Genetic and physical mapping of the grapevine powdery mildew resistance gene, Run1, using a bacterial artificial chromosome library

Vitis rotundifolia Genes Introgressed with RUN1 and RPV1: Poor Recombination and Impact on V. vinifera Berry Transcriptome

Thanks to several Vitis vinifera backcrosses with an initial V. vinifera L. × V. rotundifolia (previously Muscadinia rotundifolia) interspecific cross, the MrRUN1/MrRPV1 locus (resistance to downy and powdery mildews) was introgressed in genotypes phenotypically close to V. vinifera varieties. To check the consequences of introgressing parts of the V. rotundifolia genome on gene expression during fruit development, we conducted a comparative RNA-seq study on single berries from different V. vinifera cultivars and V. vinifera × V. rotundifolia hybrids, including 'G5' and two derivative microvine lines, 'MV102' (resistant) and 'MV32' (susceptible) segregating for the MrRUN1/RPV1 locus. RNA-Seq profiles were analyzed on a comprehensive set of single berries from the end of the herbaceous plateau to the ripe stage. Pair-end reads were aligned both on V. vinifera PN40024.V4 reference genome, V. rotundifolia cv 'Trayshed' and cv 'Carlos', and to the few resistance genes from the original V. rotundifolia cv '52' parent available at NCBI. Weighted Gene Co-expression Network Analysis (WGCNA) led to classifying the differentially expressed genes into 15 modules either preferentially correlated with resistance or berry phenology and composition. Resistance positively correlated transcripts predominantly mapped on the 4-5 Mb distal region of V. rotundifolia chromosome 12 beginning with the MrRUN1/MrRPV1 locus, while the negatively correlated ones mapped on the orthologous V. vinifera region, showing this large extremity of LG12 remained recalcitrant to internal recombination during the successive backcrosses. Some constitutively expressed V. rotundifolia genes were also observed at lower densities outside this region. Genes overexpressed in developing berries from resistant accessions, either introgressed from V. rotundifolia or triggered by these in the vinifera genome, spanned various functional groups, encompassing calcium signal transduction, hormone signaling, transcription factors, plant-pathogen-associated interactions, disease resistance proteins, ROS and phenylpropanoid biosynthesis. This transcriptomic insight provides a foundation for understanding the disease resistance inherent in these hybrid cultivars and suggests a constitutive expression of NIR NBS LRR triggering calcium signaling. Moreover, these results illustrate the magnitude of transcriptomic changes caused by the introgressed V. rotundifolia background in backcrossed hybrids, on a large number of functions largely exceeding the ones constitutively expressed in single resistant gene transformants.

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.

Novel loci associated with resistance to downy and powdery mildew in grapevine

Among the main challenges in current viticulture, there is the increasing demand for sustainability in the protection from fungal diseases, such as downy mildew (DM) and powdery mildew (PM). Breeding disease-resistant grapevine varieties is a key strategy for better managing fungicide inputs. This study explores the diversity of grapevine germplasm (cultivated and wild) from Caucasus and neighboring areas to identify genotypes resistant to DM and PM, based on 13 Simple Sequence Repeat (SSR) loci and phenotypical (artificial pathogen inoculation) analysis, and to identify loci associated with DM and PM resistance, via Genome-Wide Association Analysis (GWAS) on Single Nucleotide Polymorphism (SNP) profiles. SSR analysis revealed resistant alleles for 16 out of 88 genotypes. Phenotypic data identified seven DM and 31 PM resistant genotypes. GWAS identified two new loci associated with DM resistance, located on chromosome 15 and 16 (designated as Rpv36 and Rpv37), and two with PM resistance, located on chromosome 6 and 17 (designated as Ren14 and Ren15). The four novel loci identified genomic regions rich in genes related to biotic stress response, such as genes involved in pathogen recognition, signal transduction and resistance response. This study highlights potential candidate genes associated with resistance to DM and PM, providing valuable insights for breeding programs for resistant varieties. To optimize their utilization, further functional characterization studies are recommended.

QTL detection and candidate gene analysis of grape white rot resistance by interspecific grape (Vitis vinifera L. × Vitis davidii Foex.) crossing

Grape white rot, a devastating disease of grapevines caused by Coniella diplodiella (Speg.) Sacc., leads to significant yield losses in grape. Breeding grape cultivars resistant to white rot is essential to reduce the regular use of chemical treatments. In recent years, Chinese grape species have gained more attention for grape breeding due to their high tolerance to various biotic and abiotic factors along with changing climatic conditions. In this study, we employed whole-genome resequencing (WGR) to genotype the parents of 'Manicure Finger' (Vitis vinifera, female) and '0940' (Vitis davidii, male), along with 101 F₁ mapping population individuals, thereby constructing a linkage genetic map. The linkage map contained 9337 single-nucleotide polymorphism (SNP) markers with an average marker distance of 0.3 cM. After 3 years of phenotypic evaluation of the progeny for white rot resistance, we confirmed one stable quantitative trait locus (QTL) for white rot resistance on chromosome 3, explaining up to 17.9% of the phenotypic variation. For this locus, we used RNA-seq to detect candidate gene expression and identified PR1 as a candidate gene involved in white rot resistance. Finally, we demonstrated that recombinant PR1 protein could inhibit the growth of C. diplodiella and that overexpression of PR1 in susceptible V. vinifera increased grape resistance to the pathogen.

Discovery and genome-guided mapping of REN12 from Vitis amurensis, conferring strong, rapid resistance to grapevine powdery mildew

Powdery mildew resistance genes restrict infection attempts at different stages of pathogenesis. Here, a strong and rapid powdery mildew resistance phenotype was discovered from Vitis amurensis 'PI 588631' that rapidly stopped over 97% of Erysiphe necator conidia, before or immediately after emergence of a secondary hypha from appressoria. This resistance was effective across multiple years of vineyard evaluation on leaves, stems, rachises, and fruit and against a diverse array of E. necator laboratory isolates. Using core genome rhAmpSeq markers, resistance mapped to a single dominant locus (here named REN12) on chromosome 13 near 22.8-27.0 Mb, irrespective of tissue type, explaining up to 86.9% of the phenotypic variation observed on leaves. Shotgun sequencing of recombinant vines using skim-seq technology enabled the locus to be further resolved to a 780 kb region, from 25.15 to 25.93 Mb. RNASeq analysis indicated the allele-specific expression of four resistance genes (NLRs) from the resistant parent. REN12 is one of the strongest powdery mildew resistance loci in grapevine yet documented, and the rhAmpSeq sequences presented here can be directly used for marker-assisted selection or converted to other genotyping platforms. While no virulent isolates were identified among the genetically diverse isolates and wild populations of E. necator tested here, NLR loci like REN12 are often race-specific. Thus, stacking of multiple resistance genes and minimal use of fungicides should enhance the durability of resistance and could enable a 90% reduction in fungicides in low-rainfall climates where few other pathogens attack the foliage or fruit.

Genetic changes in the genus Vitis and the domestication of vine

The genus Vitis belongs to the Vitaceae family and is divided into two subgenera: Muscadinia and Vitis, the main difference between these subgenera being the number of chromosomes. There are many hypotheses about the origin of the genus, which have been formed with archaeological studies and lately with molecular analyses. Even though there is no consensus on the place of origin, these studies have shown that grapes have been used by man since ancient times, starting later on its domestication. Most studies point to the Near East and Greece as the beginning of domestication, current research suggests it took place in parallel in different sites, but in all cases Vitis vinifera (L.) subsp. sylvestris [Vitis vinifera (L.) subsp. sylvestris (Gmelin) Hagi] seems to be the species chosen by our ancestors to give rise to the now known Vitis vinifera (L.) subsp. vinifera [=sativa (Hegi)= caucasica (Vavilov)]. Its evolution and expansion into other territories followed the formation of new empires and their expansion, and this is where the historical importance of this crop lies. In this process, plants with hermaphrodite flowers were preferentially selected, with firmer, sweeter, larger fruits of different colors, thus favoring the selection of genes associated with these traits, also resulting in a change in seed morphology. Currently, genetic improvement programs have made use of wild species for the introgression of disease resistance genes and tolerance to diverse soil and climate environments. In addition, the mapping of genes of interest, both linked to agronomic and fruit quality traits, has allowed the use of molecular markers for assisted selection. Information on the domestication process and genetic resources help to understand the gene pool available for the development of cultivars that respond to producer and consumer requirements.

Haplotype-resolved powdery mildew resistance loci reveal the impact of heterozygous structural variation on NLR genes in Muscadinia rotundifolia

Muscadinia rotundifolia cv. Trayshed is a valuable source of resistance to grape powdery mildew. It carries 2 powdery mildew resistance-associated genetic loci, Run1.2 on chromosome 12 and Run2.2 on chromosome 18. The purpose of this study was to identify candidate resistance genes associated with each haplotype of the 2 loci. Both haplotypes of each resistance-associated locus were identified, phased, and reconstructed. Haplotype phasing allowed the identification of several structural variation events between haplotypes of both loci. Combined with a manual refinement of the gene models, we found that the heterozygous structural variants affected the gene content, with some resulting in duplicated or hemizygous nucleotide-binding leucine-rich repeat genes. Heterozygous structural variations were also found to impact the domain composition of some nucleotide-binding leucine-rich repeat proteins. By comparing the nucleotide-binding leucine-rich repeat proteins at Run1.2 and Run2.2 loci, we discovered that the 2 loci include different numbers and classes of nucleotide-binding leucine-rich repeat genes. To identify powdery mildew resistance-associated genes, we performed a gene expression profiling of the nucleotide-binding leucine-rich repeat genes at Run1.2b and Run2.2 loci with or without powdery mildew present. Several nucleotide-binding leucine-rich repeat genes were constitutively expressed, suggesting a role in powdery mildew resistance. These first complete, haplotype-resolved resistance-associated loci and the candidate nucleotide-binding leucine-rich repeat genes identified by this study are new resources that can aid the development of powdery mildew-resistant grape cultivars.

Powdery Mildew Resistance Genes in Vines: An Opportunity to Achieve a More Sustainable Viticulture

Grapevine (Vitis vinifera) is one of the main fruit crops worldwide. In 2020, the total surface area planted with vines was estimated at 7.3 million hectares. Diverse pathogens affect grapevine yield, fruit, and wine quality of which powdery mildew is the most important disease prior to harvest. Its causal agent is the biotrophic fungus Erysiphe necator, which generates a decrease in cluster weight, delays fruit ripening, and reduces photosynthetic and transpiration rates. In addition, powdery mildew induces metabolic reprogramming in its host, affecting primary metabolism. Most commercial grapevine cultivars are highly susceptible to powdery mildew; consequently, large quantities of fungicide are applied during the productive season. However, pesticides are associated with health problems, negative environmental impacts, and high costs for farmers. In paralleled, consumers are demanding more sustainable practices during food production. Therefore, new grapevine cultivars with genetic resistance to powdery mildew are needed for sustainable viticulture, while maintaining yield, fruit, and wine quality. Two main gene families confer resistance to powdery mildew in the Vitaceae, Run (Resistance to Uncinula necator) and Ren (Resistance to Erysiphe necator). This article reviews the powdery mildew resistance genes and loci and their use in grapevine breeding programs.

Chromosome-level genome sequence assembly and genome-wide association study of Muscadinia rotundifolia reveal the genetics of 12 berry-related traits

Vitis has two subgenera: Euvitis, which includes commercially important Vitis vinifera and interspecific hybrid cultivars, and Muscadinia. Of note, the market for Muscadinia grapes remains small, and only Muscadinia rotundifolia is cultivated as a commercial crop. To establish a basis for the study of Muscadinia species, we generated chromosome-level whole-genome sequences of Muscadinia rotundifolia cv. Noble. A total of 393.8 Mb of sequences were assembled from 20 haploid chromosomes, and 26 394 coding genes were identified from the sequences. Comparative analysis with the genome sequence of V. vinifera revealed a smaller size of the M. rotundifolia genome but highly conserved gene synteny. A genome-wide association study of 12 Muscadinia berry-related traits was performed among 356 individuals from breeding populations of M. rotundifolia. For the transferability of markers between Euvitis and Muscadinia, we used 2000 core genome rhAmpSeq markers developed to allow marker transferability across Euvitis species. A total of 1599 (80%) rhAmpSeq markers returned data in Muscadinia. From the GWAS analyses, we identified a total of 52 quantitative trait nucleotides (QTNs) associated with the 12 berry-related traits. The transferable markers enabled the direct comparison of the QTNs with previously reported results. The whole-genome sequences along with the GWAS results provide a new basis for the extensive study of Muscadinia species.

Analysis of the SC8-0071-014 and sc47-18 loci co-segregated with Ren1 gene in the genotypes of seedless grape varieties

Powdery mildew (Erysiphe necator) is one of the most common and economically significant diseases of grapes. The main method of controlling the disease is pesticide treatment. To reduce chemical treatments, it is necessary to select and introduce resistant varieties into production. DNA markers are currently actively used in the study of grape genetic resources. Seedless grape varieties are highly demanded by consumers. Ren1 is one of the known and mapped vine resistance genes to powdery mildew, inherited from V. vinifera; linked DNA markers for this resistance locus are known. A study of 34 seedless grape genotypes was carried out using DNA markers SC8-0071-014 and sc47-18 co-segregated with Ren1. In the studied sample of varieties, 12 types of alleles were identified in the sc47-18 locus and 9 types of alleles in the SC8-0071-014 locus. Target fragments, according to linked marker loci, indicating the presence of the Ren1 resistance gene, were identified in grape variety Lotus (Kriulyanskiy x Yangi Er).

Construction of a high-density genetic map and detection of a major QTL of resistance to powdery mildew (Erysiphe necator Sch.) in Caucasian grapes (Vitis vinifera L.)

BACKGROUND

Vitis vinifera L. is the most cultivated grapevine species worldwide. Erysiphe necator Sch., the causal agent of grape powdery mildew, is one of the main pathogens affecting viticulture. V. vinifera has little or no genetic resistances against E. necator and the grape industry is highly dependent on agrochemicals. Some Caucasian V. vinifera accessions have been reported to be resistant to E. necator and to have no genetic relationships to known sources of resistance to powdery mildew. The main purpose of this work was the study and mapping of the resistance to E. necator in the Caucasian grapes 'Shavtsitska' and 'Tskhvedianis tetra'.

RESULTS

The Caucasian varieties 'Shavtsitska' and 'Tskhvedianis tetra' showed a strong partial resistance to E. necator which segregated in two cross populations: the resistant genotypes delayed and limited the pathogen mycelium growth, sporulation intensity and number of conidia generated. A total of 184 seedlings of 'Shavtsitska' x 'Glera' population were genotyped through the Genotyping by Sequencing (GBS) technology and two high-density linkage maps were developed for the cross parents. The QTL analysis revealed a major resistance locus, explaining up to 80.15% of the phenotypic variance, on 'Shavtsitska' linkage group 13, which was associated with a reduced pathogen infection as well as an enhanced plant necrotic response. The genotyping of 105 Caucasian accessions with SSR markers flanking the QTL revealed that the resistant haplotype of 'Shavtsitska' was shared by 'Tskhvedianis tetra' and a total of 25 Caucasian grape varieties, suggesting a widespread presence of this resistance in the surveyed germplasm. The uncovered QTL was mapped in the region where the Ren1 locus of resistance to E. necator, identified in the V. vinifera 'Kishmish vatkana' and related grapes of Central Asia, is located. The genetic analysis conducted revealed that the Caucasian grapes in this study exhibit a resistant haplotype different from that of Central Asian grape accessions.

CONCLUSIONS

The QTL isolated in 'Shavtsitska' and present in the Caucasian V. vinifera varieties could be a new candidate gene of resistance to E. necator to use in breeding programmes. It co-localizes with the Ren1 locus but shows a different haplotype from that of grapevines of Central Asia. We therefore consider that the Caucasian resistance locus, named Ren1.2, contains a member of a cluster of R-genes, of which the region is rich, and to be linked with, or possibly allelic, to Ren1.

Vitis Species from the Southwestern United States Vary in Their Susceptibility to Powdery Mildew

The European grapevine (Vitis vinifera L.) has been cultivated in North America for about 500 years. One of the major limitations to its culture is the powdery mildew (PM) fungus, Erysiphe necator Schw. This study reports on the most extensive screening of Vitis species from the southwestern United States and northern Mexico for resistance to PM, testing 147 accessions of 13 Vitis species. In addition, Vitis vinifera cv. Carignane, a highly susceptible wine grape cultivar, was used as a reference to evaluate the effect of the inoculum 14 days postinoculation. Inoculation was done with a vacuum-operated settling tower using a broadly virulent isolate of E. necator, the C-strain. Resistant accessions (nine), moderately susceptible accessions (39), and highly susceptible accessions (99) were detected. The resistant accessions were then inoculated with an additional fungal isolate, e1-101, and they retained their resistance. Vitis species susceptibility was not associated with a North-South gradation, but Western species were more susceptible than Midwestern and Eastern species. All five of the V. monticola accessions were susceptible, as were the accessions of V. treleasei. The species V. acerifolia, V. candicans, V. cinerea, and V. × doaniana had significantly more resistant to moderately susceptible accessions compared with V. arizonica, V. berlandieri, V. californica, V. × champinii, V. girdiana, V. riparia, and V. rupestris, which had relatively more susceptible accessions than the other species. This research identified new sources of PM resistance in Vitis from the southwestern United States that could be incorporated into PM resistance breeding programs throughout the world.

Diploid chromosome-scale assembly of the Muscadinia rotundifolia genome supports chromosome fusion and disease resistance gene expansion during Vitis and Muscadinia divergence

Muscadinia rotundifolia, the muscadine grape, has been cultivated for centuries in the southeastern United States. M. rotundifolia is resistant to many of the pathogens that detrimentally affect Vitis vinifera, the grape species commonly used for winemaking. For this reason, M. rotundifolia is a valuable genetic resource for breeding. Single-molecule real-time reads were combined with optical maps to reconstruct the two haplotypes of each of the 20 M. rotundifolia cv. Trayshed chromosomes. The completeness and accuracy of the assembly were confirmed using a high-density linkage map. Protein-coding genes were annotated using an integrated and comprehensive approach. This included using full-length cDNA sequencing (Iso-Seq) to improve gene structure and hypothetical spliced variant predictions. Our data strongly support that Muscadinia chromosomes 7 and 20 are fused in Vitis and pinpoint the location of the fusion in Cabernet Sauvignon and PN40024 chromosome 7. Disease-related gene numbers in Trayshed and Cabernet Sauvignon were similar, but their clustering locations were different. A dramatic expansion of the Toll/Interleukin-1 Receptor-like Nucleotide-Binding Site Leucine-Rich Repeat (TIR-NBS-LRR) class was detected on Trayshed chromosome 12 at the Resistance to Uncinula necator 1 (RUN1)/Resistance to Plasmopara viticola 1 (RPV1) locus, which confers strong dominant resistance to powdery and downy mildews. A genome browser, annotation, and Blast tool for Trayshed are available at www.grapegenomics.com.

The Assessment of Agrobiological and Disease Resistance Traits of Grapevine Hybrid Populations (Vitis vinifera L. × Muscadinia rotundifolia Michx.) in the Climatic Conditions of Crimea

The Crimean autochthonous grape varieties are unique by their origin and serve as a valuable source for breeding new cultivars with increased salt and frost resistance, as well as high-quality berries. However, they suffer from fungal pathogens, as the dry and hot summer months contribute to the epiphytotic course of diseases. An increase in the resistance of Crimean grape varieties is currently achieved through interspecific hybridization. In this study, we describe the genetic and agrobiological diversity of three hybrid populations obtained using the Vitis interspecific hybrid ‘Magarach 31-77-10′ as a female parent and Muscadinia rotundifolia × Vitis vinifera BC5 hybrid plants as male parents. The hybrid nature of the populations was assessed using RADseq high-throughput genotyping. We discovered 12,734 SNPs, which were common to all three hybrid populations. We also proved with the SSR markers that the strong powdery and downy mildew resistance of the paternal genotypes is determined by the dominant Run1/Rpv1 locus inherited from M. rotundifolia. As a result, the disease development score (R, %) for both mildew diseases in the female parent ‘Magarach 31-77-10’ was three times higher than in male parents 2000-305-143 and 2000-305-163 over two years of phytopathological assessment. The highest values of yield-contributing traits (average bunch weight ~197 g and 1.3 kg as yield per plant) were detected in the population 4-11 (♀M. No. 31-77-10 × 2000-305-163). Despite the epiphytotic development of PM, the spread of oidium to the vegetative organs of hybrids 4-11 did not exceed 20%. Some hybrid genotypes with high productivity and resistance to pathogens were selected for further assessment as promising candidates for new varieties.

High-Density Genetic Linkage Map Construction and White Rot Resistance Quantitative Trait Loci Mapping for Genus Vitis Based on Restriction Site-Associated DNA Sequencing

Grape white rot (Coniothyrium diplodiella) is a major fungal disease affecting grape yield and quality. Quantitative trait locus (QTL) analysis is an important method for studying important horticultural traits of grapevine. This study was conducted to construct a high-density map and conduct QTL mapping for grapevine white rot resistance. A mapping population with 177 genotypes was developed from interspecific hybridization of a white rot-resistant cultivar (Vitis vinifera × V. labrusca 'Zhuosexiang') and white rot-susceptible cultivar (V. vinifera 'Victoria'). Single-nucleotide polymorphism (SNP) markers were developed by restriction site-associated DNA sequencing. The female, male, and integrated maps contained 2,501, 4,110, and 6,249 SNP markers with average genetic distances of adjacent markers of 1.25, 0.77, and 0.50 cM, respectively. QTL mapping was conducted based on white rot resistance identification of 177 individuals in July and August of 2017 and 2018. Notably, one stable QTL related to white rot resistance was detected and located on linkage group LG14. The phenotypic variance ranged from 12.93 to 13.43%. An SNP marker (chr14_3929380), which cosegregated with white rot resistance, was discovered and shows potential for use in marker-assisted selection to generate new grapevine cultivars with resistance to white rot.

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.

High-density genetic linkage map construction and cane cold hardiness QTL mapping for Vitis based on restriction site-associated DNA sequencing

Background

Cold hardiness is an important agronomic trait and can significantly affect grape production and quality. Until now, there are no reports focusing on cold hardiness quantitative trait loci (QTL) mapping. In this study, grapevine interspecific hybridisation was carried out with the maternal parent ‘Cabernet sauvignon’ and paternal parent ‘Zuoyouhong’. A total of 181 hybrid offspring and their parents were used as samples for restriction-site associated DNA sequencing (RAD). Grapevine cane phloem and xylem cold hardiness of the experimental material was detected using the low-temperature exotherm method in 2016, 2017 and 2018. QTL mapping was then conducted based on the integrated map.

Results

We constructed a high-density genetic linkage map with 16,076, 11,643, and 25,917 single-nucleotide polymorphism (SNP) markers anchored in the maternal, paternal, and integrated maps, respectively. The average genetic distances of adjacent markers in the maps were 0.65 cM, 0.77 cM, and 0.41 cM, respectively. Colinearity analysis was conducted by comparison with the grape reference genome and showed good performance. Six QTLs were identified based on the phenotypic data of 3 years and they were mapped on linkage group (LG) 2, LG3, and LG15. Based on QTL results, candidate genes which may be involved in grapevine cold hardiness were selected.

Conclusions

High-density linkage maps can facilitate grapevine fine QTL mapping, genome comparison, and sequence assembly. The cold hardiness QTL mapping and candidate gene discovery performed in this study provide an important reference for molecular-assisted selection in grapevine cold hardiness breeding.

Genome-wide characterization revealed role of NBS-LRR genes during powdery mildew infection in Vitis vinifera

NBS-LRR comprises a large class of disease resistance (R) proteins that play a widespread role in plant protection against pathogens. In grapevine, powdery mildew cause significant losses in its productivity and efforts are being directed towards finding of resistance loci or genes imparting resistance/tolerance against such fungal diseases. In the present study, we performed genome-wide analysis of NBS-LRR genes during PM infection in grapevine. We identified 18, 23, 12, 16, 10, 10, 9, 20 and 14 differentially expressed NBS-LRR genes in response to PM infection in seven partially PM-resistant (DVIT3351.27, Husseine, Karadzhandal, Khalchili, Late vavilov, O34-16, Sochal) and 2 PM-susceptible (Carignan and Thompson seedless) V. vinifera accessions. Further, the identified sequences were characterized based on chromosomal locations, physicochemical properties, gene structure and motif analysis, and functional annotation by Gene Ontology (GO) mapping. The NBS-LRR genes responsive to powdery mildew could potentially be exploited to improve resistance in grapes.

Emergent Ascomycetes in Viticulture: An Interdisciplinary Overview

The reduction of pesticide usage is a current imperative and the implementation of sustainable viticulture is an urgent necessity. A potential solution, which is being increasingly adopted, is offered by the use of grapevine cultivars resistant to its main pathogenic threats. This, however, has contributed to changes in defense strategies resulting in the occurrence of secondary diseases, which were previously controlled. Concomitantly, the ongoing climate crisis is contributing to destabilizing the increasingly dynamic viticultural context. In this review, we explore the available knowledge on three Ascomycetes which are considered emergent and causal agents of powdery mildew, black rot and anthracnose. We also aim to provide a survey on methods for phenotyping disease symptoms in fields, greenhouse and lab conditions, and for disease control underlying the insurgence of pathogen resistance to fungicide. Thus, we discuss fungal genetic variability, highlighting the usage and development of molecular markers and barcoding, coupled with genome sequencing. Moreover, we extensively report on the current knowledge available on grapevine-ascomycete interactions, as well as the mechanisms developed by the host to counteract the attack. Indeed, to better understand these resistance mechanisms, it is relevant to identify pathogen effectors which are involved in the infection process and how grapevine resistance genes function and impact the downstream cascade. Dealing with such a wealth of information on both pathogens and the host, the horizon is now represented by multidisciplinary approaches, combining traditional and innovative methods of cultivation. This will support the translation from theory to practice, in an attempt to understand biology very deeply and manage the spread of these Ascomycetes.

Reproductive and genetic consequences of extreme isolation in Salix herbacea L. at the rear edge of its distribution

BACKGROUND AND AIMS

At the rear edge of the distribution of species, extreme isolation and small population size influence the genetic diversity and differentiation of plant populations. This may be particularly true for Arctic-alpine species in mid-latitude mountains, but exactly how peripherality has shaped their genetic and reproductive characteristics is poorly investigated. The present study, focused on Salix herbacea, aims at providing new insights into the causes behind ongoing demographic dynamics and their consequences for peripheral populations of Arctic-alpine species.

METHODS

We performed a whole-population, highly detailed sampling of the only two S. herbacea populations in the northern Apennines, comparing their clonal and genetic diversity, sex ratio and spatial genetic structure with a reference population from the Alps. After inspecting ~1800 grid intersections in the three populations, 563 ramets were genotyped at 11 nuclear microsatellite markers (nSSRs). Past demography and mating patterns of Apennine populations were investigated to elucidate the possible causes of altered reproductive dynamics.

KEY RESULTS

Apennine populations, which experienced a Holocene bottleneck and are highly differentiated (FST = 0.15), had lower clonal and genetic diversity compared with the alpine population (RMLG = 1 and HE = 0.71), with the smaller population exhibiting the lowest diversity (RMLG = 0.03 and HE = 0.24). An unbalanced sex ratio was found in the larger (63 F:37 M) and the smaller (99 F:1 M) Apennine population. Both were characterized by the presence of extremely large clones (up to 2500 m2), which, however, did not play a dominant role in local reproductive dynamics.

CONCLUSIONS

Under conditions of extreme isolation and progressive size reduction, S. herbacea has experienced an alteration of genetic characteristics produced by the prevalence of clonal growth over sexual reproduction. However, our results showed that the larger Apennine population has maintained levels of sexual reproduction enough to counteract a dramatic loss of genetic and clonal diversity.

The cytological basis of powdery mildew resistance in wild Chinese Vitis species

The wild Chinese grapevines (Vitis spp.) show varying levels of resistance to powdery mildew caused by Erysiphe necator that is an economically important disease of cultivated grapevines (Vitis vinifera). However, little information is available regarding the cytological mechanisms of powdery mildew resistance in these wild relatives. Here, we studied the cytological responses of three wild Chinese grapevine accessions after they were infected with E. necator (En) NAFU1 in comparison to the susceptible V. vinifera cv. 'Thompson Seedless' grape. The hyphal growth and sporulation of En NAFU1 were significantly restricted in wild species compared to 'Thompson Seedless', which appears to be associated with early cell wall deposition at the attempt sites, encasement of haustoria, and hypersensitive response-like cell death of penetrated epidermal cells. Moreover, endogenous free salicylic acid (SA) was more abundant in wild Chinese Vitis species than in 'Thompson Seedless' under pathogen-free condition. During En NAFU1 colonization, SA conjugates accumulated higher in wild grapevines than in 'Thompson Seedless'. In addition, the species-specific expression patterns of defense-associated genes during En NAFU1 colonization indicated that mechanisms underlying powdery mildew resistance are divergent among different wild Chinese Vitis species. These results contribute to understanding of mechanisms underlying defense responses of wild Chinese Vitis species against powdery mildew.

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.

High-density linkage maps and loci for berry color and flower sex in muscadine grape (Vitis rotundifolia)

Linkage maps of muscadine grape generated using genotyping-by-sequencing (GBS) provide insight into genome collinearity between Muscadinia and Euvitis subgenera and genetic control of flower sex and berry color. The muscadine grape, Vitis rotundifolia, is a specialty crop native to the southeastern USA. Muscadine vines can be male, female, or perfect-flowered, and berry color ranges from bronze to black. Genetic linkage maps were constructed using genotyping-by-sequencing in two F₁ populations segregating for flower sex and berry color. The linkage maps consisted of 1244 and 2069 markers assigned to 20 linkage groups (LG) for the 'Black Beauty' × 'Nesbitt' and 'Supreme' × 'Nesbitt' populations, respectively. Data from both populations were used to generate a consensus map with 2346 markers across 20 LGs. A high degree of collinearity was observed between the genetic maps and the Vitis vinifera physical map. The higher chromosome number in muscadine (2n = 40) compared to V. vinifera (2n = 38) was accounted for by the behavior of V. vinifera chromosome 7 as two independently segregating LGs in muscadine. The muscadine sex locus mapped to an interval that aligned to 4.64-5.09 Mb on V. vinifera chromosome 2, a region which includes the previously described V. vinifera subsp. sylvestris sex locus. While the MYB transcription factor genes controlling fruit color in V. vinifera are located on chromosome 2, the muscadine berry color locus mapped to an interval aligning to 11.09-11.88 Mb on V. vinifera chromosome 4, suggesting that a mutation in a different gene in the anthocyanin biosynthesis pathway determines berry color in muscadine. These linkage maps lay the groundwork for marker-assisted breeding in muscadine and provide insight into the evolution of Vitis species.

Determination of downy and powdery mildew resistance of some Vitis spp

The Black Sea region of Turkey receives an annual rainfall of 2000-2500 mm and viticulture in the region depends on the rainfall limits significantly. In this study, the resistance of eighty different Vitis species and cultivars/genotypes to downy and powdery mildew was assessed using Marker Assisted Selection coupled with inoculation observations. Six Simple Sequence Repeats (SSR) and one Sequence Characterized Amplified Region (SCAR) markers were developed for different resistance loci (Run1, Rpv1, Ren1, Rpv3, Ren3) from different Vitis genetic resources. Eight of the cultivars/genotypes were characterised as resistant to downy mildew, seven were resistant to powdery mildew, and four were resistant to both diseases. These results, taken together with the disease inoculation observations, revealed ‘Köfteci Üzümü’ (Vitis labrusca) and ‘Giresun 3’ (Vitis labrusca) were the most resistant cultivars/genotypes.

Introgression reshapes recombination distribution in grapevine interspecific hybrids

In grapevine interspecific hybrids, meiotic recombination is suppressed in homeologous regions and enhanced in homologous regions of recombined chromosomes, whereas crossover rate remains unchanged when chromosome pairs are entirely homeologous. Vitis rotundifolia, an American species related to the cultivated European grapevine Vitis vinifera, has a high level of resistance to several grapevine major diseases and is consequently a valuable resource for grape breeding. However, crosses between both species most often lead to very few poorly fertile hybrids. In this context, identifying genetic and genomic features that make cross-breeding between both species difficult is essential. To this end, three mapping populations were generated by pseudo-backcrosses using V. rotundifolia as the donor parent and several V. vinifera cultivars as the recurrent parents. Genotyping-by-sequencing was used to establish high-density genetic linkage maps and to determine the genetic composition of the chromosomes of each individual. A good collinearity of the SNP positions was observed between parental maps, confirming the synteny between both species, except on lower arm of chromosome 7. Interestingly, recombination rate in V. rotundifolia × V. vinifera interspecific hybrids depends on the length of the introgressed region. It is similar to grapevine for chromosome pairs entirely homeologous. Conversely, for chromosome pairs partly homeologous, recombination is suppressed in the homeologous regions, whereas it is enhanced in the homologous ones. This balance leads to the conservation of the total genetic length of each chromosome between V. vinifera and hybrid maps, whatever the backcross level and the proportion of homeologous region. Altogether, these results provide new insight to optimize the use of V. rotundifolia in grape breeding and, more generally, to improve the introgression of gene of interest from wild species related to crops.

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.

Ectopic expression of Arabidopsis broad-spectrum resistance gene RPW8.2 improves the resistance to powdery mildew in grapevine (Vitis vinifera)

Powdery mildew is the most economically important disease of cultivated grapevines worldwide. Here, we report that the Arabidopsis broad-spectrum disease resistance gene RPW8.2 could improve resistance to powdery mildew in Vitis vinifera cv. Thompson Seedless. The RPW8.2-YFP fusion gene was stably expressed in grapevines from either the constitutive 35S promoter or the native promoter (NP) of RPW8.2. The grapevine shoots and plantlets transgenic for 35S::RPW8.2-YFP showed reduced rooting and reduced growth at later development stages in the absence of any pathogens. Infection tests with an adapted grapevine powdery mildew isolate En NAFU1 showed that hyphal growth and sporulation were significantly restricted in transgenic grapevines expressing either of the two constructs. The resistance appeared to be attributable to the ectopic expression of RPW8.2, and associated with the enhanced encasement of the haustorial complex (EHC) and onsite accumulation of H₂O₂. In addition, the RPW8.2-YFP fusion protein showed focal accumulation around the fungal penetration sites. Transcriptome analysis revealed that ectopic expression of RPW8.2 in grapevines not only significantly enhanced salicylic acid-dependent defense signaling, but also altered expression of other phytohormone-associated genes. Taken together, our results indicate that RPW8.2 could be utilized as a transgene for improving resistance against powdery mildew in grapevines.

Use of Natural Diversity and Biotechnology to Increase the Quality and Nutritional Content of Tomato and Grape

Improving fruit quality has become a major goal in plant breeding. Direct approaches to tackling fruit quality traits specifically linked to consumer preferences and environmental friendliness, such as improved flavor, nutraceutical compounds, and sustainability, have slowly been added to a breeder priority list that already includes traits like productivity, efficiency, and, especially, pest and disease control. Breeders already use molecular genetic tools to improve fruit quality although most advances have been made in producer and industrial quality standards. Furthermore, progress has largely been limited to simple agronomic traits easy-to-observe, whereas the vast majority of quality attributes, specifically those relating to flavor and nutrition, are complex and have mostly been neglected. Fortunately, wild germplasm, which is used for resistance against/tolerance of environmental stresses (including pathogens), is still available and harbors significant genetic variation for taste and health-promoting traits. Similarly, heirloom/traditional varieties could be used to identify which genes contribute to flavor and health quality and, at the same time, serve as a good source of the best alleles for organoleptic quality improvement. Grape (Vitis vinifera L.) and tomato (Solanum lycopersicum L.) produce fleshy, berry-type fruits, among the most consumed in the world. Both have undergone important domestication and selection processes, that have dramatically reduced their genetic variability, and strongly standardized fruit traits. Moreover, more and more consumers are asking for sustainable production, incompatible with the wide range of chemical inputs. In the present paper, we review the genetic resources available to tomato/grape breeders, and the recent technological progresses that facilitate the identification of genes/alleles of interest within the natural or generated variability gene pool. These technologies include omics, high-throughput phenotyping/phenomics, and biotech approaches. Our review also covers a range of technologies used to transfer to tomato and grape those alleles considered of interest for fruit quality. These include traditional breeding, TILLING (Targeting Induced Local Lesions in Genomes), genetic engineering, or NPBT (New Plant Breeding Technologies). Altogether, the combined exploitation of genetic variability and innovative biotechnological tools may facilitate breeders to improve fruit quality tacking more into account the consumer standards and the needs to move forward into more sustainable farming practices.

RUN1 and REN1 Pyramiding in Grapevine (Vitis vinifera cv. Crimson Seedless) Displays an Improved Defense Response Leading to Enhanced Resistance to Powdery Mildew (Erysiphe necator)

Fungal pathogens are the cause of the most common diseases in grapevine and among them powdery mildew represents a major focus for disease management. Different strategies for introgression of resistance in grapevine are currently undertaken in breeding programs. For example, introgression of several resistance genes (R) from different sources for making it more durable and also strengthening the plant defense response. Taking this into account, we cross-pollinated P09-105/34, a grapevine plant carrying both RUN1 and REN1 pyramided loci of resistance to Erysiphe necator inherited from a pseudo-backcrossing scheme with Muscadinia rotundifolia and Vitis vinifera 'Dzhandzhal Kara,' respectively, with the susceptible commercial table grape cv. 'Crimson Seedless.' We developed RUN1REN1 resistant genotypes through conventional breeding and identified them by marker assisted selection. The characterization of defense response showed a highly effective defense mechanism against powdery mildew in these plants. Our results reveal that RUN1REN1 grapevine plants display a robust defense response against E. necator, leading to unsuccessful fungal establishment with low penetration rate and poor hypha development. This resistance mechanism includes reactive oxygen species production, callose accumulation, programmed cell death induction and mainly VvSTS36 and VvPEN1 gene activation. RUN1REN1 plants have a great potential as new table grape cultivars with durable complete resistance to E. necator, and are valuable germplasm to be included in grape breeding programs to continue pyramiding with other sources of resistance to grapevine diseases.

Constitutive heterologous overexpression of a TIR-NB-ARC-LRR gene encoding a putative disease resistance protein from wild Chinese Vitis pseudoreticulata in Arabidopsis and tobacco enhances resistance to phytopathogenic fungi and bacteria

Plants use resistance (R) proteins to detect pathogen effector proteins and activate their innate immune response against the pathogen. The majority of these proteins contain an NB-ARC (nucleotide-binding adaptor shared by APAF-1, R proteins, and CED-4) domain along with a leucine-rich repeat (LRR), and some also bear a toll interleukin 1 receptor (TIR) domain. In this study, we characterized a gene encoding a TIR-NB-ARC-LRR R protein (VpTNL1) (GenBank accession number KX649890) from wild Chinese grapevine Vitis pseudoreticulata accession "Baihe-35-1", which was identified previously from a transcriptomic analysis of leaves inoculated with powdery mildew (PM; Erysiphe necator (Schw.)). The VpTNL1 transcript was found to be highly induced in V. pseudoreticulata following inoculation with E. necator, as well as treatment with salicylic acid (SA). Sequence analysis demonstrated that the deduced amino acid sequence contained a TIR domain at the N-terminus, along with an NB-ARC and four LRRs domains within the C-terminus. Constitutive expression of VpTNL1 in Arabidopsis thaliana resulted in either a wild-type or dwarf phenotype. Intriguingly, the phenotypically normal transgenic lines displayed enhanced resistance to Arabidopsis PM, Golovinomyces cichoracearum, as well as to the virulent bacterial pathogen Pseudomonas syringae pv. tomato DC3000. Similarly, constitutive expression of VpTNL1 in Nicotiana tabacum was found to confer enhanced resistance to tobacco PM, Erysiphe cichoacearum DC. Subsequent isolation of the VpTNL1 promoter and deletion analysis indicated that TC-rich repeats and TCA elements likely play an important role in its response to E. necator and SA treatment, respectively. Taken together, these results indicate that VpTNL1 contributes to PM resistance in grapevine and provide an interesting gene target for the future amelioration of grape via breeding and/or biotechnology.

Genetic dissection of powdery mildew resistance in interspecific half-sib grapevine families using SNP-based maps

Quantitative trait locus (QTL) identification in perennial fruit crops is impeded largely by their lengthy generation time, resulting in costly and labor-intensive maintenance of breeding programs. In a grapevine (genus Vitis) breeding program, although experimental families are typically unreplicated, the genetic backgrounds may contain similar progenitors previously selected due to their contribution of favorable alleles. In this study, we investigated the utility of joint QTL identification provided by analyzing half-sib families. The genetic control of powdery mildew was studied using two half-sib F₁ families, namely GE0711/1009 (MN1264 × MN1214; N = 147) and GE1025 (MN1264 × MN1246; N = 125) with multiple species in their ancestry. Maternal genetic maps consisting of 1077 and 1641 single nucleotide polymorphism (SNP) markers, respectively, were constructed using a pseudo-testcross strategy. Ratings of field resistance to powdery mildew were obtained based on whole-plant evaluation of disease severity. This 2-year analysis uncovered two QTLs that were validated on a consensus map in these half-sib families with improved precision relative to the parental maps. Examination of haplotype combinations based on the two QTL regions identified strong association of haplotypes inherited from 'Seyval blanc', through MN1264, with powdery mildew resistance. This investigation also encompassed the use of microsatellite markers to establish a correlation between 206-bp (UDV-015b) and 357-bp (VViv67) fragment sizes with resistance-carrying haplotypes. Our work is one of the first reports in grapevine demonstrating the use of SNP-based maps and haplotypes for QTL identification and tagging of powdery mildew resistance in half-sib families.

Characterization of the interaction between Oidium heveae and Arabidopsis thaliana

Oidium heveae, an obligate biotrophic pathogen of rubber trees (Hevea brasiliensis), causes significant yield losses of rubber worldwide. However, the molecular mechanisms underlying the interplay between O. heveae and rubber trees remain largely unknown. In this study, we isolated an O. heveae strain, named HN1106, from cultivated H. brasiliensis in Hainan, China. We found that O. heveae HN1106 triggers the hypersensitive response in a manner that depends on the effector-triggered immunity proteins EDS1 (Enhanced Disease Susceptibility 1) and PAD4 (Phytoalexin Deficient 4) and on salicylic acid (SA) in the model plant Arabidopsis thaliana. However, SA-independent resistance also appears to limit O. heveae infection of Arabidopsis, because the pathogen does not produce conidiospores on npr1 (nonexpressor of pr1), sid2 (SA induction deficient 2) and NahG plants, which show disruptions in SA signalling. Furthermore, we found that the callose synthase PMR4 (Powdery Mildew Resistant 4) prevents O. heveae HN1106 penetration into leaves in the early stages of infection. To elucidate the potential mechanism of resistance of Arabidopsis to O. heveae HN1106, we inoculated 47 different Arabidopsis accessions with the pathogen, and analysed the plant disease symptoms and O. heveae HN1106 hyphal growth and conidiospore formation on the leaves. We found that the accession Lag2-2 showed significant susceptibility to O. heveae HN1106. Overall, this study provides a basis for future research aimed at combatting powdery mildew caused by O. heveae in rubber trees.

Identification of two novel powdery mildew resistance loci, Ren6 and Ren7, from the wild Chinese grape species Vitis piasezkii

BACKGROUND

Grapevine powdery mildew Erysiphe necator is a major fungal disease in all grape growing countries worldwide. Breeding for resistance to this disease is crucial to avoid extensive fungicide applications that are costly, labor intensive and may have detrimental effects on the environment. In the past decade, Chinese Vitis species have attracted attention from grape breeders because of their strong resistance to powdery mildew and their lack of negative fruit quality attributes that are often present in resistant North American species. In this study, we investigated powdery mildew resistance in multiple accessions of the Chinese species Vitis piasezkii that were collected during the 1980 Sino-American botanical expedition to the western Hubei province of China.

RESULTS

A framework genetic map was developed using simple sequence repeat markers in 277 seedlings of an F1 mapping population arising from a cross of the powdery mildew susceptible Vitis vinifera selection F2-35 and a resistant accession of V. piasezkii DVIT2027. Quantitative trait locus analyses identified two major powdery mildew resistance loci on chromosome 9 (Ren6) and chromosome 19 (Ren7) explaining 74.8 % of the cumulative phenotypic variation. The quantitative trait locus analysis for each locus, in the absence of the other, explained 95.4 % phenotypic variation for Ren6, while Ren7 accounted for 71.9 % of the phenotypic variation. Screening of an additional 259 seedlings of the F1 population and 910 seedlings from four pseudo-backcross populations with SSR markers defined regions of 22 kb and 330 kb for Ren6 and Ren7 in the V. vinifera PN40024 (12X) genome sequence, respectively. Both R loci operate post-penetration through the induction of programmed cell death, but vary significantly in the speed of response and degree of resistance; Ren6 confers complete resistance whereas Ren7 confers partial resistance to the disease with reduced colony size. A comparison of the kinetics of induction of powdery mildew resistance mediated by Ren6, Ren7 and the Run1 locus from Muscadinia rotundifolia, indicated that the speed and strength of resistance conferred by Ren6 is greater than that of Run1 which, in turn, is superior to that conferred by Ren7.

CONCLUSIONS

This is the first report of mapping powdery mildew resistance in the Chinese species V. piasezkii. Two distinct powdery mildew R loci designated Ren6 and Ren7 were found in multiple accessions of this Chinese grape species. Their location on different chromosomes to previously reported powdery mildew resistance R loci offers the potential for grape breeders to combine these R genes with existing powdery mildew R loci to produce grape germplasm with more durable resistance against this rapidly evolving fungal pathogen.

Grapevine Pathogenic Microorganisms: Understanding Infection Strategies and Host Response Scenarios

Grapevine (Vitis vinifera L.) is one of the most important fruit crop worldwide. Commercial cultivars are greatly affected by a large number of pathogenic microorganisms that cause diseases during pre- and/or post-harvest periods, affecting production, processing and export, along with fruit quality. Among the potential threats, we can find bacteria, fungi, oomycete, or viruses with different life cycles, infection mechanisms and evasion strategies. While plant-pathogen interactions are cycles of resistance and susceptibility, resistance traits from natural resources are selected and may be used for breeding purposes and for a sustainable agriculture. In this context, here we summarize some of the most important diseases affecting V. vinifera together with their causal agents. The aim of this work is to bring a comprehensive review of the infection strategies deployed by significant types of pathogens while understanding the host response in both resistance and susceptibility scenarios. New approaches being used to uncover grapevine status during biotic stresses and scientific-based procedures needed to control plant diseases and crop protection are also addressed.

Identification of Powdery Mildew Responsive Genes in Hevea brasiliensis through mRNA Differential Display

Powdery mildew is an important disease of rubber trees caused by Oidium heveae B. A. Steinmann. As far as we know, none of the resistance genes related to powdery mildew have been isolated from the rubber tree. There is little information available at the molecular level regarding how a rubber tree develops defense mechanisms against this pathogen. We have studied rubber tree mRNA transcripts from the resistant RRIC52 cultivar by differential display analysis. Leaves inoculated with the spores of O. heveae were collected from 0 to 120 hpi in order to identify pathogen-regulated genes at different infection stages. We identified 78 rubber tree genes that were differentially expressed during the plant–pathogen interaction. BLAST analysis for these 78 ESTs classified them into seven functional groups: cell wall and membrane pathways, transcription factor and regulatory proteins, transporters, signal transduction, phytoalexin biosynthesis, other metabolism functions, and unknown functions. The gene expression for eight of these genes was validated by qRT-PCR in both RRIC52 and the partially susceptible Reyan 7-33-97 cultivars, revealing the similar or differential changes of gene expressions between these two cultivars. This study has improved our overall understanding of the molecular mechanisms of rubber tree resistance to powdery mildew.

Comparative transcriptomics of Central Asian Vitis vinifera accessions reveals distinct defense strategies against powdery mildew

Grape powdery mildew (PM), caused by the biotrophic ascomycete Erysiphe necator, is a devastating fungal disease that affects most Vitis vinifera cultivars. We have previously identified a panel of V. vinifera accessions from Central Asia with partial resistance to PM that possess a Ren1-like local haplotype. In this study, we show that in addition to the typical Ren1-associated late post-penetration resistance, these accessions display a range of different levels of disease development suggesting that alternative alleles or additional genes contribute to determining the outcome of the interaction with the pathogen. To identify potential Ren1-dependent transcriptional responses and functions associated with the different levels of resistance, we sequenced and analyzed the transcriptomes of these Central Asian accessions at two time points of PM infection. Transcriptomes were compared to identify constitutive differences and PM-inducible responses that may underlie their disease resistant phenotype. Responses to E. necator in all resistant accessions were characterized by an early up-regulation of 13 genes, most encoding putative defense functions, and a late down-regulation of 32 genes, enriched in transcriptional regulators and protein kinases. Potential Ren1-dependent responses included a hotspot of co-regulated genes on chromosome 18. We also identified 81 genes whose expression levels and dynamics correlated with the phenotypic differences between the most resistant accessions 'Karadzhandahal', DVIT3351.27, and O34-16 and the other genotypes. This study provides a first exploration of the functions associated with varying levels of partial resistance to PM in V. vinifera accessions that can be exploited as sources of genetic resistance in grape breeding programs.

Vitis rupestris B38 Confers Isolate-Specific Quantitative Resistance to Penetration by Erysiphe necator

Vitis rupestris B38 is a North American grapevine resistant to the major pathogen of cultivated grapevines, Erysiphe necator. Sources of powdery mildew resistance, like V. rotundifolia, are widely used in grape breeding but are already threatened, even before commercialization, by isolates that can reproduce on Run1 and other rotundifolia-derived breeding lines. Thus, complementary sources of resistance are needed to improve resistance durability. The segregation of foliar powdery mildew severity in an F1 family, derived from a cross of V. rupestris B38×V. vinifera 'Chardonnay', was observed in the field over three growing seasons and in potted vines following single-isolate inoculation. A pattern of continuous variation was observed in every instance. Mechanisms of resistance were analyzed on the resistant and susceptible parent by using microscopy to quantify the ability of the pathogen to penetrate and to form a colony on detached leaves. While 'Chardonnay' was susceptible in all tested conditions, V. rupestris B38 resistance was characterized by a reduction in pathogen penetration, with an effect of leaf position and significant differences among powdery mildew isolates. Segregation of the ability of the pathogen to penetrate and form a colony in F1 individuals showed a pattern of quantitative penetration resistance with no delay or restriction on colony formation once penetration has been achieved. Moreover, V. rupestris B38 showed an enhanced penetration resistance to a powdery mildew isolate with the ability to overcome the Run1 gene, making it an interesting resistance source to prolong the durability of this gene.

Strategies for RUN1 Deployment Using RUN2 and REN2 to Manage Grapevine Powdery Mildew Informed by Studies of Race Specificity

The Toll/interleukin-1 receptor nucleotide-binding site leucine-rich repeat gene, "resistance to Uncinula necator 1" (RUN1), from Vitis rotundifolia was recently identified and confirmed to confer resistance to the grapevine powdery mildew fungus Erysiphe necator (syn. U. necator) in transgenic V. vinifera cultivars. However, sporulating powdery mildew colonies and cleistothecia of the heterothallic pathogen have been found on introgression lines containing the RUN1 locus growing in New York (NY). Two E. necator isolates collected from RUN1 vines were designated NY1-131 and NY1-137 and were used in this study to inform a strategy for durable RUN1 deployment. In order to achieve this, fitness parameters of NY1-131 and NY1-137 were quantified relative to powdery mildew isolates collected from V. rotundifolia and V. vinifera on vines containing alleles of the powdery mildew resistance genes RUN1, RUN2, or REN2. The results clearly demonstrate the race specificity of RUN1, RUN2, and REN2 resistance alleles, all of which exhibit programmed cell death (PCD)-mediated resistance. The NY1 isolates investigated were found to have an intermediate virulence on RUN1 vines, although this may be allele specific, while the Musc4 isolate collected from V. rotundifolia was virulent on all RUN1 vines. Another powdery mildew resistance locus, RUN2, was previously mapped in different V. rotundifolia genotypes, and two alleles (RUN2.1 and RUN2.2) were identified. The RUN2.1 allele was found to provide PCD-mediated resistance to both an NY1 isolate and Musc4. Importantly, REN2 vines were resistant to the NY1 isolates and RUN1REN2 vines combining both genes displayed additional resistance. Based on these results, RUN1-mediated resistance in grapevine may be enhanced by pyramiding with RUN2.1 or REN2; however, naturally occurring isolates in North America display some virulence on vines with these resistance genes. The characterization of additional resistance sources is needed to identify resistance gene combinations that will further enhance durability. For the resistance gene combinations currently available, we recommend using complementary management strategies, including fungicide application, to reduce populations of virulent isolates.

Transcriptome characterization of three wild Chinese Vitis uncovers a large number of distinct disease related genes

BACKGROUND

Grape is one of the most valuable fruit crops and can serve for both fresh consumption and wine production. Grape cultivars have been selected and evolved to produce high-quality fruits during their domestication over thousands of years. However, current widely planted grape cultivars suffer extensive loss to many diseases while most wild species show resistance to various pathogens. Therefore, a comprehensive evaluation of wild grapes would contribute to the improvement of disease resistance in grape breeding programs.

RESULTS

We performed deep transcriptome sequencing of three Chinese wild grapes using the Illumina strand-specific RNA-Seq technology. High quality transcriptomes were assembled de novo and more than 93% transcripts were shared with the reference PN40024 genome. Over 1,600 distinct transcripts, which were absent or highly divergent from sequences in the reference PN40024 genome, were identified in each of the three wild grapes, among which more than 1,000 were potential protein-coding genes. Gene Ontology (GO) and pathway annotations of these distinct genes showed those involved in defense responses and plant secondary metabolisms were highly enriched. More than 87,000 single nucleotide polymorphisms (SNPs) and 2,000 small insertions or deletions (indels) were identified between each genotype and PN40024, and approximately 20% of the SNPs caused nonsynonymous mutations. Finally, we discovered 100 to 200 highly confident cis-natural antisense transcript (cis-NAT) pairs in each genotype. These transcripts were significantly enriched with genes involved in secondary metabolisms and plant responses to abiotic stresses.

CONCLUSION

The three de novo assembled transcriptomes provide a comprehensive sequence resource for molecular genetic research in grape. The newly discovered genes from wild Vitis, as well as SNPs and small indels we identified, may facilitate future studies on the molecular mechanisms related to valuable traits possessed by these wild Vitis and contribute to the grape breeding programs. Furthermore, we identified hundreds of cis-NAT pairs which showed their potential regulatory roles in secondary metabolism and abiotic stress responses.

Construction of a high-density genetic map and QTLs mapping for sugars and acids in grape berries

BACKGROUND

QTLs controlling individual sugars and acids (fructose, glucose, malic acid and tartaric acid) in grape berries have not yet been identified. The present study aimed to construct a high-density, high-quality genetic map of a winemaking grape cross with a complex parentage (V. vinifera × V. amurensis) × ((V. labrusca × V. riparia) × V. vinifera), using next-generation restriction site-associated DNA sequencing, and then to identify loci related to phenotypic variability over three years.

RESULTS

In total, 1 826 SNP-based markers were developed. Of these, 621 markers were assembled into 19 linkage groups (LGs) for the maternal map, 696 for the paternal map, and 1 254 for the integrated map. Markers showed good linear agreement on most chromosomes between our genetic maps and the previously published V. vinifera reference sequence. However marker order was different in some chromosome regions, indicating both conservation and variation within the genome. Despite the identification of a range of QTLs controlling the traits of interest, these QTLs explained a relatively small percentage of the observed phenotypic variance. Although they exhibited a large degree of instability from year to year, QTLs were identified for all traits but tartaric acid and titratable acidity in the three years of the study; however only the QTLs for malic acid and β ratio (tartaric acid-to-malic acid ratio) were stable in two years. QTLs related to sugars were located within ten LGs (01, 02, 03, 04, 07, 09, 11, 14, 17, 18), and those related to acids within three LGs (06, 13, 18). Overlapping QTLs in LG14 were observed for fructose, glucose and total sugar. Malic acid, total acid and β ratio each had several QTLs in LG18, and malic acid also had a QTL in LG06. A set of 10 genes underlying these QTLs may be involved in determining the malic acid content of berries.

CONCLUSION

The genetic map constructed in this study is potentially a high-density, high-quality map, which could be used for QTL detection, genome comparison, and sequence assembly. It may also serve to broaden our understanding of the grape genome.

Functions of EDS1-like and PAD4 genes in grapevine defenses against powdery mildew

The molecular interactions between grapevine and the obligate biotrophic fungus Erysiphe necator are not understood in depth. One reason for this is the recalcitrance of grapevine to genetic modifications. Using defense-related Arabidopsis mutants that are susceptible to pathogens, we were able to analyze key components in grapevine defense responses. We have examined the functions of defense genes associated with the salicylic acid (SA) pathway, including ENHANCED DISEASE SUSCEPTIBILITY 1 (EDS1), EDS1-LIKE 2 (EDL2), EDL5 and PHYTOALEXIN DEFICIENT 4 (PAD4) of two grapevine species, Vitis vinifera cv. Cabernet Sauvignon, which is susceptible to E. necator, and V. aestivalis cv. Norton, which is resistant. Both VaEDS1 and VvEDS1 were previously found to functionally complement the Arabidopsis eds1-1 mutant. Here we show that the promoters of both VaEDS1 and VvEDS1 were induced by SA, indicating that the heightened defense of Norton is related to its high SA level. Other than Va/VvEDS1, only VaEDL2 complemented Arabidopsis eds1-1, whereas Va/VvPAD4 did not complement Arabidopsis pad4-1. Bimolecular fluorescence complementation results indicated that Vitis EDS1 and EDL2 proteins interact with Vitis PAD4 and AtPAD4, suggesting that Vitis EDS1/EDL2 forms a complex with PAD4 to confer resistance, as is known from Arabidopsis. However, Vitis EDL5 and PAD4 did not interact with Arabidopsis EDS1 or PAD4, correlating with their inability to function in Arabidopsis. Together, our study suggests a more complicated EDS1/PAD4 module in grapevine and provides insight into molecular mechanisms that determine disease resistance levels in Vitis species native to the North American continent.

QTL mapping of black rot (Guignardia bidwellii) resistance in the grapevine rootstock 'Börner' (V. riparia Gm183 × V. cinerea Arnold)

In the grapevine cultivar 'Börner' QTLs for black rot resistance were detected consistently in several independent experiments. For one QTL on chromosome 14 closely linked markers were developed and a detailed map provided. Black rot is a serious grapevine disease that causes substantial yield loss under unfavourable conditions. All traditional European grapevine cultivars are susceptible to the causative fungus Guignardia bidwellii which is native to North America. The cultivar 'Börner', an interspecific hybrid of V. riparia and V. cinerea, shows a high resistance to black rot. Therefore, a mapping population derived from the cross of the susceptible breeding line V3125 ('Schiava grossa' × 'Riesling') with 'Börner' was used to carry out QTL analysis. A resistance test was established based on potted plants which were artificially inoculated in a climate chamber with in vitro produced G. bidwellii spores. Several rating systems were developed and tested. Finally, a five class scheme was applied for scoring the level of resistance. A major QTL was detected based on a previously constructed genetic map and data from six independent resistance tests in the climate chamber and one rating of natural infections in the field. The QTL is located on linkage group 14 (Rgb1) and explained up to 21.8 % of the phenotypic variation (LOD 10.5). A second stable QTL mapped on linkage group 16 (Rgb2; LOD 4.2) and explained 8.5 % of the phenotypic variation. These two QTLs together with several minor QTLs observed on the integrated map indicate a polygenic nature of the black rot resistance in 'Börner'. A detailed genetic map is presented for the locus Rgb1 with tightly linked markers valuable for the development for marker-assisted selection for black rot resistance in grapevine breeding.

Genetic dissection of a TIR-NB-LRR locus from the wild North American grapevine species Muscadinia rotundifolia identifies paralogous genes conferring resistance to major fungal and oomycete pathogens in cultivated grapevine

The most economically important diseases of grapevine cultivation worldwide are caused by the fungal pathogen powdery mildew (Erysiphe necator syn. Uncinula necator) and the oomycete pathogen downy mildew (Plasmopara viticola). Currently, grapegrowers rely heavily on the use of agrochemicals to minimize the potentially devastating impact of these pathogens on grape yield and quality. The wild North American grapevine species Muscadinia rotundifolia was recognized as early as 1889 to be resistant to both powdery and downy mildew. We have now mapped resistance to these two mildew pathogens in M. rotundifolia to a single locus on chromosome 12 that contains a family of seven TIR-NB-LRR genes. We further demonstrate that two highly homologous (86% amino acid identity) members of this gene family confer strong resistance to these unrelated pathogens following genetic transformation into susceptible Vitis vinifera winegrape cultivars. These two genes, designated resistance to Uncinula necator (MrRUN1) and resistance to Plasmopara viticola (MrRPV1) are the first resistance genes to be cloned from a grapevine species. Both MrRUN1 and MrRPV1 were found to confer resistance to multiple powdery and downy mildew isolates from France, North America and Australia; however, a single powdery mildew isolate collected from the south-eastern region of North America, to which M. rotundifolia is native, was capable of breaking MrRUN1-mediated resistance. Comparisons of gene organization and coding sequences between M. rotundifolia and the cultivated grapevine V. vinifera at the MrRUN1/MrRPV1 locus revealed a high level of synteny, suggesting that the TIR-NB-LRR genes at this locus share a common ancestor.

Identification of mildew resistance in wild and cultivated Central Asian grape germplasm

BACKGROUND

Cultivated grapevines, Vitis vinifera subsp. sativa, evolved from their wild relative, V. vinifera subsp. sylvestris. They were domesticated in Central Asia in the absence of the powdery mildew fungus, Erysiphe necator, which is thought to have originated in North America. However, powdery mildew resistance has previously been discovered in two Central Asian cultivars and in Chinese Vitis species.

RESULTS

A set of 380 unique genotypes were evaluated with data generated from 34 simple sequence repeat (SSR) markers. The set included 306 V. vinifera cultivars, 40 accessions of V. vinifera subsp. sylvestris, and 34 accessions of Vitis species from northern Pakistan, Afghanistan and China. Based on the presence of four SSR alleles previously identified as linked to the powdery mildew resistance locus, Ren1, 10 new mildew resistant genotypes were identified in the test set: eight were V. vinifera cultivars and two were V. vinifera subsp. sylvestris based on flower and seed morphology. Sequence comparison of a 620 bp region that includes the Ren1-linked allele (143 bp) of the co-segregating SSR marker SC8-0071-014, revealed that the ten newly identified genotypes have sequences that are essentially identical to the previously identified mildew resistant V. vinifera cultivars: 'Kishmish vatkana' and 'Karadzhandal'. Kinship analysis determined that three of the newly identified powdery mildew resistant accessions had a relationship with 'Kishmish vatkana' and 'Karadzhandal', and that six were not related to any other accession in this study set. Clustering procedures assigned accessions into three groups: 1) Chinese species; 2) a mixed group of cultivated and wild V. vinifera; and 3) table grape cultivars, including nine of the powdery mildew resistant accessions. Gene flow was detected among the groups.

CONCLUSIONS

This study provides evidence that powdery mildew resistance is present in V. vinifera subsp. sylvestris, the dioecious wild progenitor of the cultivated grape. Four first-degree parent progeny relationships were discovered among the hermaphroditic powdery mildew resistant cultivars, supporting the existence of intentional grape breeding efforts. Although several Chinese grape species are resistant to powdery mildew, no direct genetic link to the resistance found in V. vinifera could be established.

Three ERF transcription factors from Chinese wild grapevine Vitis pseudoreticulata participate in different biotic and abiotic stress-responsive pathways

Ethylene response factor (ERF) functions as an important plant-specific transcription factor in regulating biotic and abiotic stress response through interaction with various stress pathways. We previously obtained three ERF members, VpERF1, VpERF2, and VpERF3 from a highly powdery mildew (PM)-resistant Chinese wild Vitis pseudoreticulata cDNA full-length library. To explore their functions associated with plant disease resistance or biotic stress, we report here to characterize three ERF members from this library. PM-inoculation analysis on three different resistant grapevine genotypes revealed that three VpERFs displayed significant responses, but a different expression pattern. Over-expression of VpERF1, VpERF2, and VpERF3 in transgenic tobacco plants demonstrated that VpERF2 and VpERF3 enhanced resistance to both bacterial pathogen Ralstonia solanacearum and fungal pathogen Phytophtora parasitica var. nicotianae Tucker. Importantly, VpERF1-overexpressing transgenic Arabidopsis plants increased susceptibility toward these pathogens. Investigation on drought, cold, and heat treatments suggested, VpERF2 was distinctly induced, whereas VpERF3 displayed a very weak response and VpERF1 was distinctly induced by drought and heat. Concurrently, VpERF3 was significantly induced by salicylic acid (SA), methyl jasmonate (MeJA), and ET. Our results showed that the three VpERFs from Chinese wild V. pseudoreticulata play different roles in either preventing disease progression via regulating the expression of relevant defense genes, or directly involving abiotic stress responsive pathways.

Genetic dissection of agronomic traits within a segregating population of breeding table grapes

Grapes (Vitis vinifera) are of great economic importance worldwide. We genetically dissected a table grape breeding population, using hidden Markov models (HMM) applied to quantitative trait locus (QTL) analyses. We evaluated and dissected the following traits: total number of clusters, leaf score, peduncle length, cluster length, number of berries, weight of 10 berries, average seed number, nature of seeds, berry skin color, soluble solids, titratable acidity, and berry anthocyanin. A consensus map was developed with 255 SSR molecular markers, ordered into 19 linkage groups. The observed length of this map was 1871.4 cM, with 89.7% coverage. QTL were identified using interval mapping with HMM. The number of QTL detected for each trait varied between 1 and 8, reflecting the quantitative nature of these traits. The percentage of variation explained by these QTL was small, varying between 1.56 and 11.98%. We found QTL across linkage groups 2, 7, 12, 13, and 14 for berry anthocyanin.

A reference genetic map of Muscadinia rotundifolia and identification of Ren5, a new major locus for resistance to grapevine powdery mildew

Muscadinia rotundifolia, a species closely related to cultivated grapevine Vitis vinifera, is a major source of resistance to grapevine downy and powdery mildew, two major threats to cultivated traditional cultivars of V. vinifera respectively caused by the oomycete Plasmopara viticola and the ascomycete Erisyphe necator. The aim of the present work was to develop a reference genetic linkage map based on simple sequence repeat (SSR) markers for M. rotundifolia. This map was created using S1 M. rotundifolia cv. Regale progeny, and covers 948 cM on 20 linkage groups, which corresponds to the expected chromosome number for muscadine. The comparison of the genetic maps of V. vinifera and M. rotundifolia revealed a high macrosynteny between the genomes of both species. The S1 progeny was used to assess the general level of resistance of M. rotundifolia to P. viticola and E. necator, by scoring different parameters of pathogen development. A quantitative trait locus (QTL) analysis allowed us to highlight a major QTL on linkage group 14 controlling resistance to powdery mildew, which explained up to 58 % of the total phenotypic variance. This QTL was named 'Resistance to Erysiphe Necator 5' (Ren5). A microscopic evaluation E. necator mycelium development on resistant and susceptible genotypes of the S1 progeny showed that Ren5 exerts its action after the formation of the first appressorium, and acts by delaying, and then stopping, mycelium development.