Telomere-to-telomere and gap-free genome assembly of a susceptible grapevine species (Thompson Seedless) to facilitate grape functional genomics.

Grapes are globally recognized as economically significant fruit trees. Among grape varieties, Thompson Seedless holds paramount influence for fresh consumption and for extensive applications in winemaking, drying, and juicing. This variety is one of the most efficient genotypes for grape genetic modification. However, the lack of a high-quality genome has impeded effective breeding efforts. Here, we present the high-quality reference genome of Thompson Seedless with all 19 chromosomes represented as 19 contiguous sequences (N50 = 27.1 Mb) with zero gaps and prediction of all telomeres and centromeres. Compared with the previous assembly (TSv1 version), the new assembly incorporates an additional 31.5 Mb of high-quality sequenced data with annotation of a total of 30 397 protein-coding genes. We also performed a meticulous analysis to identify nucleotide-binding leucine-rich repeat genes (NLRs) in Thompson Seedless and two wild grape varieties renowned for their disease resistance. Our analysis revealed a significant reduction in the number of two types of NLRs, TIR-NB-LRR (TNL) and CC-NB-LRR (CNL), in Thompson Seedless, which may have led to its sensitivity to many fungal diseases, such as powdery mildew, and an increase in the number of a third type, RPW8 (resistance to powdery mildew 8)-NB-LRR (RNL). Subsequently, transcriptome analysis showed significant enrichment of NLRs during powdery mildew infection, emphasizing the pivotal role of these elements in grapevine's defense against powdery mildew. The successful assembly of a high-quality Thompson Seedless reference genome significantly contributes to grape genomics research, providing insight into the importance of seedlessness, disease resistance, and color traits, and these data can be used to facilitate grape molecular breeding efforts.

VqWRKY56 interacts with VqbZIPC22 in grapevine to promote proanthocyanidin biosynthesis and increase resistance to powdery mildew.

Powdery mildew (PM) is a severe fungal disease of cultivated grapevine world-wide. Proanthocyanidins (PAs) play an important role in resistance to fungal pathogens; however, little is known about PA-mediated PM resistance in grapevine. We identified a WRKY transcription factor, VqWRKY56, from Vitis quinquangularis, the expression of which was significantly induced by PM. Overexpression (OE) of VqWRKY56 in Vitis vinifera increased PA content and reduced susceptibility to PM. Furthermore, the transgenic plants showed more cell death and increased accumulation of salicylic acid and reactive oxygen species. Transient silencing of VqWRKY56 in V. quinquangularis and V. vinifera reduced PA accumulation and increased the susceptibility to PM. VqWRKY56 interacted with VqbZIPC22 in vitro and in planta. The protein VqWRKY56 can bind to VvCHS3, VvLAR1, and VvANR promoters, and VqbZIPC22 can bind to VvANR promoter. Co-expression of VqWRKY56 and VqbZIPC22 significantly increased the transcript level of VvCHS3, VvLAR1, and VvANR genes. Finally, transient OE of VqbZIPC22 in V. vinifera promoted PA accumulation and improved resistance to PM, while transient silencing in V. quinquangularis had the opposite effect. Our study provides new insights into the mechanism of PA regulation by VqWRKY56 in grapevine and provides a basis for further metabolic engineering of PA biosynthesis to improve PM resistance.

CRISPR/Cas9-mediated mutagenesis of VvbZIP36 promotes anthocyanin accumulation in grapevine (Vitis vinifera).

Anthocyanins are plant secondary metabolites that have a variety of biological functions, including pigmentation. The accumulation of anthocyanins is regulated by both transcriptional activators and repressors. Studies have shown that the bZIP family act primarily as positive regulators of anthocyanin biosynthesis, but there are few reports of negative regulation. Here, we report that a grapevine (Vitis vinifera) bZIP gene from group K, VvbZIP36, acts as a negative regulator of anthocyanin biosynthesis. Knocking-out one allele of VvbZIP36 in grapevine utilizing the CRISPR/Cas9 technology promoted anthocyanin accumulation. Correlation analysis of transcriptome and metabolome data showed that, compared with wild type, a range of anthocyanin biosynthesis genes were activated in VvbZIP36 mutant plants, resulting in the accumulation of related metabolites, including naringenin chalcone, naringenin, dihydroflavonols and cyanidin-3-O-glucoside. Furthermore, the synthesis of stilbenes (α-viniferin), lignans and some flavonols (including quercetin-3-O-rhamnoside, kaempferol-3-O-rhamnoside and kaempferol-7-O-rhamnoside) was significantly inhibited and several genes linked to these metabolism, were down-regulated in the mutant plants. In summary, our results demonstrate that VvbZIP36, as a negative regulator of anthocyanin biosynthesis, plays a role in balancing the synthesis of stilbenes (α-viniferin), lignans, flavonols and anthocyanins.

Overexpression of VqWRKY31 enhances powdery mildew resistance in grapevine by promoting salicylic acid signaling and specific metabolite synthesis.

Powdery mildew (PM), caused by the fungal pathogen Erysiphe necator, is one of the most destructive diseases of grapevine (Vitis vinifera and other Vitis spp). Resistance to PM is an important goal for cultivar improvement, and understanding the underlying molecular mechanisms conditioning resistance is critical. Here, we report that transgenic expression of the WRKY transcription factor gene VqWRKY31 from the PM-resistant species Vitis quinquangularis conferred resistance to powdery mildew in V. vinifera through promoting salicylic acid signaling and specific metabolite synthesis. VqWRKY31 belongs to the WRKY IIb subfamily, and expression of the VqWRKY31 gene was induced in response to E. necator inoculation. Transgenic V. vinifera plants expressing VqWRKY31 were substantially less susceptible to E. necator infection, and this was associated with increased levels of salicylic acid and reactive oxygen species. Correlation analysis of transcriptomic and metabolomic data revealed that VqWRKY31 promoted expression of genes in metabolic pathways and the accumulation of many disease resistance-related metabolites, including stilbenes, flavonoids, and proanthocyanidins. In addition, results indicated that VqWRKY31 can directly bind to the promoters of two structural genes in stilbene synthesis, STS9 and STS48, and activate their expression. Based on our results, we propose a model where VqWRKY31 enhances grapevine PM resistance through activation of salicylic acid defense signaling and promotion of specific disease resistance-related metabolite synthesis. These findings can be directly exploited for molecular breeding strategies to produce PM-resistant grapevine germplasm.

Whole-genome sequencing reveals rare off-target mutations in CRISPR/Cas9-edited grapevine.

The CRISPR (clustered regularly interspaced short palindromic repeats)-associated protein 9 (Cas9) system is a powerful tool for targeted genome editing, with applications that include plant biotechnology and functional genomics research. However, the specificity of Cas9 targeting is poorly investigated in many plant species, including fruit trees. To assess the off-target mutation rate in grapevine (Vitis vinifera), we performed whole-genome sequencing (WGS) of seven Cas9-edited grapevine plants in which one of two genes was targeted by CRISPR/Cas9 and three wild-type (WT) plants. In total, we identified between 202,008 and 272,397 single nucleotide polymorphisms (SNPs) and between 26,391 and 55,414 insertions/deletions (indels) in the seven Cas9-edited grapevine plants compared with the three WT plants. Subsequently, 3272 potential off-target sites were selected for further analysis. Only one off-target indel mutation was identified from the WGS data and validated by Sanger sequencing. In addition, we found 243 newly generated off-target sites caused by genetic variants between the Thompson Seedless cultivar and the grape reference genome (PN40024) but no true off-target mutations. In conclusion, we observed high specificity of CRISPR/Cas9 for genome editing of grapevine.

Grapevine VlbZIP30 improves drought resistance by directly activating VvNAC17 and promoting lignin biosynthesis through the regulation of three peroxidase genes.

Drought stress severely affects grapevine quality and yield, and recent reports have revealed that lignin plays an important role in protection from drought stress. Since little is known about lignin-mediated drought resistance in grapevine, we investigated its significance. Herein, we show that VlbZIP30 mediates drought resistance by activating the expression of lignin biosynthetic genes and increasing lignin deposition. Transgenic grapevine plants overexpressing VlbZIP30 exhibited lignin deposition (mainly G and S monomers) in the stem secondary xylem under control conditions, which resulted from the upregulated expression of VvPRX4 and VvPRX72. Overexpression of VlbZIP30 improves drought tolerance, characterized by a reduction in the water loss rate, maintenance of an effective photosynthesis rate, and increased lignin content (mainly G monomer) in leaves under drought conditions. Electrophoretic mobility shift assay, luciferase reporter assays, and chromatin immunoprecipitation-qPCR assays indicated that VlbZIP30 directly binds to the G-box cis-element in the promoters of lignin biosynthetic (VvPRX N1) and drought-responsive (VvNAC17) genes to regulate their expression. In summary, we report a novel VlbZIP30-mediated mechanism linking lignification and drought tolerance in grapevine. The results of this study may be of value for the development of molecular breeding strategies to produce drought-resistant fruit crops.

VlbZIP30 of grapevine functions in dehydration tolerance via the abscisic acid core signaling pathway.

Drought stress limits the growth and development of grapevines, thereby reducing productivity, but the mechanisms by which grapevines respond to drought stress remain largely uncharacterized. Here, we characterized a group A bZIP gene from "Kyoho" grapevine, VlbZIP30, which was shown to be induced by abscisic acid (ABA) and dehydration stress. Overexpression of VlbZIP30 in transgenic Arabidopsis thaliana enhanced dehydration tolerance. Transcriptome analysis revealed that a major proportion of ABA-responsive and/or drought-responsive genes are transcriptionally regulated by VlbZIP30 during ABA or mannitol treatment at the cotyledon greening stage. We identified an A. thaliana G-box motif (CACGTG) and a potential grapevine G-box motif (MCACGTGK) in the promoters of the 39 selected A. thaliana genes upregulated in the transgenic plants and in the 35 grapevine homologs, respectively. Subsequently, using two grapevine-related databases, we found that 74% (23/31) and 84% (21/25) of the detected grapevine genes were significantly upregulated by ABA and drought stress, respectively, suggesting that these genes are involved in ABA or dehydration stress and may be regulated by VlbZIP30 in grapevine. We propose that VlbZIP30 functions as a positive regulator of dehydration-responsive signaling in the ABA core signaling pathway.

The Grape VlWRKY3 Gene Promotes Abiotic and Biotic Stress Tolerance in Transgenic Arabidopsis thaliana.

WRKY transcription factors are known to play important roles in plant responses to various abiotic and biotic stresses. The grape WRKY gene, WRKY3 was previously reported to respond to salt and drought stress, as well as methyl jasmonate and ethylene treatments in Vitis labrusca × V. vinifera cv. 'Kyoho.' In the current study, WRKY3 from the 'Kyoho' grape cultivar was constitutively expressed in Arabidopsis thaliana under control of the cauliflower mosaic virus 35S promoter. The 35S::VlWRKY3 transgenic A. thaliana plants showed improved salt and drought stress tolerance during the germination, seedling and the mature plant stages. Various physiological traits related to abiotic stress responses were evaluated to gain further insight into the role of VlWRKY3, and it was found that abiotic stress caused less damage to the transgenic seedlings than to the wild-type (WT) plants. VlWRKY3 over-expression also resulted in altered expression levels of abiotic stress-responsive genes. Moreover, the 35S::VlWRKY3 transgenic A. thaliana lines showed improved resistance to Golovinomyces cichoracearum, but increased susceptibility to Botrytis cinerea, compared with the WT plants. Collectively, these results indicate that VlWRKY3 plays important roles in responses to both abiotic and biotic stress, and modification of its expression may represent a strategy to enhance stress tolerance in crops.

CRISPR/Cas9-mediated efficient targeted mutagenesis in grape in the first generation.

The clustered regularly interspaced short palindromic repeats-associated protein 9 (CRISPR/Cas9) system is a powerful tool for editing plant genomes. Efficient genome editing of grape (Vitis vinifera) suspension cells using the type II CRISPR/Cas9 system has been demonstrated; however, it has not been established whether this system can be applied to get biallelic mutations in the first generation of grape. In this current study, we designed four guide RNAs for the VvWRKY52 transcription factor gene for using with the CRISPR/Cas9 system, and obtained transgenic plants via Agrobacterium-mediated transformation, using somatic embryos of the Thompson Seedless cultivar. Analysis of the first-generation transgenic plants verified 22 mutant plants of the 72 T-DNA-inserted plants. Of these, 15 lines carried biallelic mutations and seven were heterozygous. A range of RNA-guided editing events, including large deletions, were found in the mutant plants, while smaller deletions comprised the majority of the detected mutations. Sequencing of potential off-target sites for all four targets revealed no off-target events. In addition, knockout of VvWRKY52 in grape increased the resistance to Botrytis cinerea. We conclude that the CRISPR/Cas9 system allows precise genome editing in the first generation of grape and represents a useful tool for gene functional analysis and grape molecular breeding.

Ectopic Expression of the Wild Grape WRKY Transcription Factor VqWRKY52 in Arabidopsis thaliana Enhances Resistance to the Biotrophic Pathogen Powdery Mildew But Not to the Necrotrophic Pathogen Botrytis cinerea.

WRKY transcription factors are known to play important roles in plant responses to biotic stresses. We previously showed that the expression of the WRKY gene, VqWRKY52, from Chinese wild Vitis quinquangularis was strongly induced 24 h post inoculation with powdery mildew. In this study, we analyzed the expression levels of VqWRKY52 following treatment with the defense related hormones salicylic acid (SA) and methyl jasmonate, revealing that VqWRKY52 was strongly induced by SA but not JA. We characterized the VqWRKY52 gene, which encodes a WRKY III gene family member, and found that ectopic expression in Arabidopsis thaliana enhanced resistance to powdery mildew and Pseudomonas syringae pv. tomato DC3000, but increased susceptibility to Botrytis cinerea, compared with wild type (WT) plants. The transgenic A. thaliana lines displayed strong cell death induced by the biotrophic powdery mildew pathogen, the hemibiotrophic P. syringe pathogen and the necrotrophic pathogen B. cinerea. In addition, the relative expression levels of various defense-related genes were compared between the transgenic A. thaliana lines and WT plants following the infection by different pathogens. Collectively, the results indicated that VqWRKY52 plays essential roles in the SA dependent signal transduction pathway and that it can enhance the hypersensitive response cell death triggered by microbial pathogens.

Expression of a grape (Vitis vinifera) bZIP transcription factor, VlbZIP36, in Arabidopsis thaliana confers tolerance of drought stress during seed germination and seedling establishment.

Drought is one of the most serious factors that limit agricultural productivity and there is considerable interest in understanding the molecular bases of drought responses and their regulation. While numbers of basic leucine zipper (bZIP) transcription factors (TFs) are known to play key roles in response of plants to various abiotic stresses, only a few group K bZIP TFs have been functionally characterized in the context of stress signaling. In this study, we characterized the expression of the grape (Vitis vinifera) group K bZIP gene, VlbZIP36, and found evidence for its involvement in response to drought and the stress-associated phytohormone abscisic acid (ABA). Transgenic Arabidopsis thaliana lines over-expressing VlbZIP36 under the control of a constitutive promoter showed enhanced dehydration tolerance during the seed germination stage, as well as in the seedling and mature plant stages. The results indicated that VlbZIP36 plays a role in drought tolerance by improving the water status, through limiting water loss, and mitigating cellular damage. The latter was evidenced by reduced cell death, lower electrolyte leakage in the transgenic plants, as well as by increased activities of antioxidant enzymes. We concluded that VlbZIP36 enhances drought tolerance through the transcriptional regulation of ABA-/stress-related genes.

Ectopic expression of a grape aspartic protease gene, AP13, in Arabidopsis thaliana improves resistance to powdery mildew but increases susceptibility to Botrytis cinerea.

The grape aspartic protease gene, AP13 was previously reported to be responsive, in Chinese wild Vitis quinquangularis cv. 'Shang-24', to infection by Erysiphe necator, the causal agent of powdery mildew disease, as well as to treatment with salicylic acid in V. labrusca×V. vinifera cv. 'Kyoho'. In the current study, we evaluated the expression levels of AP13 in 'Shang-24' in response to salicylic acid (SA), methyl jasmonate (MeJA) and ethylene (ET) treatments, as well as to infection by the necrotrophic fungus, Botrytis cinerea, and the transcript levels of VqAP13 decreased after B. cinerea infection and MeJA treatment, but increased following ET and SA treatments. Transgenic Arabidopsis thaliana lines over-expressing VqAP13 under the control of a constitutive promoter showed enhanced resistance to powdery mildew and to the bacterium Pseudomonas syringae pv. tomato DC3000, and accumulated more callose than wild type plants, while the resistance of transgenic A. thaliana lines to B. cinerea inoculation was reduced. In addition, the expression profiles of various disease resistance- related genes in the transgenic A. thaliana lines following infection by different pathogens were compared to the equivalent profiles in the wild type plants. The results suggest that VqAP13 action promotes the SA dependent signal transduction pathway, but suppresses the JA signal transduction pathway.