Population genetic structure of Plasmopara viticola in the Western Cape Province of South Africa

The pathogenicity of Plasmopara viticola: a review of evolutionary dynamics, infection strategies and effector molecules

Oomycetes are filamentous organisms that resemble fungi in terms of morphology and life cycle, primarily due to convergent evolution. The success of pathogenic oomycetes lies in their ability to adapt and overcome host resistance, occasionally transitioning to new hosts. During plant infection, these organisms secrete effector proteins and other compounds during plant infection, as a molecular arsenal that contributes to their pathogenic success. Genomic sequencing, transcriptomic analysis, and proteomic studies have revealed highly diverse effector repertoires among different oomycete pathogens, highlighting their adaptability and evolution potential.The obligate biotrophic oomycete Plasmopara viticola affects grapevine plants (Vitis vinifera L.) causing the downy mildew disease, with significant economic impact. This disease is devastating in Europe, leading to substantial production losses. Even though Plasmopara viticola is a well-known pathogen, to date there are scarce reviews summarising pathogenicity, virulence, the genetics and molecular mechanisms of interaction with grapevine.This review aims to explore the current knowledge of the infection strategy, lifecycle, effector molecules, and pathogenicity of Plasmopara viticola. The recent sequencing of the Plasmopara viticola genome has provided new insights into understanding the infection strategies employed by this pathogen. Additionally, we will highlight the contributions of omics technologies in unravelling the ongoing evolution of this oomycete, including the first in-plant proteome analysis of the pathogen.

A Comparison of Three Types of “Vineyard Management” and Their Effects on the Structure of Plasmopara viticola Populations and Epidemic Dynamics of Grape Downy Mildew

Grape downy mildew (GDM) is a destructive grapevine disease caused by Plasmopara viticola that occurs worldwide. In this study, we determined the characteristics of GDM epidemics and the grapevine canopy micro-climate in open-field, fungicide-spray, and rain-shelter plots during two constitutive years (2016 and 2017). It was found that rain shelter can significantly delay the disease occurrence by 28 and 21 days, reduce the epidemic phase by 28 and 21 days, and decrease the final disease index by 82% and 83%. Furthermore, it can block precipitation, reduce the relative humidity by 11% and 8%, and reduce the leaf wetness duration by 85% and 76% compared with open-field cultivation. A total of 3861, 783, and 1145 lesions were collected from the open-field, fungicide-managed, and rain-shelter plots, respectively, for analyses of the genetic diversity, population differentiation, and epidemic mode with seven microsatellite markers. In terms of genetic diversity, the Nei’s diversity index ranged from 0.569 to 0.680 and Shannon’s information index ranged from 0.958 to 1.226, showing high levels of diversity across populations. Similar to fungicide management, a rain shelter can significantly reduce the population’s genetic diversity. Low pairwise FST values (0.003–0.047) and high gene flow (Nm = 1.548–20.699) were observed among the three populations each year. In addition, most of the genetic variation occurred within populations. The epidemic mode of GDM in the open-field, fungicide-managed, and rain-shelter cultivation showed moderate, low, and high levels of clonality, respectively, in the case study.

Evidence for Differences in the Temporal Progress of Plasmopara viticola Clades riparia and aestivalis Airborne Inoculum Monitored in Vineyards in Eastern Canada Using a Specific Multiplex Quantitative PCR Assay

Four clades of Plasmopara viticola isolated from wild and cultivated Vitis species were described in 2013. Only P. viticola clades riparia and aestivalis have been detected in eastern Canada. To increase our understanding of the epidemiology of these clades of P. viticola, airborne sporangia were monitored with spore samplers at two experimental vineyards from 2015 to 2018 and at 11, 14, and 15 commercial vineyards in 2016, 2017, and 2018, respectively. At each vineyard and in each year, airborne sporangia were assessed three times weekly from grapevine budbreak to harvest. To accurately monitor airborne inoculum, a specific and sensitive quantitative PCR assay for simultaneous quantification of P. viticola clades riparia and aestivalis was developed. At the experimental site, in the vineyard planted with the hybrid grape variety Chancellor, mostly P. viticola clade riparia was detected. In vineyards planted with multiple grape varieties, airborne sporangia of P. viticola clade riparia were prevalent at the beginning of the season, whereas P. viticola clade aestivalis was mostly detected from midseason to harvest. At the commercial sites, airborne sporangia of P. viticola clade riparia were more prevalent in 2016, whereas P. viticola clade aestivalis was more prevalent in 2017 and 2018. The only significant difference between the inoculum progress curves was the time at which 50% of the seasonal inoculum was reached, with an average for the 3 years of 100.8 and 117.9 days since 1 May for P. viticola clade riparia and clade aestivalis, respectively. When airborne sporangium concentrations were expressed as the proportion of the two clades, in general, the proportion of clade aestivalis to that of clade riparia was low at the beginning of the season and increased to reach approximately 0.9 to 1.0 at the end of the season. These results suggest that both clades of P. viticola coexist, but that clade aestivalis is predominant and that downy mildew epidemics caused by P. viticola clade riparia occur 2 to 3 weeks before those caused by clade aestivalis.

Europe as a bridgehead in the worldwide invasion history of grapevine downy mildew, Plasmopara viticola

Europe is the historical cradle of viticulture, but grapevines (Vitis vinifera) have been increasingly threatened by pathogens of American origin. The invasive oomycete Plasmopara viticola causes downy mildew, one of the most devastating grapevine diseases worldwide. Despite major economic consequences, its invasion history remains poorly understood. We analyzed a comprehensive dataset of ∼2,000 samples, collected from the most important wine-producing countries, using nuclear and mitochondrial gene sequences and microsatellite markers. Population genetic analyses revealed very low genetic diversity in invasive downy mildew populations worldwide and little evidence of admixture. All the invasive populations originated from only one of the five native North American lineages, the one parasitizing wild summer grape (V. aestivalis). An approximate Bayesian computation-random forest approach allowed inferring the worldwide invasion scenario of P. viticola. After an initial introduction into Europe, invasive European populations served as a secondary source of introduction into vineyards worldwide, including China, South Africa, and twice independently, Australia. Only the invasion of Argentina probably represents a tertiary introduction, from Australia. Our findings provide a striking example of a global pathogen invasion resulting from secondary dispersal of a successful invasive population. Our study will also help designing quarantine regulations and efficient breeding for resistance against grapevine downy mildew.

The Climate-Driven Genetic Diversity Has a Higher Impact on the Population Structure of Plasmopara viticola Than the Production System or QoI Fungicide Sensitivity in Subtropical Brazil

Downy mildew, caused by Plasmopara viticola, is the main disease affecting vineyards in subtropical Brazil. Here, we collected 94 P. viticola isolates from four organic and conventional vineyards in the two main grape-growing states of Brazil to evaluate the sensitivity to the quinone outside inhibitor (QoI) azoxystrobin by pheno- and genotyping assays. The impact of location, production system and sensitivity to QoI fungicides on the population genetics and structure of P. viticola was determined using 10 microsatellite markers. Cytochrome b sequencing revealed that 28 and 100% of the isolates from vineyards under organic and conventional management carried the G143A mutation, respectively. The G143A mutation was associated with high levels of azoxystrobin resistance. Three out of the 94 isolates analyzed carried the M125I alteration, not previously described in P. viticola, which was associated with a five-fold reduction in azoxystrobin sensitivity compared to wild-type isolates. Haplotype network analysis based on cytochrome b gene sequences suggested that the Brazilian populations are more closely related to the European than the North American population. A total of six haplotypes were identified, with two of them carrying the G143A mutation. Microsatellite analysis revealed high allelic and genotypic variation among the four populations. Population differentiation analyses indicated that state of origin directly influences the population biology of P. viticola, while production system and QoI sensitivity have little effect. Great genetic diversity, sexual reproduction and high levels of admixture were observed in Rio Grande do Sul State. In contrast, populations in São Paulo State were dominated by a few clonal genotypes, and no admixed genotype was detected between the two genetic pools identified in the state. This study raises the hypothesis that winter weather conditions influence the overwinter survival strategy with profound effects in the population biology of P. viticola.

A study of the genetic polymorphism of Plasmopara viticola in the vineyards of the Krasnodar Territory

Plasmopara viticola oomycete is a seasonal pathogen that causes one of the most harmful diseases of the grapevine – downy mildew. The study of the biodiversity of Plasmopara viticola in various zones of viticulture has fundamental goals, as well as practical ones, as it is important for understanding the epidemiological cycle of P. viticola and for refining disease prediction models. The purpose of the work is to study the genetic diversity of P. viticola in the vineyards of the Krasnodar Territory, including on the grape varieties with different levels of resistance to downy mildew. The study was conducted on pathogens samples collected on grape plants of varieties with varying degrees of resistance to downy mildew. The collection of material was carried out in May-August 2019 in various zones of the Krasnodar Territory. 48 samples of P. viticola were analyzed. The DNA markers BER, ISA, CES, GOB, PV91, PV137, PV143, PV144 recommended for studying the genetic diversity of P. viticola were used. The work was performed by PCR. The amplification products were evaluated by the method of fragment analysis. DNA-marker GOB identified 37 alleles of different sizes, PV144 – 20, CES – 10, BER – 3, PV91 – 3, PV137 – 2, ISA – 1, PV143 – 1. It was shown that P. viticola populations are variable on different varieties and in different geographical areas. This study was conducted in the Krasnodar Territory for the first time.

Population Genetic Structure and Cryptic Species of Plasmopara viticola in Australia

Downy mildew of grape caused by Plasmopara viticola is a global pathogen of economic importance to commercial viticulture. In contrast to populations in the northern hemisphere, few studies have investigated the population biology, genetic diversity, and origin of the pathogen in Australian production systems. DNA was extracted from 381 P. viticola samples from Vitis vinifera and alternate hosts collected via fresh and herbarium leaves from populations within Australia and Whatman FTA cards from North America, Brazil, and Uruguay. A total of 32 DNA samples were provided from a French population. The populations were genotyped using 16 polymorphic microsatellite markers. Representative samples from within Australia, Brazil, and Uruguay were also genotyped to determine which of the cryptic species (clades) within the P. viticola species complex were present. Our findings suggest the Australian and South American populations of P. viticola are more closely related to the European population than the North American population, the reported source of origin of the pathogen. The Western Australian population had similarities to the South Australian population, and the tight clustering of samples suggests a single introduction into Western Australia. P. viticola clade aestivalis was the only clade detected in Australian and South American populations. Analysis of the Western Australian population suggests that it is reproducing clonally, but additional research is required to determine the mechanism as to how this is occurring.

Factors Affecting the Vineyard Populational Diversity of Plasmopara viticola

Vitis vinifera is very susceptible to downy mildew (Plasmopara viticola). A number of authors have suggested different genetic populations of this fungus exist in Europe, each showing a different degree of virulence. Work performed to date indicates this diversity to be the result of different factors. In areas where gene flow is greater and recombination more frequent, the diversity of P. viticola appears to be wider. In vineyards isolated by geographic barriers, a race may become dominant and produce clonal epidemics driven by asexual reproduction. The aim of the present work was to identify the conditions that influence the genetic diversity of P. viticola populations in the vineyards of northwestern Spain, where the climatic conditions for the growth of this fungus are very good. Vineyards situated in a closed, narrow valley of the interior, in more open valleys, and on the coast were sampled and the populations of P. viticola detected were differentiated at the molecular level through the examination of microsatellite markers. The populations of P. viticola represented in primary and secondary infections were investigated in the same way. The concentration of airborne sporangia in the vegetative cycle was also examined, as was the virulence of the different P. viticola populations detected. The epidemiological characteristics of the fungus differed depending on the degree of isolation of the vineyard, the airborne spore concentration, and on whether the attack was primary or secondary. Strong isolation was associated with the appearance of dominant fungal races and, therefore, reduced populational diversity.

Multiple gene genealogy reveals high genetic diversity and evidence for multiple origins of Chinese Plasmopara viticola population

Downy mildew caused by Plasmopara viticola is one of the most devastating diseases of grapevines worldwide. So far, the genetic diversity and origin of the Chinese P. viticola population are unclear. In the present study, 103 P. viticola isolates were sequenced at four gene regions: internal transcribed spacer one (ITS), large subunit of ribosomal RNA (LSU), actin gene (ACT) and beta-tubulin (TUB). The sequences were analyzed to obtain polymorphism and diversity information of the Chinese population as well as to infer the relationships between Chinese and American isolates. High genetic diversity was observed for the Chinese population, with evidence of sub-structuring based on climate. Phylogenetic analysis and haplotype networks showed evidence of close relationships between some American and Chinese isolates, consistent with recent introduction from America to China via planting materials. However, there is also evidence for endemic Chinese P. viticola isolates. Our results suggest that the current Chinese Plasmopara viticola population is an admixture of endemic and introduced isolates.

Ten polymorphic microsatellite loci identified from a small insert genomic library for Peronospora tabacina

Ten polymorphic microsatellite loci for the obligate biotrophic, oomycete pathogen of tobacco, Peronospora tabacina, were identified from a small insert genomic library enriched for GT motifs. Eighty-five percent of the 162 loci identified were composed of dinucleotide repeats, whereas only 4% and 11% were tri-and tetra-nucleotide repeats respectively. About 82% of all the microsatellites were perfect and within the library; only about 7% of the loci were duplicated. Primers were designed for 63 loci; 10 loci were polymorphic, 19 were monomorphic and 34 either failed to amplify or produced ambiguous/inconsistent results. The 10 polymorphic loci were characterized with 44 isolates of P. tabacina collected from tobacco plants growing in Europe, the Near East and North and South America. The number of alleles per locus was either three or four with a mean of 3.2, and the mean number of genotypes per locus was 3.6. Observed heterozygosity was 0.32-0.95, whereas expected heterozygosity was 0.44-0.69 for these loci. All loci except PT054 did not conform to the Hardy-Weinberg distribution. Polymorphic information content (PIC) for the loci was 0.35-0.69 with a mean of 0.50. These microsatellite loci provide a set of markers sufficient to perform genetic diversity and population studies of P. tabacina, and possibly other species of Peronospora.

Evaluation of a Warning System for Controlling Primary Infections of Grapevine Downy Mildew

A warning system based on (i) a model that simulates the development of all cohorts of Plasmopara viticola oospores, from oospore germination to infection; (ii) short-term weather forecasts; and (iii) a mobile phone short message system was tested in Northern Italy, from 2006 to 2008. An unsprayed control was compared with a "Warning A" treatment (WA, fungicides were applied whenever the warning system predicted an infection period), a "Warning B" treatment (WB, fungicides were applied as in the WA treatment but only when the relative dimension of any oospore cohort predicted by the model exceeded a threshold), and a "grower" treatment (fungicides were applied according to a conventional schedule). Average disease incidence on leaves was reduced by up to 90% in sprayed plots compared with unsprayed plots. On bunches, efficacy was always >90% at fruit set; when most berries were touching, efficacy was higher for the WA (96%) than for grower (89%) and WB (85%) treatments. On average, 6.8 fungicide sprays were applied following the grower's schedule; use of the warning system reduced applications by about one-half (WA treatment) or two-thirds (WB treatment). The grower's schedule had an average cost of 337 €/ha; the average saving with the WA and the WB treatments was 174 and 224 €/ha, respectively.