Selective sweep at the Rpv3 locus during grapevine breeding for downy mildew resistance

The Transcriptional Landscape of Berry Skin in Red and White PIWI ("Pilzwiderstandsfähig") Grapevines Possessing QTLs for Partial Resistance to Downy and Powdery Mildews

PIWI, from the German word Pilzwiderstandsfähig, meaning "fungus-resistant", refers to grapevine cultivars bred for resistance to fungal pathogens such as Erysiphe necator (the causal agent of powdery mildew) and Plasmopara viticola (the causal agent of downy mildew), two major diseases in viticulture. These varieties are typically developed through traditional breeding, often crossbreeding European Vitis vinifera with American or Asian species that carry natural disease resistance. This study investigates the transcriptional profiles of exocarp tissues in mature berries from four PIWI grapevine varieties compared to their elite parental counterparts using RNA-seq analysis. We performed RNA-seq on four PIWI varieties (two red and two white) and their noble parents to identify differential gene expression patterns. Comprehensive analyses, including Differential Gene Expression (DEGs), Gene Set Enrichment Analysis (GSEA), Weighted Gene Co-expression Network Analysis (WGCNA), and tau analysis, revealed distinct gene clusters and individual genes characterizing the transcriptional landscape of PIWI varieties. Differentially expressed genes indicated significant changes in pathways related to organic acid metabolism and membrane transport, potentially contributing to enhanced resilience. WGCNA and k-means clustering highlighted co-expression modules linked to PIWI genotypes and their unique tolerance profiles. Tau analysis identified genes uniquely expressed in specific genotypes, with several already known for their defense roles. These findings offer insights into the molecular mechanisms underlying grapevine resistance and suggest promising avenues for breeding strategies to enhance disease resistance and overall grape quality in viticulture.

Multiple deletions of candidate effector genes lead to the breakdown of partial grapevine resistance to downy mildew

Grapevine downy mildew, caused by the oomycete Plasmopara viticola (P. viticola, Berk. & M. A. Curtis; Berl. & De Toni), is a global threat to Eurasian wine grapes Vitis vinifera. Although resistant grapevine varieties are becoming more accessible, P. viticola populations are rapidly evolving to overcome these resistances. We aimed to uncover avirulence genes related to Rpv3.1-mediated grapevine resistance. We sequenced the genomes and characterized the development of 136 P. viticola strains on resistant and sensitive grapevine cultivars. A genome-wide association study was conducted to identify genomic variations associated with resistant-breaking phenotypes. We identified a genomic region associated with the breakdown of Rpv3.1 grapevine resistance (avrRpv3.1 locus). A diploid-aware reassembly of the P. viticola INRA-Pv221 genome revealed structural variations in this locus, including a 30 kbp deletion. Virulent P. viticola strains displayed multiple deletions on both haplotypes at the avrRpv3.1 locus. These deletions involve two paralog genes coding for proteins with 800-900 amino acids and signal peptides. These proteins exhibited a structure featuring LWY-fold structural modules, common among oomycete effectors. When transiently expressed, these proteins induced cell death in grapevines carrying Rpv3.1 resistance, confirming their avirulence nature. This discovery sheds light on the genetic mechanisms enabling P. viticola to adapt to grapevine resistance, laying a foundation for developing strategies to manage this destructive crop pathogen.

A Sustainable Strategy for Marker-Assisted Selection (MAS) Applied in Grapevine (Vitis spp.) Breeding for Resistance to Downy (Plasmopara Viticola) and Powdery (Erysiphe Necator) Mildews

Plant breeders utilize marker-assisted selection (MAS) to identify favorable or unfavorable alleles in seedlings early. In this task, they need methods that provide maximum information with minimal input of time and economic resources. Grape breeding aimed at producing cultivars resistant to pathogens employs several resistance loci (Rpv, Ren, and Run) that are ideal for implementing MAS. In this work, a sustainable MAS protocol was developed based on non-purified DNA (crude), multiplex PCR of SSR markers, and capillary electrophoresis, and its application on grapevine seedlings to follow some main resistance loci was described. The optimized protocol was utilized on 8440 samples and showed high efficiency, reasonable throughput (2-3.2 min sample), easy handling, flexibility, and tolerable costs (reduced by at least 3.5 times compared to a standard protocol). The Rpv, Ren, and Run allelic data analysis did not show limitations to loci combination and pyramiding, but segregation distortions were frequent and displayed both low (undesired) and high rates of inheritance. The protocol and results presented are useful tools for grape breeders and beyond, and they can address sustainable changes in MAS. Several progenies generated have valuable pyramided resistance and will be the subject of new studies and implementation in the breeding program.

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.

In Vitro Collection for the Safe Storage of Grapevine Hybrids and Identification of the Presence of Plasmopara viticola Resistance Genes

This paper focuses on the creation of an in vitro collection of grapevine hybrids from the breeding program of the Kazakh Scientific Research Institute of Fruit Growing and Viticulture and investigates the presence of Plasmopara viticola resistance mediated by Rpv3 and Rpv12 loci. We looked at the optimization of in vitro establishment using either shoots taken directly from field-grown plants or from budwood cuttings forced indoors. We further screened for the presence of endophyte contamination in the initiated explants and optimized the multiplication stage. Finally, the presence of the resistance loci against P. viticola was studied. The shoots initiated from the field-sourced explants were the more effective method of providing plant sources for in vitro initiation once all plant accessions met the goal of in vitro establishment. The concentration of phytohormones and the acidity of the culture medium have a great effect on the multiplication rate and the quality of in vitro stock cultures. Out of 17 grapevine accessions, 16 showed the presence of single or combined resistance loci against P. viticola. The grapevine accessions identified as carrying Rpv3 and Rpv12 alleles represent important genetic resources for disease resistance breeding programs. These accessions may further contribute to the creation of new elite cultivars of economic interest.

Breeding new seedless table grapevines for a more sustainable viticulture in Mediterranean climate

The growing demand for sustainable and environmentally friendly viticulture is leading to a multiplication of breeding programs aimed at obtaining vines that are resistant to powdery mildew (PM) and downy mildew (DM), the two most damaging vine diseases. In Puglia, the most important Italian region for the production of table grapes, an extensive crossing program was launched in 2015 with 113 crosses, including elite table varieties, seedless varieties, and resistant varieties. The main seedling production parameters were measured for each cross. In particular, berries harvested as well as the number of seeds and seedlings obtained were considered. Approximately 103,119 seedlings were obtained and subjected to marker-assisted selection for seedlessness using the marker VvAGL11 and for resistance to PM and DM with appropriate markers. Approximately one third (32,638) of the progenies were selected as putative seedless and seventeen thousand five hundred-nine (17,509) were transferred to the field for phenotypic evaluation, including 527 seedless individuals putatively resistant, of which 208 confirmed to be resistant to DM, 22 resistant to PM, and 20 individuals that combined resistance and seedlessness traits. The work discusses the effects of parental combinations and other variables in obtaining surviving progeny and pyramiding genes in table grapes and provides useful information for selecting genotypes and increasing the efficiency of breeding programs for seedless disease-resistant grapes.

Fungicide-Saving Potential and Economic Advantages of Fungus-Resistant Grapevine Cultivars

The high susceptibility of European grapevine cultivars to downy mildew (DM) and powdery mildew (PM) causes the intensive use of fungicides. Fungus-resistant cultivars (FRCs) with different resistance (R) loci have been bred and could play an important role in reducing plant protection treatments (PPTs). However, little information is available about the extent to which PPTs can be reduced in the field through the use of FRCs and the associated economic advantages. In this study, different strategies with reduced PPTs on FRCs were tested in field experiments. The results demonstrated that the number of PPTs can be reduced by 60 to 90%, resulting in reductions in applied copper and sulfur by 52 to 79% through the use of FRCs compared with susceptible cultivars, without affecting grape or plant health. The saving potential varied among years, depending on the type of R loci and climatic conditions. Furthermore, this study highlights that completely omitting PPTs in the cultivation of FRCs can result in PM or DM infections and possible loss of yield and fruit quality. In addition to the field experiments, a two-year observation of the performance of FRCs in commercial vineyards was undertaken, which highlighted not only the significant reduction in PPTs but also the financial savings that can be achieved through the use of FRCs.

Genetic structure of the population of wild-growing vines of the Utrish Nature Reserve

Grapes are one of the most common agricultural crops in the world. Currently, the analysis of genotypes directly at the DNA level is considered to be the most accurate method for studying the plant gene pool. The study of wild vines and ancient varieties in various regions of viticulture is an important direction of research in this field. The purpose of this work was to study the population of wild grapes growing on the territory of the Utrish Nature Reserve on the Black Sea coast of Krasnodar Region. The territory of the reserve is of interest as it is a site of ancient settlements, and the environmental conditions are suitable for the growth of wild grapes. During the survey of the territory, 24 samples of wild grapes were found, which were described according to the main morphological characteristics and analyzed by the molecular genetic method. The found vines were genotyped using 15 DNA markers, including nine commonly used for DNA fingerprinting (VVS2, VVMD5, VVMD7, VVMD25, VVMD27, VVMD28, VVMD32, VrZAG62, VrZAG79) and VVIb23, which allows determining hermaphrodite and dioecious vines. Statistical processing of microsatellite loci polymorphism data was carried out using the GenAlEx 6.5 program. The genetic relationships of the studied vines were evaluated using the PAST 2.17c program. The samples were found to be morphologically and genetically polymorphic. The number of alleles identified in the sample varied from 5 to 18 and averaged 8 alleles per locus. Statistical processing of DNA analysis data made it possible to identify two genetically different populations among the wild discovered vines. An assessment of genetic similarity of the found vines with some local varieties of geographically close viticulture regions, rootstocks and representatives of Vitis sylvestris from other territories was made. One of the populations found in the Utrish Nature Reserve is close to a number of V. sylvestris genotypes, the DNA profiles of which are presented in the Vitis International Variety Catalogue.

Phased grapevine genome sequence of an Rpv12 carrier for biotechnological exploration of resistance to Plasmopara viticola

The downy mildew disease caused by the oomycete Plasmopara viticola is a serious threat for grapevine and can cause enormous yield losses in viticulture. The quantitative trait locus Rpv12, mediating resistance against P. viticola, was originally found in Asian Vitis amurensis. This locus and its genes were analyzed here in detail. A haplotype-separated genome sequence of the diploid Rpv12-carrier Gf.99-03 was created and annotated. The defense response against P. viticola was investigated in an infection time-course RNA-seq experiment, revealing approximately 600 upregulated Vitis genes during host-pathogen interaction. The Rpv12 regions of the resistance and the sensitivity encoding Gf.99-03 haplotype were structurally and functionally compared with each other. Two different clusters of resistance-related genes were identified within the Rpv12 locus. One cluster carries a set of four differentially expressed genes with three ACCELERATED CELL DEATH 6-like genes. The other cluster carries a set of six resistance gene analogs related to qualitative pathogen resistance. The Rpv12 locus and its candidate genes for P. viticola resistance provide a precious genetic resource for P. viticola resistance breeding. Newly developed co-segregating simple sequence repeat markers in close proximity to the R-genes enable its improved applicability in marker-assisted grapevine breeding.

DNA marker identification of downy mildew resistance locus Rpv10 in grapevine genotypes

One of the most common and harmful diseases of grapevine is downy mildew, caused by Plasmopara viticola. Cultivars of Vitis vinifera, the basis of high-quality viticulture, are mainly not resistant to downy mildew. Varieties with natural resistance to downy mildew belong to the vine species of North America and Asia (V. aestivalis, V. berlandieri, V. cinerea, V. labrusca, V. amurensis, etc.), as well as Muscadinia rotundifolia. The breeding of resistant cultivars is based on interspecific crossing. Currently, molecular genetic methods are increasingly used in pre-selection work and directly in breeding. One of the major loci of downy mildew resistance, Rpv10, was first identified in the variety Solaris and was originally inherited from wild V. amurensis. DNA markers that allow detecting Rpv10 in grapevine genotypes are known. We used PCR analysis to search for donors of resistance locus among 30 grape cultivars that, according to their pedigrees, could carry Rpv10. The work was performed using an automatic genetic analyzer, which allows obtaining high-precision data. Rpv10 locus allele, which determines resistance to the downy mildew pathogen, has been detected in 10 genotypes. Fingerprinting of grape cultivars with detected Rpv10 was performed at 6 reference SSR loci. DNA marker analysis revealed the presence of a resistance allele in the cultivar Korinka russkaya, which, according to publicly available data, is the offspring of the cultivar Zarya Severa and cannot carry Rpv10. Using the microsatellite loci polymorphism analysis and the data from VIVC database, it was found that Korinka russkaya is the progeny of the cultivar Severnyi, which is the donor of the resistance locus Rpv10. The pedigree of the grapevine cultivar Korinka russkaya was also clarified.

Towards Marker-Assisted Breeding for Black Rot Bunch Resistance: Identification of a Major QTL in the Grapevine Cultivar 'Merzling'

Black rot (BR), caused by Guignardia bidwellii, is an emergent fungal disease threatening viticulture and affecting several mildew-tolerant varieties. However, its genetic bases are not fully dissected yet. For this purpose, a segregating population derived from the cross 'Merzling' (hybrid, resistant) × 'Teroldego' (V. vinifera, susceptible) was evaluated for BR resistance at the shoot and bunch level. The progeny was genotyped with the GrapeReSeq Illumina 20K SNPchip, and 7175 SNPs were combined with 194 SSRs to generate a high-density linkage map of 1677 cM. The QTL analysis based on shoot trials confirmed the previously identified Resistance to Guignardia bidwellii (Rgb)1 locus on chromosome 14, which explained up to 29.2% of the phenotypic variance, reducing the genomic interval from 2.4 to 0.7 Mb. Upstream of Rgb1, this study revealed a new QTL explaining up to 79.9% of the variance for bunch resistance, designated Rgb3. The physical region encompassing the two QTLs does not underlie annotated resistance (R)-genes. The Rgb1 locus resulted enriched in genes belonging to phloem dynamics and mitochondrial proton transfer, while Rgb3 presented a cluster of pathogenesis-related Germin-like protein genes, promoters of the programmed cell death. These outcomes suggest a strong involvement of mitochondrial oxidative burst and phloem occlusion in BR resistance mechanisms and provide new molecular tools for grapevine marker-assisted breeding.

The Characterization of Pathotypes in Grapevine Downy Mildew Provides Insights into the Breakdown of Rpv3, Rpv10, and Rpv12 Factors in Grapevines

We describe a standard method for characterizing the virulence profile of Plasmopara viticola, the causal agent of grapevine downy mildew. We used 33 European strains to inoculate six grapevine varieties carrying the principal factors for resistance to downy mildew (Rpv1, Rpv3.1, Rpv3.2, Rpv5, Rpv6, Rpv10, and Rpv12) and the susceptible Vitis vinifera 'Chardonnay'. For each interaction, we characterized the level of sporulation by image analysis and the intensity of the grapevine hypersensitive response by visual score. We propose a definition for the breakdown of grapevine quantitative resistances combining these two traits. Among the 33 strains analyzed, 28 are virulent on at least one resistance factor. We identified five different pathotypes across the 33 strains analyzed: two pathotypes overcoming a single resistance factor (vir3.1 and vir3.2) and three complex pathotypes overcoming multiple resistance factors (vir3.1,3.2; vir3.2,12; vir3.1,3.2,10). Our findings confirm the widespread occurrence of P. viticola strains overcoming the Rpv3 haplotypes (28 strains). We also detected the first breakdown of resistance to the Rpv10 by a strain from Germany and the breakdown of Rpv12 factors by a strain from Hungary. The pathotyping method proposed here and the associated differential host range lay the groundwork for the early detection of resistance breakdown in grapevines. This approach will also facilitate the monitoring of the evolution of P. viticola populations at large spatial scales. This is an essential step forward to promoting durable management of the resistant grapevine varieties currently available.

A cool climate perspective on grapevine breeding: climate change and sustainability are driving forces for changing varieties in a traditional market

A multitude of diverse breeding goals need to be combined in a new cultivar, which always forces to compromise. The biggest challenge grapevine breeders face is the extraordinarily complex trait of wine quality, which is the all-pervasive and most debated characteristic. Since the 1920s, Germany runs continuous grapevine breeding programmes. This continuity was the key to success and lead to various new cultivars on the market, so called PIWIs. Initially, introduced pests and diseases such as phylloxera, powdery and downy mildew were the driving forces for breeding. However, preconceptions about the wine quality of new resistant selections impeded the market introduction. These preconceptions are still echoing today and may be the reason in large parts of the viticultural community for: (1) ignoring substantial breeding progress, and (2) sticking to successful markets of well-known varietal wines or blends (e.g. Chardonnay, Cabernet Sauvignon, Riesling). New is the need to improve viticulture´s sustainability and to adapt to changing environmental conditions. Climate change with its extreme weather will impose the need for a change in cultivars in many wine growing regions. Therefore, a paradigm shift is knocking on the door: new varieties (PIWIs) versus traditional varieties for climate adapted and sustainable viticulture. However, it will be slow process and viticulture is politically well advised to pave the way to variety innovation. In contrast to the widely available PIWIs, competitive cultivars created by means of new breeding technologies (NBT, e.g. through CRISPR/Cas) are still decades from introduction to the market.

Pathogen Adaptation to American (Rpv3-1) and Eurasian (Rpv29) Grapevine Loci Conferring Resistance to Downy Mildew

Durable resistance is a key objective in genetic improvement for disease resistance in grapevines, which must survive for years in the field in the presence of adaptable pathogen populations. In this study, the adaptation of 72 Northern Italian isolates of Plasmopara viticola, the downy mildew agent, has been investigated into Bianca, possessing Rpv3-1, the most frequently exploited resistance locus for genetic improvement, and Mgaloblishvili, a Vitis vinifera variety possessing the newly discovered Rpv29 locus. Infection parameters (latency period, infection frequency, and disease severity) and oospore production and viability were evaluated and compared to those of Pinot noir, the susceptible reference. The expected levels of disease control were achieved by both resistant cultivars (>90% on Bianca; >25% on Mgaloblishvili), despite the high frequency of isolates able to grow on one (28%) or both (46%) accessions. The disease incidence and severity were limited by both resistant cultivars and the strains able to grow on resistant accessions showed signatures of fitness penalties (reduced virulence, infection frequency, and oospore density). Together, these results indicate an adequate pathogen control but suitable practices must be adopted in the field to prevent the diffusion of the partially adapted P. viticola strains to protect resistance genes from erosion.

Deep semantic segmentation for the quantification of grape foliar diseases in the vineyard

Plant disease evaluation is crucial to pathogen management and plant breeding. Human field scouting has been widely used to monitor disease progress and provide qualitative and quantitative evaluation, which is costly, laborious, subjective, and often imprecise. To improve disease evaluation accuracy, throughput, and objectiveness, an image-based approach with a deep learning-based analysis pipeline was developed to calculate infection severity of grape foliar diseases. The image-based approach used a ground imaging system for field data acquisition, consisting of a custom stereo camera with strobe light for consistent illumination and real time kinematic (RTK) GPS for accurate localization. The deep learning-based pipeline used the hierarchical multiscale attention semantic segmentation (HMASS) model for disease infection segmentation, color filtering for grapevine canopy segmentation, and depth and location information for effective region masking. The resultant infection, canopy, and effective region masks were used to calculate the severity rate of disease infections in an image sequence collected in a given unit (e.g., grapevine panel). Fungicide trials for grape downy mildew (DM) and powdery mildew (PM) were used as case studies to evaluate the developed approach and pipeline. Experimental results showed that the HMASS model achieved acceptable to good segmentation accuracy of DM (mIoU > 0.84) and PM (mIoU > 0.74) infections in testing images, demonstrating the model capability for symptomatic disease segmentation. With the consistent image quality and multimodal metadata provided by the imaging system, the color filter and overlapping region removal could accurately and reliably segment grapevine canopies and identify repeatedly imaged regions between consecutive image frames, leading to critical information for infection severity calculation. Image-derived severity rates were highly correlated (r > 0.95) with human-assessed values, and had comparable statistical power in differentiating fungicide treatment efficacy in both case studies. Therefore, the developed approach and pipeline can be used as an effective and efficient tool to quantify the severity of foliar disease infections, enabling objective, high-throughput disease evaluation for fungicide trial evaluation, genetic mapping, and breeding programs.

Phenotyping for QTL identification: A case study of resistance to Plasmopara viticola and Erysiphe necator in grapevine

Vitis vinifera is the most widely cultivated grapevine species. It is highly susceptible to Plasmopara viticola and Erysiphe necator, the causal agents of downy mildew (DM) and powdery mildew (PM), respectively. Current strategies to control DM and PM mainly rely on agrochemical applications that are potentially harmful to humans and the environment. Breeding for resistance to DM and PM in wine grape cultivars by introgressing resistance loci from wild Vitis spp. is a complementary and more sustainable solution to manage these two diseases. During the last two decades, 33 loci of resistance to P. viticola (Rpv) and 15 loci of resistance to E. necator (Ren and Run) have been identified. Phenotyping is salient for QTL characterization and understanding the genetic basis of resistant traits. However, phenotyping remains a major bottleneck for research on Rpv and Ren/Run loci and disease resistance evaluation. A thorough analysis of the literature on phenotyping methods used for DM and PM resistance evaluation highlighted phenotyping performed in the vineyard, greenhouse or laboratory with major sources of variation, such as environmental conditions, plant material (organ physiology and age), pathogen inoculum (genetic and origin), pathogen inoculation (natural or controlled), and disease assessment method (date, frequency, and method of scoring). All these factors affect resistance assessment and the quality of phenotyping data. We argue that the use of new technologies for disease symptom assessment, and the production and adoption of standardized experimental guidelines should enhance the accuracy and reliability of phenotyping data. This should contribute to a better replicability of resistance evaluation outputs, facilitate QTL identification, and contribute to streamline disease resistance breeding programs.

Pathogenesis of Plasmopara viticola Depending on Resistance Mediated by Rpv3_1, and Rpv10 and Rpv3_3, and by the Vitality of Leaf Tissue

Grapevine cultivars vary in their resistance to Plasmopara viticola, causal agent of downy mildew. Genes from various Vitis species confer pathogen resistance (Rpv), resulting in reduced compatibility of the host-pathogen interaction and partial disease resistance that may become apparent at different stages of pathogenesis. This study describes the pathogenesis of P. viticola on the partially resistant cultivars Regent (Rpv3-1) and Solaris (Rpv3-3, Rpv10) as compared with the susceptible cultivar Mueller-Thurgau using various microscopic techniques, visual disease rating as well as qPCR. Host plant resistance had no effect on the initial steps of pathogenesis outside the host plant cells (zoospore attachment, formation of substomatal vesicle) and became detectable only after the formation of primary haustoria. The restricted compatibility resulted in reductions in haustorium size and in the number of secondary haustoria and was associated with callose depositions around haustoria and stomatal guard cells, collapsed mesophyll cells (hypersensitive reaction), and additional production of an amorphous substance in the intercellular space of cultivar Solaris. Resistance mechanisms reduced the efficiency of P. viticola haustoria and largely restricted tissue colonization to the spongy parenchyma; resistance of cultivar Solaris having thicker leaves was more effective than that of cultivar Regent. Despite of the effects of resistance genes, P. viticola was able to complete its life cycle by forming sporangiophores with sporangia through the stomata on both resistant cultivars indicating partial resistance. Differences in the pathogenesis on detached and attached grapevine leaves highlighted the impact of host tissue vitality on both resistance and susceptibility to the biotrophic pathogen.

Genetic polymorphism of local Abkhazian grape cultivars

Local grape cultivars from different countries of the world are an important part of the gene pool of this culture. Of particular interest are the genotypes of the most ancient regions of viticulture. The territories of the subtropical zone of Georgia and the central part of Abkhazia belong to one of the centers of origin of the cultural grapevine. The purpose of the work was to genotype native Abkhazian grape cultivars, to study their genetic diversity based on DNA profiling data and to compare them with the genotypes of local varieties of other viticultural regions. Samples of plants were taken on the territory of the Republic of Abkhazia in private farmsteads and in the collection of the agricultural firm “Vina i Vody Abkhazii“ (“Wines and Waters of Abkhazia”). The genotyping of the Abkhazian cultivars Avasirhva, Agbizh, Azhapsh, Azhizhkvakva, Azhikvaca, Atvizh, Atyrkuazh, Achkykazh, Kachich was carried out using 14 DNA markers, 9 of which are standard microsatellite markers recommended for the identification of grape varieties. To improve our knowledge about the sizes of the identified alleles, we used the DNA of grape cultivars with a known allelic composition at the analyzed loci. Statistical analysis of the data showed that the observed heterozygosity for the analyzed loci exceeded expected values, which indicates a genetic polymorphism of the studied sample of varieties. Evaluation of genetic similarity within the analyzed group based on the results of genotyping at 14 loci showed that the cultivars Kachich and Azhapsh differed from the other Abkhazian varieties. The obtained DNA profiles of the Abkhazian cultivars were checked for compliance with DNA-fingerprints of grape varieties in the Vitis International Variety Catalogue. The Georgian varieties Azhizhkvakva and Tsitska turned out to be synonyms according to DNA profiles, two varieties from the Database (Italian Albana bianca and Georgian Ojaleshi) have differences in DNA-fingerprints from the varieties Atyrkuazh and Azhikvatsa only in one allele, respectively. When comparing the identified Abkhazian grape genotypes, their difference from the sample of Dagestan, Don, Greek, Turkish, Italian, Spanish, and French varieties and genetic similarity with the genotypes of Georgian grapes were shown.

Vitis OneGenE: A Causality-Based Approach to Generate Gene Networks in Vitis vinifera Sheds Light on the Laccase and Dirigent Gene Families

The abundance of transcriptomic data and the development of causal inference methods have paved the way for gene network analyses in grapevine. Vitis OneGenE is a transcriptomic data mining tool that finds direct correlations between genes, thus producing association networks. As a proof of concept, the stilbene synthase gene regulatory network obtained with OneGenE has been compared with published co-expression analysis and experimental data, including cistrome data for MYB stilbenoid regulators. As a case study, the two secondary metabolism pathways of stilbenoids and lignin synthesis were explored. Several isoforms of laccase, peroxidase, and dirigent protein genes, putatively involved in the final oxidative oligomerization steps, were identified as specifically belonging to either one of these pathways. Manual curation of the predicted sequences exploiting the last available genome assembly, and the integration of phylogenetic and OneGenE analyses, identified a group of laccases exclusively present in grapevine and related to stilbenoids. Here we show how network analysis by OneGenE can accelerate knowledge discovery by suggesting new candidates for functional characterization and application in breeding programs.

Grapevine Rpv3-, Rpv10- and Rpv12-mediated defense responses against Plasmopara viticola and the impact of their deployment on fungicide use in viticulture

BACKGROUND

The high susceptibility of European grapevine cultivars (Vitis vinifera) to downy mildew (Plasmopara viticola) leads to the intensive use of fungicides in viticulture. To reduce this input, breeding programs have introgressed resistance loci from wild Vitis species into V. vinifera, resulting in new fungus-resistant grapevine cultivars (FRC). However, little is known about how these different resistance loci confer resistance and what the potential reduction in fungicide applications are likely to be if these FRCs are deployed. To ensure a durable and sustainable resistance management and breeding, detailed knowledge about the different defense mechanisms mediated by the respective Rpv (Resistance to P. viticola) resistance loci is essential.

RESULTS

A comparison of the resistance mechanisms mediated by the Rpv3-1, Rpv10 and/or Rpv12-loci revealed an early onset of programmed cell death (PCD) at 8 hours post infection (hpi) in Rpv12-cultivars and 12 hpi in Rpv10-cultivars, whereas cell death was delayed in Rpv3-cultivars and was not observed until 28 hpi. These temporal differences correlated with an increase in the trans-resveratrol level and the formation of hydrogen peroxide shortly before onset of PCD. The differences in timing of onset of Rpv-loci specific defense reactions following downy mildew infection could be responsible for the observed differences in hyphal growth, sporulation and cultivar-specific susceptibility to this pathogen in the vineyard. Hereby, Rpv3- and Rpv12/Rpv3-cultivars showed a potential for a significant reduction of fungicide applications, depending on the annual P. viticola infection pressure and the Rpv-loci. Furthermore, we report on the discovery of a new P. viticola isolate that is able to overcome both Rpv3- and Rpv12-mediated resistance.

CONCLUSION

This study reveals that differences in the timing of the defense reaction mediated by the Rpv3-, Rpv10- and Rpv12-loci, result in different degrees of natural resistance to downy mildew in field. Vineyard trials demonstrate that Rpv12/Rpv3- and Rpv3-cultivars are a powerful tool to reduce the dependence of grape production on fungicide applications. Furthermore, this study indicates the importance of sustainable breeding and plant protection strategies based on resistant grapevine cultivars to reduce the risk of new P. viticola isolates that are able to overcome the respective resistance mechanism.

Mono-Locus and Pyramided Resistant Grapevine Cultivars Reveal Early Putative Biomarkers Upon Artificial Inoculation With Plasmopara viticola

One of the most economically important grapevine diseases is Downy mildew (DM) caused by the oomycete Plasmopara viticola. A strategy to reduce the use of fungicides to compensate for the high susceptibility of V. vinifera is the selection of grapevine varieties showing pathogen-specific resistance. We applied a metabolomics approach to evaluate the metabolic modulation in mono-locus resistant genotypes carrying one locus associated with P. viticola resistance (Rpv) (BC4- Rpv1, Bianca- Rpv3-1, F12P160- Rpv12, Solaris- Rpv10), as well as in pyramided resistant genotypes carrying more than one Rpv (F12P60- Rpv3-1; Rpv12 and F12P127- Rpv3-1, Rpv3-3; Rpv10) taking as a reference the susceptible genotype Pinot Noir. In order to understand if different sources of resistance are associated with different degrees of resistance and, implicitly, with different responses to the pathogen, we considered the most important classes of plant metabolite primary compounds, lipids, phenols and volatile organic compounds at 0, 12, 48, and 96 h post-artificial inoculation (hpi). We identified 264 modulated compounds; among these, 22 metabolites were found accumulated in significant quantities in the resistant cultivars compared to Pinot Noir. In mono-locus genotypes, the highest modulation of the metabolites was noticed at 48 and 96 hpi, except for Solaris, that showed a behavior similar to the pyramided genotypes in which the changes started to occur as early as 12 hpi. Bianca, Solaris and F12P60 showed the highest number of interesting compounds accumulated after the artificial infection and with a putative effect against the pathogen. In contrast, Pinot Noir showed a less effective defense response in containing DM growth.

Screening of Croatian Native Grapevine Varieties for Susceptibility to Plasmopara viticola Using Leaf Disc Bioassay, Chlorophyll Fluorescence, and Multispectral Imaging

In the era of sustainable grapevine production, there is a growing demand to define differences between Vitis vinifera varieties in susceptibility to downy mildew. Croatia, as a country with a long tradition of grapevine cultivation, preserves a large number of native grapevine varieties. A leaf disc bioassay has been conducted on 25 of them to define their response to downy mildew, according to the International Organisation of Vine and Wine (OIV) descriptor 452-1, together with the stress response of the leaf discs using chlorophyll fluorescence and multispectral imaging with 11 parameters included. Time points of measurement were as follows: before treatment (T₀), one day post-inoculation (dpi) (T₁), two dpi (T₂), three dpi (T₃), four dpi (T₄), six dpi (T₅), and eight dpi (T₆). Visible changes in form of developed Plasmopara viticola (P. viticola) sporulation were evaluated on the seventh day upon inoculation. Results show that methods applied here distinguish varieties of different responses to downy mildew. Based on the results obtained, a phenotyping model in the absence of the pathogen is proposed, which is required to confirm by conducting more extensive research.

Georgian Grapevine Cultivars: Ancient Biodiversity for Future Viticulture

Grapevine (Vitis vinifera) is one of the most widely cultivated plant species of agricultural interest, and is extensively appreciated for its fruits and the wines made from its fruits. Considering the high socio-economic impact of the wine sector all over the world, in recent years, there has been an increase in work aiming to investigate the biodiversity of grapevine germplasm available for breeding programs. Various studies have shed light on the genetic diversity characterizing the germplasm from the cradle of V. vinifera domestication in Georgia (South Caucasus). Georgian germplasm is placed in a distinct cluster from the European one and possesses a rich diversity for many different traits, including eno-carpological and phenological traits; resistance to pathogens, such as oomycetes and phytoplasmas; resistance to abiotic stresses, such as sunburn. The aim of this review is to assess the potential of Georgian cultivars as a source of useful traits for breeding programs. The unique genetic and phenotypic aspects of Georgian germplasm were unraveled, to better understand the diversity and quality of the genetic resources available to viticulturists, as valuable resources for the coming climate change scenario.

Evaluation and Pre-selection of New Grapevine Genotypes Resistant to Downy and Powdery Mildew, Obtained by Cross-Breeding Programs in Spain

The need to develop an environmentally friendly, sustainable viticulture model has led to numerous grapevine improvement programmes aiming to increase resistance to downy and powdery mildew. The success of such programmes relies on the availability of protocols that can quantify the resistance/susceptibility of new genotypes, and on the existence of molecular markers of resistance loci that can aid in the selection process. The present work assesses the degree of phenotypic resistance/susceptibility to downy and powdery mildew of 28 new genotypes obtained from crosses between "Monastrell" and "Regent." Three genotypes showed strong combined resistance, making them good candidates for future crosses with other sources of resistance to these diseases (pyramiding). In general, laboratory and glasshouse assessments of resistance at the phenotype level agreed with the resistance expected from the presence of resistance-associated alleles of simple sequence repeat (SSR) markers for the loci Rpv3 and Ren3 (inherited from "Regent"), confirming their usefulness as indicators of likely resistance to downy and powdery mildew, respectively, particularly so for downy mildew.

Discovery of the REN11 Locus From Vitis aestivalis for Stable Resistance to Grapevine Powdery Mildew in a Family Segregating for Several Unstable and Tissue-Specific Quantitative Resistance Loci

Race-specific resistance loci, whether having qualitative or quantitative effects, present plant-breeding challenges for phenotypic selection and deciding which loci to select or stack with other resistance loci for improved durability. Previously, resistance to grapevine powdery mildew (GPM, caused by Erysiphe necator) was predicted to be conferred by at least three race-specific loci in the mapping family B37-28 × C56-11 segregating for GPM resistance from Vitis aestivalis. In this study, 9 years of vineyard GPM disease severity ratings plus a greenhouse and laboratory assays were genetically mapped, using a rhAmpSeq core genome marker platform with 2,000 local haplotype markers. A new qualitative resistance locus, named REN11, on the chromosome (Chr) 15 was found to be effective in nearly all (11 of 12) vineyard environments on leaves, rachis, berries, and most of the time (7 of 12) stems. REN11 was independently validated in a pseudo-testcross with the grandparent source of resistance, "Tamiami." Five other loci significantly predicted GPM severity on leaves in only one or two environments, which could indicate race-specific resistance or their roles in different timepoints in epidemic progress. Loci on Chr 8 and 9 reproducibly predicted disease severity on stems but not on other tissues and had additive effects with REN11 on the stems. The rhAmpSeq local haplotype sequences published in this study for REN11 and Chr 8 and 9 stem quantitative trait locus (QTL) can be used directly for marker-assisted selection or converted to SNP assays. In screening for REN11 in a diversity panel of 20,651 vines representing the diversity of Vitis, this rhAmpSeq haplotype had a false positive rate of 0.034% or less. The effects of the other foliar resistance loci detected in this study seem too unstable for genetic improvement regardless of quantitative effect size, whether due to race specificity or other environmental variables.

Potential of genetic resistance of new table grape hybrids to fungal pathogens

Downy mildew (Plasmopara viticola) and powdery mildew (Erysiphe necator) are the most common and economically significant fungal diseases in vineyards. The task of this work is to study the genotypes of new promising hybrid forms of table grapes for the presence of resistance genes to downy mildew (Rpv10 and Rpv3) and powdery mildew (Ren9) using DNA-markers. The study was carried out on table grape hybrids under the working names Agat dubovskiy, Akelo, Arabella, Artek, Dubovskiy rozovyi, Gamlet, Ispolin, Kishmish dubovskiy, Kurazh, Pestryi, Valensiya and registered variety Liviya. The studied genes were analyzed using markers UDV305 and UDV737 (Rpv3), GF09-46 (Rpv10), CenGen6 (Ren9). The following cultivars were used as reference genotypes: Saperavi severnyi (carries Rpv10 gene) and Regent (Rpv3 and Ren9). It was established that Rpv3 gene is carried by hybrids Kishmish dubovskiy, Agat dubovskiy, Kurazh, Valensiya, Akelo, Gamlet, Dubovskiy rozovyi, Pestryi. Ren9 gene was found in Artek, Agat dubovskiy, Kurazh, Ispolin, Valensiya, Arabella, Gamlet, Dubovskiy rozovyi, Pestryi. The Rpv10 gene was not detected in any of the analyzed grapevine samples. genotypes Agat dubovskiy, Kurazh, Gamlet, Dubovskiy rozovyi, Pestryi, Valensiya carry Rpv3 and Ren9 genes simultaneously. These grapevines have an elegant bunch and large berries that are attractive to consumers.

Plasmopara viticola infection affects mineral elements allocation and distribution in Vitis vinifera leaves

Plasmopara viticola is one of the most important pathogens infecting Vitis vinifera plants. The interactions among P. viticola and both susceptible and resistant grapevine plants have been extensively characterised, at transcriptomic, proteomic and metabolomic levels. However, the involvement of plants ionome in the response against the pathogen has been completely neglected so far. Therefore, this study was aimed at investigating the possible role of leaf ionomic modulation during compatible and incompatible interactions between P. viticola and grapevine plants. In susceptible cultivars, a dramatic redistribution of mineral elements has been observed, thus uncovering a possible role for mineral nutrients in the response against pathogens. On the contrary, the resistant cultivars did not present substantial rearrangement of mineral elements at leaf level, except for manganese (Mn) and iron (Fe). This might demonstrate that, resistant cultivars, albeit expressing the resistance gene, still exploit a pathogen response mechanism based on the local increase in the concentration of microelements, which are involved in the synthesis of secondary metabolites and reactive oxygen species. Moreover, these data also highlight the link between the mineral nutrition and plants' response to pathogens, further stressing that appropriate fertilization strategies can be fundamental for the expression of response mechanisms against pathogens.

DNA-marker identification of Rpv3 and Rpv12 resistance loci in genotypes of table and seedless grape varieties

DNA markers are widely used in grapevine breeding to create forms with combined resistance genes. Downy mildew is one of the most common fungal diseases of the vine in the world. Growing grapevines with increased resistance allows to reduce the number of chemical treatments. The decrease in the use of pesticides is especially significant for viticulture of table varieties, since berries are directly consumed by humans for food. Currently, more than 20 resistance genes have been identified by molecular methods, and DNA markers for many genes have been developed. The genes Rpv3 (inherited from North American grape species) and Rpv12 (derived from V. amurensis) are among the most effective and have an additive effect. The study of 14 table grape varieties for the presence of the Rpv3 gene and 8 varieties for the presence of the Rpv12 gene was performed by using DNA-marker analysis. The analysis included varieties that could inherit these genes from the parent forms, according to their ancestry. The study was conducted using an automatic genetic analyzer ABI Prism 3130 and special software GeneMapper and PeakScanner, DNA-markers were taken from literature sources. According to the results of DNA-marker analysis, 9 varieties were identified, including 2 seedless varieties, with the Rpv3299-279 allele in the genotypes, which determines resistance to downy mildew, and 3 table varieties with the Rpv12 gene in the genotypes. One table grape genotype was identified with Rpv3 and Rpv12.

Rpv Mediated Defense Responses in Grapevine Offspring Resistant to Plasmopara viticola

Downy mildew, caused by the biotrophic oomycete Plasmopara viticola, is one of the most serious grapevine diseases. The development of new varieties, showing partial resistance to downy mildew, through traditional breeding provides a sustainable and effective solution for disease management. Marker-assisted-selection (MAS) provide fast and cost-effective genotyping methods, but phenotyping remains necessary to characterize the host-pathogen interaction and assess the effective resistance level of new varieties as well as to validate MAS selection. In this study, the Rpv mediated defense responses were investigated in 31 genotypes, encompassing susceptible and resistant varieties and 26 seedlings, following inoculation of leaf discs with P. viticola. The offspring differed in Rpv loci inherited (none, one or two): Rpv3-3 and Rpv10 from Solaris and Rpv3-1 and Rpv12 from Kozma 20-3. To improve the assessment of different resistance responses, pathogen reaction (sporulation) and host reaction (necrosis) were scored separately as independent features. They were differently expressed depending on Rpv locus: offspring carrying Rpv3-1 and Rpv12 loci showed the strongest resistance response (scarce sporulation and necrosis), those carrying Rpv3-3 locus showed the highest levels of necrosis while Rpv10 carrying genotypes showed intermediate levels of both sporulation and necrosis.

Genome-Wide Changes in Genetic Diversity in a Population of Myotis lucifugus Affected by White-Nose Syndrome

Novel pathogens can cause massive declines in populations, and even extirpation of hosts. But disease can also act as a selective pressure on survivors, driving the evolution of resistance or tolerance. Bat white-nose syndrome (WNS) is a rapidly spreading wildlife disease in North America. The fungus causing the disease invades skin tissues of hibernating bats, resulting in disruption of hibernation behavior, premature energy depletion, and subsequent death. We used whole-genome sequencing to investigate changes in allele frequencies within a population of Myotis lucifugus in eastern North America to search for genetic resistance to WNS. Our results show low F_ST values within the population across time, i.e., prior to WNS (Pre-WNS) compared to the population that has survived WNS (Post-WNS). However, when dividing the population with a geographical cut-off between the states of Pennsylvania and New York, a sharp increase in values on scaffold GL429776 is evident in the Post-WNS samples. Genes present in the diverged area are associated with thermoregulation and promotion of brown fat production. Thus, although WNS may not have subjected the entire M. lucifugus population to selective pressure, it may have selected for specific alleles in Pennsylvania through decreased gene flow within the population. However, the persistence of remnant sub-populations in the aftermath of WNS is likely due to multiple factors in bat life history.

Novel Aspects on The Interaction Between Grapevine and Plasmopara viticola: Dual-RNA-Seq Analysis Highlights Gene Expression Dynamics in The Pathogen and The Plant During The Battle For Infection

Mgaloblishvili, a Vitis vinifera cultivar, exhibits unique resistance traits against Plasmopara viticola, the downy mildew agent. This offers the unique opportunity of exploring the molecular responses in compatible and incompatible plant-pathogen interaction. In this study, whole transcriptomes of Mgaloblishvili, Pinot noir (a V. vinifera susceptible cultivar), and Bianca (a resistant hybrid) leaves, inoculated and non-inoculated with the pathogen, were used to identify P. viticola effector-encoding genes and plant susceptibility/resistance genes. Multiple effector-encoding genes were identified in P. viticola transcriptome, with remarkable expression differences in relation to the inoculated grapevine cultivar. Intriguingly, five apoplastic effectors specifically associated with resistance in V. vinifera. Gene coexpression network analysis identified specific modules and metabolic changes occurring during infection in the three grapevine cultivars. Analysis of these data allowed, for the first time, the detection in V. vinifera of a putative P. viticola susceptibility gene, encoding a LOB domain-containing protein. Finally, the de novo assembly of Mgaloblishvili, Pinot noir, and Bianca transcriptomes and their comparison highlighted novel candidate genes that might be at the basis of the resistant phenotype. These results open the way to functional analysis studies and to new perspectives in molecular breeding of grapevine for resistance to P. viticola.

Gene duplication and transposition of mobile elements drive evolution of the Rpv3 resistance locus in grapevine

A wild grape haplotype (Rpv3-1) confers resistance to Plasmopara viticola. We mapped the causal factor for resistance to an interval containing a TIR-NB-LRR (TNL) gene pair that originated 1.6-2.6 million years ago by a tandem segmental duplication. Transient coexpression of the TNL pair in Vitis vinifera leaves activated pathogen-induced necrosis and reduced sporulation compared with control leaves. Even though transcripts of the TNL pair from the wild haplotype appear to be partially subject to nonsense-mediated mRNA decay, mature mRNA levels in a homozygous resistant genotype were individually higher than the mRNA trace levels observed for the orthologous single-copy TNL in sensitive genotypes. Allelic expression imbalance in a resistant heterozygote confirmed that cis-acting regulatory variation promotes expression in the wild haplotype. The movement of transposable elements had a major impact on the generation of haplotype diversity, altering the DNA context around similar TNL coding sequences and the GC-content in their proximal 5'-intergenic regions. The wild and domesticated haplotypes also diverged in conserved single-copy intergenic DNA, but the highest divergence was observed in intraspecific and not in interspecific comparisons. In this case, introgression breeding did not transgress the genetic boundaries of the domesticated species, because haplotypes present in modern varieties sometimes predate speciation events between wild and cultivated species.

Assessment of Resistance Components for Improved Phenotyping of Grapevine Varieties Resistant to Downy Mildew

Grapevine varieties showing partial resistance to downy mildew, caused by Plasmopara viticola, are a promising alternative to fungicides for disease control. Resistant varieties are obtained through breeding programs aimed at incorporating Rpv loci controlling the quantitative resistance into genotypes characterized by valuable agronomic and wine quality traits by mean of crossing. Traditional phenotyping methods used in these breeding programs are mostly based on the assessment of the resistance level after artificial inoculation of leaf discs in bioassays, by using the visual score proposed in the 2nd Edition of the International Organization of Vine and Wine (OIV) Descriptor List for Grape Varieties and Vitis species (2009). In this work, the OIV score was compared with an alternative approach, not used for the grapevine-downy mildew pathosystem so far, based on the measurement of components of resistance (RCs); 15 grapevine resistant varieties were used in comparison with the susceptible variety 'Merlot'. OIV scores were significantly correlated with P. viticola infection frequency (IFR), the latent period for the downy mildew (DM) lesions to appear (LP50), and the number of sporangia produced per lesion (SPOR), so that when the OIV score increased (i.e., the resistance level increases), IFR and SPOR decreased, while LP50 increased. The relationship was linear for LP50, monomolecular for IFR and hyperbolic for SPOR. No significant correlation was found between OIV score and DM lesion size, sporangia produced per unit area of lesion, length of infectious period, and infection efficiency of the sporangia produced on DM lesions. The correlation between OIV score and area under the disease progress curve (AUDPC) calculated by using the RCs and a simulation model was significant and fit an inverse exponential function. Based on the results of this study, the measurement of the RCs to P. viticola in grapevine varieties by means of monocyclic, leaf disc bioassays, as well as their incorporation into a model able to simulate their effect on the polycyclic development of DM epidemics in vineyards, represents an improved method for phenotyping resistance level.

Rpv3-1 mediated resistance to grapevine downy mildew is associated with specific host transcriptional responses and the accumulation of stilbenes

BACKGROUND

European grapevine cultivars (Vitis vinifera spp.) are highly susceptible to the downy mildew pathogen Plasmopara viticola. Breeding of resistant V. vinifera cultivars is a promising strategy to reduce the impact of disease management. Most cultivars that have been bred for resistance to downy mildew, rely on resistance mediated by the Rpv3 (Resistance to P. viticola) locus. However, despite the extensive use of this locus, little is known about the mechanism of Rpv3-mediated resistance.

RESULTS

In this study, Rpv3-mediated defense responses were investigated in Rpv3+ and Rpv3- grapevine cultivars following inoculation with two distinct P. viticola isolates avrRpv3+ and avrRpv3-, with the latter being able to overcome Rpv3 resistance. Based on comparative microscopic, metabolomic and transcriptomic analyses, our results show that the Rpv3-1-mediated resistance is associated with a defense mechanism that triggers synthesis of fungi-toxic stilbenes and programmed cell death (PCD), resulting in reduced but not suppressed pathogen growth and development. Functional annotation of the encoded protein sequence of genes significantly upregulated during the Rpv3-1-mediated defense response revealed putative roles in pathogen recognition, signal transduction and defense responses.

CONCLUSION

This study used histochemical, transcriptomic and metabolomic analyses of Rpv3+ and susceptible cultivars inoculated with avirulent and virulent P. viticola isolates to investigate mechanism underlying the Rpv3-1-mediated resistance response. We demonstrated a strong correlation between the expressions of stilbene biosynthesis related genes, the accumulation of fungi-toxic stilbenes, pathogen growth inhibition and PCD.

R-Loci Arrangement Versus Downy and Powdery Mildew Resistance Level: A Vitis Hybrid Survey

For the viticulture of the future, it will be an essential prerequisite to manage grapevine diseases with fewer chemical inputs. The development and the deployment of novel mildew resistant varieties are considered one of the most promising strategies towards a sustainable viticulture. In this regard, a collection of 102 accessions derived from crossing Vitis hybrids with V. vinifera varieties was studied. In addition to the true-to-type analysis, an exhaustive genetic characterization was carried out at the 11 reliable mildew resistance (R) loci available in the literature to date. Our findings highlight the pyramiding of R-loci against downy mildew in 15.7% and against powdery mildew in 39.2% of the total accessions. The genetic analysis was coupled with a three-year evaluation of disease symptoms in an untreated field in order to assess the impact of the R-loci arrangement on the disease resistance degree at leaf and bunch level. Overall, our results strongly suggest that R-loci pyramiding does not necessarily mean to increase the overall disease resistance, but it guarantees the presence of further barriers in case of pathogens overcoming the first. Moreover, our survey allows the discovery of new mildew resistance sources useful for novel QTL identifications towards marker-assisted breeding.

The Rpv3-3 Haplotype and Stilbenoid Induction Mediate Downy Mildew Resistance in a Grapevine Interspecific Population

The development of new resistant varieties to the oomycete Plasmopara viticola (Berk.& Curt) is a promising way to combat downy mildew (DM), one of the major diseases threatening the cultivated grapevine (Vitis vinifera L.). Taking advantage of a segregating population derived from "Merzling" (a mid-resistant hybrid) and "Teroldego" (a susceptible landrace), 136 F1 individuals were characterized by combining genetic, phenotypic, and gene expression data to elucidate the genetic basis of DM resistance and polyphenol biosynthesis upon P. viticola infection. An improved consensus linkage map was obtained by scoring 192 microsatellite markers. The progeny were screened for DM resistance and production of 42 polyphenols. QTL mapping showed that DM resistance is associated with the herein named Rpv3-3 specific haplotype and it identified 46 novel metabolic QTLs linked to 30 phenolics-related parameters. A list of the 95 most relevant candidate genes was generated by specifically exploring the stilbenoid-associated QTLs. Expression analysis of 11 genes in Rpv3-3 +/- genotypes displaying disparity in DM resistance level and stilbenoid accumulation revealed significant new candidates for the genetic control of stilbenoid biosynthesis and oligomerization. These overall findings emphasized that DM resistance is likely mediated by the major Rpv3-3 haplotype and stilbenoid induction.

Identification of disease resistance-linked alleles in Vitis vinifera germplasm

Introgression of genetic resistance to fungal diseases from American and Asian Vitis species traditionally pursued in grape breeding programs, although facilitated by molecular tools, has an impact on wine quality that still slows down development of competitive varieties. A contribution to the genetic improvement of grapevines for resistance to pathogens may come from unexplored genetic resources of the Eurasian Vitis vinifera L. In the present study, a hundred grapevine accessions from Georgia, Armenia and Azerbaijan were genotyped with SSR markers linked to QTLs for resistance to downy and powdery mildew, and with 21 SSR markers widely used for genetic diversity and relationship analysis. Looking at population genetic structure, Armenian and Azerbaijani accessions fell within the same cluster and were included among the Central Asian grape varieties of a homogeneous dataset, while Georgian accessions formed a separate group. Pattern of SSR alleles flanking the locus Ren1 and associated with resistance to Erysiphe necator in 'Kishmish vatkana', 'Dzhandzhal kara' and other Central Asian cultivars were found in three varieties from the Azerbaijani population that reached very high scores when assessed for PM resistance.

Construction of a high-density linkage map and QTL detection of downy mildew resistance in Vitis aestivalis-derived 'Norton'

A major QTL for downy mildew resistance was detected on chromosome 18 (Rpv27) in Vitis aestivalis-derived 'Norton' based on a high-resolution linkage map with SNP and SSR markers as well as 2 years of field and laboratory phenotyping data. Grapevine downy mildew caused by the oomycete Plasmopara viticola is one of the most widespread and destructive diseases, particularly in humid viticultural areas where it damages green tissues and defoliates vines. Traditional Vitis vinifera wine grape cultivars are susceptible to downy mildew whereas several North American and a few Asian cultivars possess various levels of resistance to this disease. To identify genetic determinants of downy mildew resistance in V. aestivalis-derived 'Norton,' a mapping population with 182 genotypes was developed from a cross between 'Norton' and V. vinifera 'Cabernet Sauvignon' from which a consensus map was constructed via 411 simple sequence repeat (SSR) markers. Using genotyping-by-sequencing, 3825 single nucleotide polymorphism (SNP) markers were also generated. Of these, 1665 SNP and 407 SSR markers were clustered into 19 linkage groups in 159 genotypes, spanning a genetic distance of 2203.5 cM. Disease progression in response to P. viticola was studied in this population for 2 years under both laboratory and field conditions, and strong correlations were observed among data sets (Spearman correlation coefficient = 0.57-0.79). A quantitative trait loci (QTL) analysis indicated a resistance locus on chromosome 18, here named Rpv27, explaining 33.8% of the total phenotypic variation. Flanking markers closely linked with the trait can be further used for marker-assisted selection in the development of new cultivars with resistance to downy mildew.

Genetic analysis of stilbenoid profiles in grapevine stems reveals a major mQTL hotspot on chromosome 18 associated with disease-resistance motifs

Grapevine (Vitis spp.) contains a wealth of phytochemicals that have received considerable attention due to health-promoting properties and biological activities as phytoalexins. To date, the genetic basis of the quantitative variations for these potentially beneficial compounds has been limited. Here, metabolic quantitative trait locus (mQTL) mapping was conducted using grapevine stems of a segregating F₂ population. Metabolic profiling of grapevine stems was performed using liquid chromatography-high-resolution mass spectrometry (LC-HRMS), resulting in the detection of 1317 ions/features. In total, 19 of these features matched with literature-reported stilbenoid masses and were genetically mapped using a 1449-SNP linkage map and R/qtl software, resulting in the identification of four mQTLs. Two large-effect mQTLs that corresponded to a stilbenoid dimer and a trimer were mapped on chromosome 18, accounting for phenotypic variances of 29.0% and 38.4%. Functional annotations of these large-effect mQTLs on the VitisNet network database revealed a major hotspot of disease-resistance motifs on chromosome 18. This 2.8-Mbp region contains 48 genes with R-gene motifs, including variants of TIR, NBS, and LRR, that might potentially confer resistance to powdery mildew, downy mildew, or other pathogens. The locus also encompasses genes associated with flavonoid and biosynthetic pathways that are likely involved in the production of secondary metabolites, including phytoalexins. In addition, haplotype dosage effects of the five mQTLs further characterized the genomic regions for differential production of stilbenoids that can be applied in resistance breeding through manipulation of stilbenoid production in planta.

DNA-marker based identification of the RPV3 gene determining downy mildew resistance in grapevines

Downy mildew is one of the most common fungal diseases of the vine, caused by Plasmopara viticola. An effective way to control the spread of the pathogen is to cultivate resistant varieties. Cultivars of Vitis vinifera, being the basis of high-quality viticulture, practically do not possess genetic resistance to P. viticola, so screening for resistance donors is an important stage in breeding. One of the major resistance loci to downy mildew, the Rpv3 gene, was identified in the genotype of a complex interspecific hybrid of grapes Bianca. Later, it was found that this gene had seven haplotypes of resistance inherited from North American grape species, and that it was possible to identify the allelic status of the gene using DNA-markers UDV305, UDV737. However, only two haplotypes can be combined in one diploid form. To determine the Rpv3 gene in the grape gene pool we, using these markers, studied 35 different genotypes of grapevines, most of which are interspecies cultivars. Three varieties with known allelic status of the Rpv3 gene (Dunavski lazur, Noah, Seyve Villard 12-375) were included in the study as reference genotypes. The genotypes were studied through polymerase chain reaction with separation of amplification products by capillary electrophoresis in automatic genetic analyzer ABI Prism 3130. In the studied grape cultivars DNA marker analysis indentified the Rpv3 gene in sixteen genotypes of interspecific origin, including haplotype Rpv3299-279 found in twelve varieties, Rpv3321-312 – in three, and haplotype Rpv3null-271 – in one variety. Seyve Villard 12-375 turned out to be the donor of resistance gene in the most of the genotypes carrying Rpv3 in this study. The obtained data can be useful in selection of mildew resistant grape varieties and screening for hybridization pairs.

SNP markers tightly linked to root knot nematode resistance in grapevine (Vitis cinerea) identified by a genotyping-by-sequencing approach followed by Sequenom MassARRAY validation

Plant parasitic nematodes, including root knot nematode Meloidogyne species, cause extensive damage to agriculture and horticultural crops. As Vitis vinifera cultivars are susceptible to root knot nematode parasitism, rootstocks resistant to these soil pests provide a sustainable approach to maintain grapevine production. Currently, most of the commercially available root knot nematode resistant rootstocks are highly vigorous and take up excess potassium, which reduces wine quality. As a result, there is a pressing need to breed new root knot nematode resistant rootstocks, which have no impact on wine quality. To develop molecular markers that predict root knot nematode resistance for marker assisted breeding, a genetic approach was employed to identify a root knot nematode resistance locus in grapevine. To this end, a Meloidogyne javanica resistant Vitis cinerea accession was crossed to a susceptible Vitis vinifera cultivar Riesling and results from screening the F1 individuals support a model that root knot nematode resistance, is conferred by a single dominant allele, referred as MELOIDOGYNE JAVANICA RESISTANCE1 (MJR1). Further, MJR1 resistance appears to be mediated by a hypersensitive response that occurs in the root apical meristem. Single nucleotide polymorphisms (SNPs) were identified using genotyping-by-sequencing and results from association and genetic mapping identified the MJR1 locus, which is located on chromosome 18 in the Vitis cinerea accession. Validation of the SNPs linked to the MJR1 locus using a Sequenom MassARRAY platform found that only 50% could be validated. The validated SNPs that flank and co-segregate with the MJR1 locus can be used for marker-assisted selection for Meloidogyne javanica resistance in grapevine.

Identification of Biomarkers for Defense Response to Plasmopara viticola in a Resistant Grape Variety

Downy mildew (Plasmopara viticola) is one of the most destructive diseases of the cultivated species Vitis vinifera. The use of resistant varieties, originally derived from backcrosses of North American Vitis spp., is a promising solution to reduce disease damage in the vineyards. To shed light on the type and the timing of pathogen-triggered resistance, this work aimed at discovering biomarkers for the defense response in the resistant variety Bianca, using leaf discs after inoculation with a suspension of P. viticola. We investigated primary and secondary metabolism at 12, 24, 48, and 96 h post-inoculation (hpi). We used methods of identification and quantification for lipids (LC-MS/MS), phenols (LC-MS/MS), primary compounds (GC-MS), and semi-quantification for volatile compounds (GC-MS). We were able to identify and quantify or semi-quantify 176 metabolites, among which 53 were modulated in response to pathogen infection. The earliest changes occurred in primary metabolism at 24-48 hpi and involved lipid compounds, specifically unsaturated fatty acid and ceramide; amino acids, in particular proline; and some acids and sugars. At 48 hpi, we also found changes in volatile compounds and accumulation of benzaldehyde, a promoter of salicylic acid-mediated defense. Secondary metabolism was strongly induced only at later stages. The classes of compounds that increased at 96 hpi included phenylpropanoids, flavonols, stilbenes, and stilbenoids. Among stilbenoids we found an accumulation of ampelopsin H + vaticanol C, pallidol, ampelopsin D + quadrangularin A, Z-miyabenol C, and α-viniferin in inoculated samples. Some of these compounds are known as phytoalexins, while others are novel biomarkers for the defense response in Bianca. This work highlighted some important aspects of the host response to P. viticola in a commercial variety under controlled conditions, providing biomarkers for a better understanding of the mechanism of plant defense and a potential application in field studies of resistant varieties.

Prelude to a panzootic: Gene flow and immunogenetic variation in northern little brown myotis vulnerable to bat white-nose syndrome

The fungus that causes bat white-nose syndrome (WNS) recently leaped from eastern North America to the Pacific Coast. The pathogen’s spread is associated with the genetic population structure of a host ( Myotis lucifugus). To understand the fine-scale neutral and immunogenetic variation among northern populations of M. lucifugus, we sampled 1142 individuals across the species’ northern range. We used genotypes at 11 microsatellite loci to reveal the genetic structure of, and directional gene flow among, populations to predict the likely future spread of the pathogen in the northwest and to estimate effective population size ( Ne). We also pyrosequenced the DRB1-like exon 2 of the class II major histocompatibility complex (MHC) in 160 individuals to explore immunogenetic selection by WNS. We identified three major neutral genetic clusters: Eastern, Montane Cordillera (and adjacent sampling areas), and Haida Gwaii, with admixture at intermediate areas and significant substructure west of the prairies. Estimates of Ne were unexpectedly low (289–16 000). Haida Gwaii may provide temporary refuge from WNS, but the western mountain ranges are not barriers to its dispersal in M. lucifugus and are unlikely to slow its spread. Our major histocompatibility complex (MHC) data suggest potential selection by WNS on the MHC, but gene duplication limited the immunogenetic analyses.

Genome sequence of Plasmopara viticola and insight into the pathogenic mechanism

Plasmopara viticola causes downy mildew disease of grapevine which is one of the most devastating diseases of viticulture worldwide. Here we report a 101.3 Mb whole genome sequence of P. viticola isolate 'JL-7-2' obtained by a combination of Illumina and PacBio sequencing technologies. The P. viticola genome contains 17,014 putative protein-coding genes and has ~26% repetitive sequences. A total of 1,301 putative secreted proteins, including 100 putative RXLR effectors and 90 CRN effectors were identified in this genome. In the secretome, 261 potential pathogenicity genes and 95 carbohydrate-active enzymes were predicted. Transcriptional analysis revealed that most of the RXLR effectors, pathogenicity genes and carbohydrate-active enzymes were significantly up-regulated during infection. Comparative genomic analysis revealed that P. viticola evolved independently from the Arabidopsis downy mildew pathogen Hyaloperonospora arabidopsidis. The availability of the P. viticola genome provides a valuable resource not only for comparative genomic analysis and evolutionary studies among oomycetes, but also enhance our knowledge on the mechanism of interactions between this biotrophic pathogen and its host.

Genetic and Phenotypic Characterization of Grapevine vein clearing virus from Wild Vitis rupestris

Grapevine vein clearing virus (GVCV), a new member of the genus Badnavirus in the family Caulimoviridae, is associated with a vein clearing and vine decline disease that severely affects grape production and berry quality in commercial vineyards in the Midwest region of the United States. In this paper, the genetic and phenotypic characteristics of GVCV-VRU1 and GVCV-VRU2, two isolates from wild Vitis rupestris grapevines in their native habitat, are described. The GVCV-VRU1 genome is 7,755 bp long while the GVCV-VRU2 genome consists of 7,725 bp, both of which are different from the genome of the GVCV-CHA isolate (7,753 bp), which was originally discovered in the grape cultivar 'Chardonel'. The nucleotide sequence identity among GVCV-VRU1, GVCV-VRU2, and GVCV-CHA ranges from 91.6 to 93.4%, and open reading frame (ORF) II is the most divergent ORF with only 83.3 to 88.5% identity. Sequence analysis of the ORF II indicated that GVCV isolates genetically similar to GVCV-VRU1 and GVCV-VRU2 also are present in commercial vineyards. Symptoms of GVCV-VRU1- or GVCV-VRU2-infected wild V. rupestris grapevine appeared initially as translucent vein clearing on young leaves and progressed to vein necrosis on mature leaves. Inoculation of GVCV-VRU1 or GVCV-VRU2 by grafting onto grape cultivar Chardonel resulted in mild mottle and leaf distortion. The natural range of wild V. rupestris grapevines overlaps with commercial vineyards in the Midwestern United States. Therefore, the discovery of GVCV isolates in wild V. rupestris grapevines has important implications for epidemics and management of the GVCV-associated disease.

A stilbene synthase allele from a Chinese wild grapevine confers resistance to powdery mildew by recruiting salicylic acid signalling for efficient defence

Stilbenes are central phytoalexins in Vitis, and induction of the key enzyme stilbene synthase (STS) is pivotal for disease resistance. Here, we address the potential for breeding resistance using an STS allele isolated from Chinese wild grapevine Vitis pseudoreticulata (VpSTS) by comparison with its homologue from Vitis vinifera cv. 'Carigane' (VvSTS). Although the coding regions of both alleles are very similar (>99% identity on the amino acid level), the promoter regions are significantly different. By expression in Arabidopsis as a heterologous system, we show that the allele from the wild Chinese grapevine can confer accumulation of stilbenes and resistance against the powdery mildew Golovinomyces cichoracearum, whereas the allele from the vinifera cultivar cannot. To dissect the upstream signalling driving the activation of this promoter, we used a dual-luciferase reporter system in a grapevine cell culture. We show elevated responsiveness of the promoter from the wild grape to salicylic acid (SA) and to the pathogen-associated molecular pattern (PAMP) flg22, equal induction of both alleles by jasmonic acid (JA), and a lack of response to the cell death-inducing elicitor Harpin. This elevated SA response of the VpSTS promoter depends on calcium influx, oxidative burst by RboH, mitogen-activated protein kinase (MAPK) signalling, and JA synthesis. We integrate the data in the context of a model where the resistance of V. pseudoreticulata is linked to a more efficient recruitment of SA signalling for phytoalexin synthesis.

Hyperspectral phenotyping of the reaction of grapevine genotypes to Plasmopara viticola

A major aim in grapevine breeding is the provision of cultivars resistant to downy mildew. As Plasmopara viticola produces sporangia on the abaxial surface of susceptible cultivars, disease symptoms on both leaf sides may be detected and quantified by technical sensors. The response of cultivars 'Mueller-Thurgau', 'Regent', and 'Solaris', which differ in resistance to P. viticola, was characterized under controlled conditions by using hyperspectral sensors. Spectral reflectance was suitable to differentiate between non-infected cultivars and leaf sides of the bicolored grapevine. Brown discoloration of tissue became visible on both leaf sides of resistant cultivars 2 days before downy mildew symptoms appeared on the susceptible 'Mueller-Thurgau' cultivar. Infection of this cultivar resulted in significant (P<0.05) reflectance changes 1-2 days prior to abaxial sporulation induced by high relative humidity, or the formation of adaxial oil spots. Hyperspectral imaging was more sensitive in disease detection than non-imaging and provided spatial information on the leaf level. Spectral indices provided information on the variability of chlorophyll content, photosynthetic activity, and relative water content of leaf tissue in time and space. On 'Mueller-Thurgau' downy mildew translated reflectance to higher values as detectable by the index DMI_3=(R₄₇₀+R₆₈₂+R₈₀₀)/(R₈₀₀/R₆₈₂) and affected reflectance at 1450nm. Tissue discoloration on 'Regent' and 'Solaris' cultivars was associated with lower reflectance between 750 and 900nm; blue and red reflectance demonstrated differences from leaf necroses. With high inoculum densities, P. viticola sporulated on even resistant cultivars. Hyperspectral characterization at the tissue level proved suitable for phenotyping plant resistance to pathogens and provided information on resistance mechanisms.