Assessment of heat tolerance and identification of miRNAs during high-temperature response in grapevine.

With global warming, heat stress has been recognized as a significant factor limiting grapevine development and fruit quality. MicroRNAs (miRNAs) are a class of small non-coding RNAs known to play crucial regulatory roles in stress resistance. Hence, there is an immediate requirement to cultivate and identify grapevine varieties that are resistant to heat and explore miRNA-mediated heat stress defense mechanisms. In this study, we assessed the thermal resistance of 38 grape germplasm resources and identified a series of miRNAs involved in heat stress resistance. The CK (25°C) and HS (45°C) groups of "Shenyue" cuttings of grapes were used as experimental materials for next-generation sequencing and construct libraries of small RNAs. A total of 177 known and 20 novel miRNAs were detected in the libraries. Differential expression analysis identified 65 differentially expressed miRNAs (DEMs) using the DE-Seq procedure. Furthermore, RT-qPCR validation confirmed complementary expression profiles of eight DEMs and their target genes between the HS and CK groups. Heterologous transformation further identified the function of Vvi-miR3633a downregulated under heat stress in Arabidopsis. In the heterologous expression lines, the survival rate was reduced by high temperature treatment indicating the ability of Vvi-miR3633a to regulate heat resistance. Assessing the heat resistance of grape species and the expression patterns of miRNA in response to high temperatures may reveal the molecular processes of heat resistance regulation mediated by miRNA in grapes under heat stress.

Carbon pools and microbial indicators in vineyard soils under organic and conventional fertilization in the São Francisco Valley, in a semi-arid tropical climate.

Soil management systems that do not prioritize conservation contribute to carbon (C) depletion in tropical environments. In the semi-arid region of Brazil, fruit farming has been a key driver for economic development, yet high agricultural yields depend on the use of costly inputs. We conducted a groundbreaking study in São Francisco Valley, northeastern Brazil, to investigate the effects of organic (OF) and synthetic fertilizers (CF) on carbon stock and stability, organic matter fractions, microorganismal carbon biomass (C-mic) and quality indexes, and C-CO2 emissions up to the 1 m of depth in grapevine soils. Additionally, we compared the fertilized soils with their nearby native vegetation under the Caatinga biome. Compared to native vegetation, the OF and CF grapevine soils store 33 Mg ha-1 in one year and 26 Mg ha-1 in two years of establishment, respectively. The total labile C stock was found to be 10.2 Mg ha-1 and 6.0 Mg ha-1 at a depth of 1 m. We observed the development of C-mic at 40-100 cm (approximately 280 mg kg-1) in the OF soil, which resulted in efficient C mineralization without disrupting microbial metabolism, which produced roughly 8.0 mg kg-1 day-1 of C-CO2. The isotopic signature shows that C3 plants partially influence carbon and nutrient cycling in deeper OF soil layers. The soil in OF exhibited a high concentration of carbonate equivalent (32 g kg-1) and calcium (6 g kg-1), which resulted in the protection of labile C from decomposition. The Cambisols of viticultural farm under organic fertilization exhibited a balance of humic and fulvic acids fractions of organic matter, consequently, a potential stability of C. Our findings show that organic fertilization based on cassava juice, fish amino acids, and straw combined with manure under intensive irrigation contributes to an increase in C storage and microbial indicators in the soil. Therefore, this type of fertilization could be employed as a sustainable management system in grape farming in the Brazilian Northeast to improve soil conditions and crop yield under harsh environmental conditions.

Characterization of varietal effects on the acidity and pH of grape berries for selection of varieties better adapted to climate change.

Climate change is drastically modifying berry composition and wine quality across the world. Most wine regions with a history of winemaking are suffering from a loss of typicity and terroir expression because of climate change impact on berry components at harvest, including wine acidity, with total acidity decreasing and pH increasing. Such changes can have a major impact on wine stability and quality. One important option for adaptation is the selection of grapevine varieties better adapted to warmer and drier conditions. Weekly measurement of tartaric acid, malic acid, pH and titratable acidity from veraison until maturity were carried out on 51 varieties over seven years in two experimental plots. Varietal differences were shown for the rate of malic acid degradation during the ripening period, with some varieties metabolizing malic acid faster per unit of thermal time than others. Some varietal differences were also noticed regarding tartaric acid modulation, which can occur under exceptionally high temperatures. Differences in the dynamics of pH evolution in grape must over the growing season were evaluated and varieties characterized with regard to organic acids (tartaric acid and malic acid), inorganic compounds (cations) as well as pH levels and stability. This multi-trait approach allows the selection of grapevine varieties based on parameters linked to their acidity, which is of particular importance in the context of climate change.

Organogenesis in a Broad Spectrum of Grape Genotypes and Agrobacterium-Mediated Transformation of the Podarok Magaracha Grapevine Cultivar.

We present data on the ability for organogenesis in 22 genotypes of grapevine and developed a direct organogenesis protocol for the cultivar Podarok Magaracha and the rootstock Kober 5BB. The protocol does not require replacement of culture media and growth regulators, and the duration is 11 weeks. The cultivation of explants occurs on modified MS medium with the addition of 2.0 mg L-1 benzyladenine and indole-3-butyric acid (0.15 mg L-1 for the rootstock Kober 5BB or 0.05 mg L-1 for the cultivar Podarok Magaracha). The direct organogenesis protocol consists of three time periods: (1) culturing explants for 2 weeks in dark conditions for meristematic bulk tissue, (2) followed by 4 weeks of cultivation in light conditions for regeneration, and (3) 5 weeks of cultivation in dark conditions for shoot elongation. Based on this protocol, conditions for the Agrobacterium-mediated transformation of the Podarok Magaracha cultivar were developed with an efficiency of 2.0% transgenic plants per 100 explants. Two stably transformed lines with integration into the genome of the pBin35SGFP plasmid construction, confirmed by Southern blotting, were obtained.

Complete genome sequence of Microbacterium sp. che218, an endophyte isolated from Vitis vinifera cv. Chardonnay shoot xylem.

Microbacterium species are bacterial endophytes that live inside plants. We report the complete genome sequence of Microbacterium sp. che218, an endophyte isolated from the shoot xylem of the wine grape Vitis vinifera cv. Chardonnay.

High-Throughput Sequencing Identified Multiple Fig Viruses and Viroids Associated with Fig Mosaic Disease in Iraq.

Mosaic is the most common viral disease affecting fig plants. Although the Fig mosaic virus is the leading cause of mosaic disease, other viruses are also involved. High-throughput sequencing was used to assess viral infections in fig plants with mosaic. The genomic DNA and total RNAseq of mosaic-symptomatic fig leaves were sequenced using the Illumina platform. The analysis revealed the presence of fig badnavirus 1 (FBV-1), grapevine badnavirus 1 (GBV-1), citrus exocortis viroid (CEVd), and apple dimple fruit viroid (ADFVd). The FBV-1 and GBV-1 sequences were 7,140 bp and 7,239 bp long, respectively. The two genomes encode one open reading frame containing five major protein domains. The viroids, CEVd and ADFVd, were 397 bp and 305 bp long. Phylogenetic analyses revealed a close relationship between FBV-1 and Iranian isolates of the same species, while GBV-1 was closely related to Russian grapevine badnavirus isolates (Tem64, Blu17, KDH48, and Pal9). CEVd was closely related to other Iraqi isolates, while ADFVd was strongly related to a Spanish isolate. A registered endogenous pararetrovirus, caulimovirus-Fca1, with a size of 7,556 bp, was found in the RNA transcripts with a low expression level. This integrant was also detected in the genomes of the two lines 'Horaishi' (a female line) and 'Caprifig 6085' (a male line). Phylogenetic analyses revealed that caulimovirus-Fca1 was distinct from two other clades of different endogenous virus genera.

Insight into the new infection pathway resulting from above-ground pathogen infection of grapevine crown gall.

Grapevine crown gall (GCG), a soil-borne plant disease caused by tumorigenic Allorhizobium vitis (TAV) (=tumorigenic Rhizobium vitis) strains, poses a significant threat to grapevines worldwide. Recently, outbreaks of GCG have been reported in several vineyards, necessitating investigation into potential alternative infection pathways beyond soil transmission. The spatiotemporal distribution of GCG in vineyards from 2020 to 2022 was analyzed using the binary power law (BPL) model, with variations in quadrat shapes. Both total and newly observed diseased plants exhibited an aggregated distribution, indicating that new infections clustered around existing diseased plants, with secondary infections appearing as independent cluster points. This study provides evidence that infected pruning tools can transmit the pathogen to healthy grapevines and that TAV inoculation through spraying contributes more to GCG incidence than planting in infected soil alone. This represents the first documented case of secondary above-ground TAV infection contributing to GCG in commercial vineyards.

Identification of Grape Laccase Genes and Their Potential Role in Secondary Metabolite Synthesis.

Laccase, a copper-containing oxidoreductase, has close links with secondary metabolite biosynthesis in plants. Its activity can affect the synthesis and accumulation of secondary metabolites, thereby influencing plant growth, development, and stress resistance. This study aims to identify the grape laccases (VviLAC) gene family members in grape (Vitis vinifera L.) and explore the transcriptional regulatory network in berry development. Here, 115 VviLACs were identified and divided into seven (Type I-VII) classes. These were distributed on 17 chromosomes and out of 47 VviLACs on chromosome 18, 34 (72.34%) were involved in tandem duplication events. VviLAC1, VviLAC2, VviLAC3, and VviLAC62 were highly expressed before fruit color development, while VviLAC4, VviLAC12, VviLAC16, VviLAC18, VviLAC20, VviLAC53, VviLAC60 and VviLAC105 were highly expressed after fruit color transformation. Notably, VviLAC105 showed a significant positive correlation with important metabolites including resveratrol, resveratrol dimer, and peonidin-3-glucoside. Analysis of the transcriptional regulatory network predicted that the 12 different transcription factors target VviLACs genes. Specifically, WRKY and ERF were identified as potential transcriptional regulatory factors for VviLAC105, while Dof and MYB were identified as potential transcriptional regulatory factors for VviLAC51. This study identifies and provides basic information on the grape LAC gene family members and, in combination with transcriptome and metabolome data, predicts the upstream transcriptional regulatory network of VviLACs.

Expression of the grapevine anion transporter ALMT2 in Arabidopsis root decreases shoot Cl-/NO3- ratio under salt stress.

Grapevines (Vitis vinifera, Vvi) are economically important crop plants which, when challenged with salt (NaCl) in soil and/or irrigation water, tend to accumulate Na+ and Cl- in aerial tissues impacting yield, and berry acceptability for winemaking. Grapevine (Vitis spp.) rootstocks vary in their capacity for shoot Cl- exclusion. Here, we characterise two putative anion transporter genes - Aluminium-activated Malate Transporter VviALMT2 and VviALMT8 - that were differentially expressed in the roots of efficient (140 Ruggeri) and inefficient (K51-40) Cl- excluding rootstocks, to explore their potential for impacting shoot Cl- exclusion. Using the Xenopus laevis oocyte expression system, VviALMT2 and VviALMT8 formed conductive channels that were highly permeable to NO3-, slightly-to-moderately permeable to other substrates including Cl- and malate, but impermeable to SO42-. RT-qPCR analyses revealed that VviALMT2 was more highly expressed in the root vasculature and up-regulated by high [NO3-] re-supply post starvation, while fluorescently tagged translational fusion VviALMT2 localised to the plasma membrane. As VviALMT8 showed no such features, we selected VviALMT2 as our salt exclusion candidate and assessed its function in planta. Expression of VviALMT2 in Arabidopsis thaliana root vasculature reduced shoot [Cl-]/[NO3-] after NaCl treatment, which suggests that VviALMT2 can be beneficial to plants under salt stress.

Artificial Intelligence Techniques in Grapevine Research: A Comparative Study with an Extensive Review of Datasets, Diseases, and Techniques Evaluation.

In the last few years, the agricultural field has undergone a digital transformation, incorporating artificial intelligence systems to make good employment of the growing volume of data from various sources and derive value from it. Within artificial intelligence, Machine Learning is a powerful tool for confronting the numerous challenges of developing knowledge-based farming systems. This study aims to comprehensively review the current scientific literature from 2017 to 2023, emphasizing Machine Learning in agriculture, especially viticulture, to detect and predict grape infections. Most of these studies (88%) were conducted within the last five years. A variety of Machine Learning algorithms were used, with those belonging to the Neural Networks (especially Convolutional Neural Networks) standing out as having the best results most of the time. Out of the list of diseases, the ones most researched were Grapevine Yellow, Flavescence Dorée, Esca, Downy mildew, Leafroll, Pierce's, and Root Rot. Also, some other fields were studied, namely Water Management, plant deficiencies, and classification. Because of the difficulty of the topic, we collected all datasets that were available about grapevines, and we described each dataset with the type of data (e.g., statistical, images, type of images), along with the number of images where they were mentioned. This work provides a unique source of information for a general audience comprising AI researchers, agricultural scientists, wine grape growers, and policymakers. Among others, its outcomes could be effective in curbing diseases in viticulture, which in turn will drive sustainable gains and boost success. Additionally, it could help build resilience in related farming industries such as winemaking.

Vitis vinifera Lipoxygenase LoxA is an Allosteric Dimer Activated by Lipidic Surfaces.

Lipoxygenases catalyze the peroxidation of poly-unsaturated fatty acid chains either free or esterified in membrane lipids. Vitis vinifera LoxA is transcriptionally induced at ripening onset and localizes at the inner chloroplast membrane where it is responsible for galactolipid regiospecific mono- and di-peroxidation. Here we present a kinetic and structural characterization of LoxA. Our X-ray structures reveal a constitutive dimer with detergent induced conformational changes affecting substrate binding and catalysis. In a closed conformation, a LID domain prevents substrate access to the catalytic site by steric hindrance. Detergent addition above the CMC destabilizes the LID and opens the dimer with both catalytic sites accessible from the same surface framed by the PLAT domains. As a consequence, detergent molecules occupy allosteric sites in the PLAT/catalytic domain interface. These structural changes are mirrored by increased enzymatic activity and positive cooperativity when the substrate is provided in micelles. The ability to interact with micelles is lost upon dimer destabilization by site-directed mutagenesis as assessed by tryptophan fluorescence. Our data allow to propose a model for protein activation at the membrane, classifying LoxA as an interfacial enzyme acting on fatty acid chains directly from the membrane similar to mammalian 15-LOX and 5-LOX.

VvbHLH036, a basic helix-loop-helix transcription factor regulates the cold tolerance of grapevine.

Cold stress is an adverse environmental factor that limits the growth and productivity of horticulture crops such as grapes (Vitis vinifera). In this study, we identified a grapevine cold-induced basic helix-loop-helix (bHLH) transcription factor (VvbHLH036). Overexpression and CRISPR/Cas9-mediated knockout (KO) of VvbHLH036 enhanced and decreased cold tolerance in grapevine roots, respectively. Transcriptome analysis of VvbHLH036-overexpressed roots identified threonine synthase (VvThrC1) as a potential downstream target of VvbHLH036. We confirmed that VvbHLH036 could bind the VvThrC1 promoter and activate its expression. Both the transcripts of VvThrC1 and the content of threonine were significantly induced in the leaves and roots of grapevine under cold treatment compared to controls. Conversely, these dynamics were significantly suppressed in the roots of CRISPR/Cas9-induced knockout of VvbHLH036. These observations support the regulation of threonine accumulation by VvbHLH036 through VvThrC1 during cold stress in grapevine. Furthermore, overexpression and CRISPR/Cas9-mediated knockout of VvThrC1 also confirmed its role in regulating threonine content and cold tolerance in transgenic roots at low temperature. Exogenous threonine treatment increased cold tolerance and reduced the accumulation of superoxide anions and hydrogen peroxide in grapevine leaves. Together, these findings point to the pivotal role of VvbHLH036 and VvThrC1 in the cold stress response in grapes by regulating threonine biosynthesis.

Exogenous strigolactone alleviates post-waterlogging stress in grapevine.

With global climate change, the frequent occurrence of intense rainfall and aggravation of waterlogging disasters have severely threatened the plant growth and fruit quality of grapevines, which are commercially important fruit crops worldwide. There is accordingly an imperative to clarify the responses of grapevine to waterlogging and to propose appropriate remedial measures. Strigolactone (SL) is a phytohormone associated with plant abiotic stress tolerance, while, its function in plant responses to waterlogging stress remain undetermined. In this study, systematic analyses of the morphology, physiology, and transcriptome changes in grapevine leaves and roots under post-waterlogging and GR24 (a synthetic analog of SL) treatments were performed. Morphological and physiological changes in grapevines in response to post-waterlogging stress, including leaf wilting and yellowing, leaf senescence, photosynthesis inhibition, and increased anti-oxidative systems, could be alleviated by the application of GR24. Moreover, transcriptome analysis revealed that the primary gene functions induced by post-waterlogging stress changed over time; however, they were consistently associated with carbohydrate metabolism. The GR24-induced leaf genes were closely associated with carbohydrate metabolism, photosynthesis, antioxidant systems, and hormone signal transduction, which were considered vital aspects that were influenced by GR24 in grapevine to induce post-waterlogging tolerance. Concerning the roots, an enhancement of microtubules and cytoskeleton for cell construction in GR24 application was proposed to facilitate root system recovery after waterlogging. With this study, we comprehend the knowledge regarding the responses of grapevines to post-waterlogging and the ameliorative effect of GR24 with the insight to the transcriptome changes during these processes.

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.

Rpv10.2: A Haplotype Variant of Locus Rpv10 Enables New Combinations for Pyramiding Downy Mildew Resistance Traits in Grapevine.

In viticulture, pathogens like the oomycete Plasmopara viticola, the causal agent of downy mildew, can cause severe yield loss and require extensive application of plant protection chemicals. Breeders are generating pathogen-resistant varieties exploiting American and Asian wild Vitis germplasm as sources of resistance. Several loci mediating resistance to P. viticola have been identified in the past but may be overcome by specifically adapted strains of the pathogen. Aiming to find and characterize novel loci, a cross population with Vitis amurensis ancestry was investigated searching for resistance-correlated quantitative trait loci (QTL). As a prerequisite, a genetic map was generated by analyzing the 244 F1 individuals derived from a cross of the downy mildew susceptible Vitis vinifera cultivar 'Tigvoasa' and the resistant V. amurensis pBC1 breeding line We 90-06-12. This genetic map is based on the information from 627 molecular markers including 56 simple sequence repeats and 571 rhAmpSeq markers. A phenotypic characterization of the progeny showed a clear segregation of the resistance traits in the F1 population after an experimental inoculation of leaf discs with downy mildew. Combining genetic and phenotypic data, an analysis for QTL revealed a major locus on linkage Group 9 that correlates strongly with the resistance to downy mildew. The locus was mapped to a region of about 80 kb on the PN40024 (12x.V2) grapevine reference genome. This genomic region co-localizes with the formerly identified locus Rpv10 from the grapevine cultivar 'Solaris'. As we found different allele sizes of the locus-linked SSR markers than those characterizing the known Rpv10 locus and differences in the sequence of a candidate gene, it was regarded as a haplotype variant and named Rpv10.2.

Assessing the Potential of Tortistilus (Hemiptera: Membracidae) from Northern California Vineyards as Vector Candidates of Grapevine Red Blotch Virus.

Ceresini treehoppers are present in northern California vineyard ecosystems, including the closely related Spissistilus and Tortistilus (Hemiptera: Membracidae). These membracids are not direct pests of wine grapes, but S. festinus is a vector of grapevine red blotch virus (GRBV). No information is available on the ability of Tortistilus spp. to transmit GRBV. In this study, Tortistilus were collected on yellow panel cards across 102 vineyard sites and surrounding areas in Napa Valley, California, USA in 2021-2023. Specimens were morphotyped, sexed and tested for GRBV ingestion and acquisition by multiplex PCR or qPCR. Phylogenetic analysis of the partial sequence of mt-COI and ITS gene fragments of a subset of 40 Tortistilus specimens revealed clustering in a monophyletic clade with T. wickhami with the former barcode sequence. Only 6% (48/758) of the T. wickhami tested positive for GRBV, but none of the heads with salivary glands (0%, 0/50) of the dissected specimens tested positive for GRBV, indicating no virus acquisition. In contrast, half of the dissected heads with salivary glands of S. festinus (52%, 12/23), from the same collection vineyard sites, tested positive for GRBV. Together, our findings confirmed the presence of T. wickhami in northern California vineyards and suggested a dubious role of this treehopper as a vector of GRBV.

Quantitative Proteomics Analysis of ABA- and GA3-Treated Malbec Berries Reveals Insights into H2O2 Scavenging and Anthocyanin Dynamics.

Abscisic acid (ABA) and gibberellic acid (GA3) are regulators of fruit color and sugar levels, and the application of these hormones is a common practice in commercial vineyards dedicated to the production of table grapes. However, the effects of exogenous ABA and GA3 on wine cultivars remain unclear. We investigated the impact of ABA and GA3 application on Malbec grapevine berries across three developmental stages. We found similar patterns of berry total anthocyanin accumulation induced by both treatments, closely associated with berry H2O2 levels. Quantitative proteomics from berry skins revealed that ABA and GA3 positively modulated antioxidant defense proteins, mitigating H2O2. Consequently, proteins involved in phenylpropanoid biosynthesis were downregulated, leading to decreased anthocyanin content at the almost ripe stage, particularly petunidin-3-G and peonidin-3-G. Additionally, we noted increased levels of the non-anthocyanins E-viniferin and quercetin in the treated berries, which may enhance H2O2 scavenging at the almost ripe stage. Using a linear mixed-effects model, we found statistical significance for fixed effects including the berry H2O2 and sugar contents, demonstrating their roles in anthocyanin accumulation. In conclusion, our findings suggest a common molecular mechanism by which ABA and GA3 influence berry H2O2 content, ultimately impacting anthocyanin dynamics during ripening.

Unveiling Iso- and Aniso-Hydric Disparities in Grapevine-A Reanalysis by Transcriptome Portrayal Machine Learning.

Mechanisms underlying grapevine responses to water(-deficient) stress (WS) are crucial for viticulture amid escalating climate change challenges. Reanalysis of previous transcriptome data uncovered disparities among isohydric and anisohydric grapevine cultivars in managing water scarcity. By using a self-organizing map (SOM) transcriptome portrayal, we elucidate specific gene expression trajectories, shedding light on the dynamic interplay of transcriptional programs as stress duration progresses. Functional annotation reveals key pathways involved in drought response, pinpointing potential targets for enhancing drought resilience in grapevine cultivation. Our results indicate distinct gene expression responses, with the isohydric cultivar favoring plant growth and possibly stilbenoid synthesis, while the anisohydric cultivar engages more in stress response and water management mechanisms. Notably, prolonged WS leads to converging stress responses in both cultivars, particularly through the activation of chaperones for stress mitigation. These findings underscore the importance of understanding cultivar-specific WS responses to develop sustainable viticultural strategies in the face of changing climate.

Genome-wide identification of the grapevine ß-1,3-glucanase gene (VviBG) family and expression analysis under different stresses.

BACKGROUND: The ß-1,3-glucanase gene is widely involved in plant development and stress defense. However, an identification and expression analysis of the grape ß-1,3-glucanase gene (VviBG) family had not been conducted prior to this study. RESULTS: Here, 42 VviBGs were identified in grapevine, all of which contain a GH-17 domain and a variable C-terminal domain. VviBGs were divided into three clades α, ß and γ, and six subgroups A-F, with relatively conserved motifs/domains and intron/exon structures within each subgroup. The VviBG gene family contained four tandem repeat gene clusters. There were intra-species synteny relationships between two pairs of VviBGs and inter-species synteny relationships between 20 pairs of VviBGs and AtBGs. The VviBG promoter contained many cis-acting elements related to stress and hormone responses. Tissue-specific analysis showed that VviBGs exhibited distinct spatial and temporal expression patterns. Transcriptome analysis indicated that many VviBGs were induced by wounds, UV, downy mildew, cold, salt and drought, especially eight VviBGs in subgroup A of the γ clade. RT-qPCR analysis showed that these eight VviBGs were induced under abiotic stress (except for VviBG41 under cold stress), and most of them were induced at higher expression levels by PEG6000 and NaCl than under cold treatment. CONCLUSIONS: The chromosome localization, synteny and phylogenetic analysis of the VviBG members were first conducted. The cis-acting elements, transcriptome data and RT-qPCR analysis showed that VviBG genes play a crucial role in grape growth and stress (hormone, biotic and abiotic) responses. Our study laid a foundation for understanding their functions in grape resistance to different stresses.

Characterization of Genetic Diversity in the Capsid Protein Gene of Grapevine Fleck Virus and Development of a New Real-Time RT-PCR Assay.

The grapevine fleck virus (GFkV) is a ubiquitous grapevine-infecting virus found worldwide, is associated with the grapevine fleck complex, and is often found in mixed infections with viruses of the grapevine leafroll complex and/or vitiviruses. Although GFkV has been studied for a long time, limited sequence information is available in the public databases. In this study, the GFkV sequence data available in GenBank and data generated at the Foundation Plant Services, University of California, Davis, were used to perform nucleotide sequence comparisons, construct a phylogenetic tree, and develop a new RT-qPCR assay. Sequence comparisons showed high genetic diversity among the GFkV isolates, and the phylogenetic analyses revealed a new group comprised of GFkV isolates identified in the present study. A new assay, referred to as GFkV-CP, was designed and validated using an existing GFkV positive control together with 11 samples known to be infected with combinations of different marafiviruses and maculaviruses but not GFkV. In addition, the newly designed assay was used in a field survey to screen grapevines from diverse geographical locations that are maintained at the United States Department of Agriculture (USDA) National Clonal Germplasm Repository (NCGR) in Winters, CA.