves; (iii) infection; and (iv) onset of disease symptoms. The model uses weather and host phenology to predict infection periods and disease progress during the season. Model output was validated against 11 independent PCLS epidemics that occurred in Italy (4 vineyards in 2019 and 2020) and Montenegro (3 vineyards in 2020). The model accurately predicted PCLS disease progress, with a concordance correlation coefficient (CCC) = 0.925 between observed and predicted data. A ROC analysis (AUROC>0.7) confirmed the ability of the model to predict the infection periods leading to an increase in PCLS severity in the field, indicating that growers could use the model to perform risk-based fungicide applications.

Dynamics of Diaporthe ampelina Conidia Released from Grape Canes that Overwintered in the Vineyard

Phomopsis cane and leaf spot (PCLS) is an important disease of grapevines that is mainly caused by Diaporthe ampelina. Dispersal dynamics of D. ampelina spores were investigated in two vineyards, one in northern Italy and one in Montenegro, by using spore samplers that collected α- and β-conidia from rain water running off from PCLS-affected canes. The canes were collected from each vineyard, deployed, and overwintered in the corresponding vineyards. In each of three years (2016, 2017, and 2018), conidial dispersal was investigated during one (Montenegro) or two (Italy) growing seasons following the deployment of the PCLS-affected canes. In the first growing season following cane deployment in both vineyards, α-conidia were mostly found in runoff water after grapevine bud break, especially in April and May, and β-conidia were regularly found in numbers comparable to those of α-conidia, most frequently from June to September. In Italy, high numbers of α- and β-conidia were also collected during the second growing season following cane deployment. The dispersal dynamics of α-conidia over time were described by a Gompertz equation using hydrothermal time (i.e., the accumulated effect of temperature on the maturation rate of pycnidia on days in which the number of hours of wetness was ≥6 or 9 h), with R² and concordance correlation coefficient >0.9. Rain (≥0.2 mm) was a good predictor of conidial dispersal, with an overall accuracy of 0.97. These results increase our understanding of D. ampelina spore dispersal and should be integrated into warning systems for PCLS management.

Etiology of Halo Blight in Michigan Hopyards

Michigan's hop acreage ranks fourth nationally, but the state's growers contend with unique disease challenges resulting from frequent rainfall and high humidity. In August 2018, a Michigan hop grower reported necrosis and blighting of foliage and shattering of cones resulting in yield loss. Irregular-shaped lesions developed on leaves, surrounded by a halo of chlorotic tissue, and cone bracts became brown. Pycnidia were observed in symptomatic tissue. The goal of this study was to identify and characterize the causal agent of symptoms in leaf and cone tissue. In symptomatic leaves, 15 of 19 isolates recovered had 96.4% internal transcribed spacer rDNA (ITSrDNA) homology with Diaporthe nomurai. Bayesian and maximum likelihood analyses were performed on a subset of isolates using ITSrDNA, histone H3, beta-tubulin, and elongation factor 1 alpha. Bootstrap and posterior probabilities supported a unique cluster of Diaporthe sp. 1-MI isolates most closely related to the Diaporthe arecae species complex, Diaporthe hongkongensis, and Diaporthe multigutullata. Diaporthe sp. 1-MI was pathogenic in detached leaf and whole plant assays. Single-spore isolates from pycnidia originating from cones and leaves shared 100% ITSrDNA homology with Diaporthe sp. 1-MI obtained from the lesion margins of leaves collected in 2018. The distribution of Diaporthe sp. 1-MI was widespread among 347 cones collected from 15 Michigan hop yards and accounted for >38% of fungi recovered from cones in three hop yards. Diaporthe sp. 1-MI causing halo and cone blight presents a new disease management challenge for Michigan hop growers.

Ecology of Diaporthe eres, the causal agent of hazelnut defects

Diaporthe eres has been recently reported as the causal agent of hazelnut defects, with characteristic brown spots on the kernels surface and internal fruit discoloration. Knowledge regarding the ecology of this fungus is poor but, is critical to support a rationale and effective hazelnut crop protection strategy. Therefore, a study was performed to describe and model the effect of different abiotic factors such as temperature (T, 5-35°C, step 5°C) and water activity (aw 0.83-0.99, step 0.03) regimes on D. eres mycelial growth, pycnidial conidiomata development and asexual spore production during a 60-day incubation period. Alpha conidia germination was tested in the same T range and at different relative humidities (RH = 94, 97 and 100%) over 48 h incubation period. Fungal growth was observed from the first visual observation; regarding pycnidia and cirrhi, their development started after 8 and 19 days of incubation, respectively and increased over time. The optimum T for growth was 20-25°C and for pycnidia and cirrhi development was 30°C; aw ≥ 0.98 was optimal for the tested steps of the fungal cycle. The best condition for conidial germination of D. eres was at 25°C with RH = 100%. Quantitative data obtained were fitted using non- linear regression functions (Bete, logistic and polynomial), which provided a very good fit of the biological process (R2 = 0.793-0.987). These functions could be the basis for the development of a predictive model for the infection of D. eres of hazelnuts.

Determining the Sources of Primary and Secondary Inoculum and Seasonal Inoculum Dynamics of Fungal Pathogens Causing Fruit Rot of Deciduous Holly

Fruit rot of deciduous holly, caused by species of the genera Alternaria, Colletotrichum, Diaporthe, and Epicoccum, is affecting plant production in Midwestern and Eastern U.S. nurseries. To determine the sources of inoculum, dormant twigs and mummified fruit were collected, and leaf spot development was monitored throughout the season from three Ohio nurseries over two consecutive years. Mummified fruit was the main source of primary inoculum for species of Alternaria and Epicoccum, whereas mummified fruit and bark were equally important for species of Colletotrichum and Diaporthe. Brown, irregular leaf spots developed in the summer, and disease incidence and severity increased along with leaf and fruit development. Coalesced leaf spots eventually resulted in early plant defoliation. When tested for their pathogenicity on fruit, leaf spot isolates were able to infect wounded mature fruit and induce rot symptoms, which indicated that leaf spots could serve as a source of secondary inoculum for fruit infections. In addition, spore traps were used to monitor seasonal inoculum abundance in the nurseries. Fruit rot pathogens were captured by the spore traps throughout the season, with peak dissemination occurring during flowering. In this study, we also attempted to understand the role of environmental factors on leaf spot development. Although leaf spot incidence and severity were negatively correlated to mean maximum, minimum and average temperature, a decrease in temperature also coincided with leaf senescence. The role of temperature on leaf spot development should be further studied to fully interpret these results.

Two dominant loci determine resistance to Phomopsis cane lesions in F1 families of hybrid grapevines

KEY MESSAGE

Rapid characterization of novel NB-LRR-associated resistance to Phomopsis cane spot on grapevine using high-throughput sampling and low-coverage sequencing for genotyping, locus mapping and transcriptome analysis provides insights into genetic resistance to a hemibiotrophic fungus. Phomopsis cane and leaf spot, caused by the hemibiotrophic fungus Diaporthe ampelina (syn = Phomopsis viticola), reduces the productivity in grapevines. Host resistance was studied on three F1 families derived from crosses involving resistant genotypes 'Horizon', Illinois 547-1, Vitis cinerea B9 and V. vinifera 'Chardonnay'. All families had progeny with extremely susceptible phenotypes, developing lesions on both dormant canes and maturing fruit clusters. Segregation of symptoms was observed under natural levels of inoculum in the field, while phenotypes on green shoots were confirmed under controlled inoculations in greenhouse. High-density genetic maps were used to localize novel qualitative resistance loci named Rda1 and Rda2 from V. cinerea B9 and 'Horizon', respectively. Co-linearity between reference genetic and physical maps allowed localization of Rda2 locus between 1.5 and 2.4 Mbp on chromosome 7, and Rda1 locus between 19.3 and 19.6 Mbp of chromosome 15, which spans a cluster of five NB-LRR genes. Further dissection of this locus was obtained by QTL mapping of gene expression values 14 h after inoculation across a subset of the 'Chardonnay' × V. cinerea B9 progeny. This provided evidence for the association between transcript levels of two of these NB-LRR genes with Rda1, with increased NB-LRR expression among susceptible progeny. In resistant parent V. cinerea B9, inoculation with D. ampelina was characterized by up-regulation of SA-associated genes and down-regulation of ethylene pathways, suggesting an R-gene-mediated response. With dominant effects associated with disease-free berries and minimal symptoms on canes, Rda1 and Rda2 are promising loci for grapevine genetic improvement.

Phomopsis Dieback: A Grapevine Trunk Disease Caused by Phomopsis viticola in California

Field surveys recently conducted in California and in other grape-growing regions in the United States showed Phomopsis viticola to be one of the most prevalent fungi isolated from grapevine perennial cankers in declining vines. The current study has not only confirmed the presence of P. viticola from grapevine cankers in California but also has for the first time revealed the occurrence of Diaporthe ambigua, D. eres, and D. neotheicola in symptomatic grapevine wood in California by means of morphological studies and multi-gene sequence analysis. Pathogenicity trials conducted on mature cordons of Vitis vinifera 'Syrah' and 'Red Globe', as well as on lignified Syrah dormant canes, showed P. viticola isolates from California to be capable of causing perennial cankers. Lengths of vascular discoloration caused by P. viticola were similar to those caused by Eutypa lata and several Botryosphaeriaceae spp., which are well-known grapevine trunk disease pathogens. Additionally, a lack of spring growth was commonly observed in dormant canes inoculated with P. viticola spore suspensions in two pathogenicity trials. As part of this study, V. vinifera 'Cabernet Sauvignon' and 'Zinfandel' wood was shown to be more susceptible to infection by P. viticola than 'Barbera', 'Chardonnay', 'Merlot', and 'Thompson Seedless' wood. After more than 40 years overlooking P. viticola as a grapevine wood pathogen, this study provides strong evidence of the role of P. viticola as a canker-causing organism, and suggests its addition to the fungi involved in the grapevine trunk disease complex. Results from this study suggest D. ambigua and D. neotheicola to be saprophytes or weak pathogens on grapevine wood.

Effects of Temperature and Wetness Duration on the Sporulation Rate of Phomopsis viticola on Infected Grape Canes

Controlled-environment studies were conducted to examine effects of temperature (T) and wetness duration (W) on the sporulation rate of Phomopsis viticola on infected grape canes and to determine effects of interrupted wetness duration (IWD) on sporulation. A split-plot design was used to determine T and W effects, with T (5, 12, 15, 18, 20, 22, 25, 28, and 35°C) as the whole-plot and W (11, 23, 35, 47, and 71 h) as the subplot. Linear and nonlinear mixed models were fitted to the data. Lower and upper limits of sporulation were estimated to be 4 and 36°C, respectively, based on the modeling results, optimum sporulation was near 21°C, and sporulation increased monotonically with increasing wetness duration. Of the examined models, a generalization of the Analytis Beta model fit the data best, based on a collection of goodness-of-fit statistical criteria. To determine effects of IWD, a split-plot was used, with T (12, 15, and 20°C) as the whole-plot and IWD (0, 2, 4, 8, 12, and 24 h) as the subplot. Generally, sporulation declined with increasing IWD. An IWD of 8 h or more resulted in significantly and substantially less sporulation compared to the control (0 h IWD) (P < 0.01). Temporal patterns of spore density in the field were determined using a repeated-measures design, in which spore density and environmental data were measured in the vineyard during and following individual rain events over 3 years. The developed model from the controlled-environment study, coupled with a time-of-season weight function and a dispersal index (based on total rain per rain episode), predicted the trend in spore density over time reasonably well, although the total magnitude of spore density could not be predicted because the density of lesions was not known. Results can be used for improving the accuracy of a disease warning system that currently only considers infection of grapes by P. viticola.