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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.

Chinese wild Vitis is a useful gene source for resistance to biotic and abiotic stresses, although there is little research on its genetic diversity and structure. In this study, nine simple sequence repeat (SSR) markers were used to assess the genetic diversity and genetic structure among 100 Vitis materials. These materials included 77 indigenous accessions representing 23 of 38 wild Vitis species/cultivars in China, 18 V. vinifera cultivars, and the five North American species V. aestivalis, V. girdiana, V. monticola, V. acerifolia, and V. riparia. The SSR loci used in this study for establishing an international database (Vitis International Variety Catalogue) revealed a total of 186 alleles in 100 Vitis accessions. The mean values for the gene diversity (GD) and polymorphism information content (PIC) per locus were 0.91 and 0.90, respectively, which indicates that the discriminatory power of the markers is high. Based on the genetic distance data, the 100 Vitis accessions were divided into five primary clusters by cluster analysis, and five populations by structure analysis; these results indicate these Chinese wild grapes were more genetically close to European grapes than to North American species. In addition, the clustering patterns of most accessions correlated with the geographic distribution. An analysis of molecular variance (AMOVA) revealed that 3.28%, 3.27%, and 93.46% of the variance occurred between populations, between individuals within populations, and between individuals within the entire population, respectively. In addition, we identified three previously undescribed accessions (Wuzhi-1, MZL-5, and MZL-6) by cluster analysis. Our results reveal a high level of genetic diversity and variability in Vitis from China, which will be helpful in the use of genetic resources in future breeding programs. In addition, our study demonstrates that SSR markers are highly suitable for further genetic diversity analyses of Chinese wild grapes.

As one of the largest transcription factor family, basic helix-loop-helix (bHLH) transcription factor family plays an important role in plant metabolism, physiology and growth. Berry color is one of the important factors that determine grape quality. However, the bHLH transcription factor family’s function in anthocyanin synthesis of grape berry has not been studied systematically. We identified 115 bHLH transcription factors in grape genome and phylogenetic analysis indicated that bHLH family could be classified into 25 subfamilies. First, we screened six candidate genes by bioinformatics analysis and expression analysis. We found one of the candidate genes VdbHLH037 belonged to III (f) subfamily and interacted with genes related to anthocyanin synthesis through phylogenetic analysis and interaction network prediction. Therefore, we speculated that VdbHLH037 participated in the anthocyanin synthesis process. To confirm this, we transiently expressed VdbHLH037 in grape and Arabidopsis transformation. Compared with the control, transgenic materials can accumulate more anthocyanins. These results provide a good base to study the function of the VdbHLH family in anthocyanin synthesis of grape berry.

Downy mildew is a fungal disease that seriously threatens the normal growth and fruit quality of grapes; therefore, it is urgent to identify resistant germplasm resources. To identify the differences in the resistance rates of various Chinese wild grapevine plants to downy mildew, 120 grapevine germplasm resources were selected as experimental materials. Leaf disk in vitro testing was applied to evaluate the downy mildew resistance level of plants, and quantitative reverse transcription-polymerase chain reaction (RT-qPCR) was used to test the expression patterns of some key genes at different time courses after inoculation with Plasmopara viticola. Additionally, simple sequence repeat (SSR) markers were selected to identify resistance in different grapevine cultivars and to provide a basis for marker-assisted selection. The results showed that the disease index of 120 grapevine germplasm resources ranged from 0 to 78.70. Among the 120 grapevine varieties, 5 Vitis rotundifolia presented immunity to downy mildew; 3 wild grapevine strains, including Yunnan-Yuanmou 2, Yunnan-2, and Muzhaling-3, were highly resistant strains; 38 grapevine strains were resistant varieties, 71 grapevine strains were susceptible varieties, and 3 V. vinifera strains, namely Italian Riesling, Medoc Noir, and Gamay Teinturier were highly susceptible to downy mildew. After infection with P. viticola, the expression patterns of key genes in resistant and susceptible plants were different. Except for WRKY33, which showed a low expression level in all plants, all the genes presented an initial increasing trend followed by a decreasing trend over the inoculation period. Among the 30 pairs of SSR markers, 22 SSR markers, including CHr14V015, UDV-370 and GF09-46, could explain only 25.83–48.33% of the phenotypic variation, which means that they cannot be applied for downy mildew resistance identification. The RGA9 marker explained the highest phenotypic variation, at 80.83%, and was expected to be a standard marker that can be applied in disease-resistance production, thus providing the basis for both the rapid and mass identification of downy mildew resistance in grapevine germplasm resources and marker-assisted selection.

Background Grapevine is an important fruit crop grown worldwide, and its cultivars are mostly derived from the European species Vitis vinifera, which has genes for high fruit quality and adaptation to a wide variety of climatic conditions. Disease resistance varies substantially across grapevine species; however, the molecular mechanisms underlying such variation remain uncharacterized. Results The anatomical structure and disease symptoms of grapevine leaves were analyzed for two grapevine species, and the critical period of resistance of grapevine to pathogenic bacteria was determined to be 12 h post inoculation (hpi). Differentially expressed genes (DEGs) were identified from transcriptome analysis of leaf samples obtained at 12 and 36 hpi, and the transcripts in four pathways (cell wall genes, LRR receptor-like genes, WRKY genes, and pathogenesis-related (PR) genes) were classified into four co-expression groups by using weighted correlation network analysis (WGCNA). The gene VdWRKY53, showing the highest transcript level, was introduced into Arabidopsis plants by using a vector containing the CaMV35S promoter. These procedures allowed identifying the key genes contributing to differences in disease resistance between a strongly resistant accession of a wild grapevine species Vitis davidii (VID) and a susceptible cultivar of V. vinifera, ‘Manicure Finger’ (VIV). Vitis davidii, but not VIV, showed a typical hypersensitive response after infection with a fungal pathogen (Coniella diplodiella) causing white rot disease. Further, 20 defense-related genes were identified, and their differential expression between the two grapevine species was confirmed using quantitative real-time PCR analysis. VdWRKY53, showing the highest transcript level, was selected for functional analysis and therefore over-expressed in Arabidopsis under the control of the CaMV35S promoter. The transgenic plants showed enhanced resistance to C. diplodiella and to two other pathogens, Pseudomonas syringae pv. tomato DC3000 and Golovinomyces cichoracearum. Conclusion The consistency of the results in VID and transgenic Arabidopsis indicated that VdWRKY53 might be involved in the activation of defense-related genes that enhance the resistance of these plants to pathogens. Thus, the over-expression of VdWRKY53 in transgenic grapevines might improve their resistance to pathogens.

Melatonin (N-acetyl-5-methoxytryptamine) plays important roles in the regulation of development and the response to biotic and abiotic stresses in plants. Serotonin-N-acetyltransferase (SNAT) functions as a key catalytic enzyme involved in melatonin biosynthesis. In this study, the candidate gene VvSNAT1 (SNAT isogene) was isolated from grape (Vitis vinifera L. cv. Merlot). Tissue-specific expression and external treatment revealed that VvSNAT1 is a salt-inducible gene that is highly expressed in leaves. Subcellular localisation results revealed that VvSNAT1 was located in the chloroplasts, which is similar to other plant SNAT proteins. Ectopic overexpression of VvSNAT1 in Arabidopsis resulted in increased melatonin production and salt tolerance. Transgenic Arabidopsis overexpressing VvSNAT1 exhibited enhanced growth and physiological performance, including a lower degree of leaf wilting, higher germination rate, higher fresh weight, and longer root length under salt stress. Moreover, overexpression of VvSNAT1 in Arabidopsis protected cells from oxidative damage by reducing the accumulation of malondialdehyde (MDA) and hydrogen peroxide (H2O2). These results indicate that VvSNAT1 positively responds to salt stress. Our results provide a novel perspective for VvSNAT1 to improve salt tolerance, mediated by melatonin accumulation, plant growth promotion and oxidative damage reduction.

Evaluation of volatile aroma compounds from Chinese wild grape species aimed to explore new grape species via fruit aroma. In this study, the volatile organic compounds (VOCs) from ten grape cultivars belonging to nine different grape species were detected, by using headspace solid-phase microextraction with GC-MS. Chinese wild grape species were studied along with table grape (Muscat Hamburg, Concord) and wine grape (Cabernet Sauvignon) cultivars belonging to different origins. Total forty-five volatile compounds were detected, upon which several VOCs including pentanoic acid, cyclobutyl ester, maltol, (+)-neoisomenthol, and 8-methyloctahydrocoumarin were detected in Chinese wild grapes that have not been detected in other Vitis species. The results revealed that C6 volatile compounds were pre-dominant VOCs. Esters were found abundant in V. labrusca (Concord) and terpenoids were dominant in V. vinafera (Hamburg Muscat). The principal component analysis showed that Chinese wild grape cultivars V. yeshanensis, V. facifolia, V. davidii, V. betulifolia V. heyneana, V. amurensis and V. adenoclada are correlated with wine grape cultivar ‘Cabernet Sauvignon’, while table grape cultivars are distributed separately. These results can provide a reference for the utilization of new germplasm for specific purposes.

Grape white rot caused by Coniella diplodiella (Speg.) affects the production and quality of grapevine in China and other grapevine-growing countries. Despite the importance of C. diplodiella as a serious disease-causing agent in grape, the genome information and molecular mechanisms underlying its pathogenicity are poorly understood. To bridge this gap, 40.93 Mbp of C. diplodiella strain WR01 was de novo assembled. A total of 9,403 putative protein-coding genes were predicted. Among these, 608 and 248 genes are potentially secreted proteins and candidate effector proteins (CEPs), respectively. Additionally, the transcriptome of C. diplodiella was analyzed after feeding with crude grapevine leaf homogenates, which reveals the transcriptional expression of 9,115 genes. Gene ontology enrichment analysis indicated that the highly enriched genes are related with carbohydrate metabolism and secondary metabolite synthesis. Forty-three putative effectors were cloned from C. diplodiella, and applied for further functional analysis. Among them, one protein exhibited strong effect in the suppression of BCL2-associated X (BAX)-induced hypersensitive response after transiently expressed in Nicotiana benthamiana leaves. This work facilitates valuable genetic basis for understanding the molecular mechanism underlying C. diplodiella-grapevine interaction.

Background Berry color is an important trait in grapes and is mainly determined by the anthocyanin content and composition. To further explore the coloring mechanism of grape berries, the F1 population of Vitis vinifera ‘Red Globe’ × ‘Muscat Hamburg’ was used to map the color locus, and transcriptome analysis was performed to assist in screening candidate genes. Results A total of 438,407 high-quality single-nucleotide polymorphisms (SNPs) were obtained from whole-genome resequencing (WGS) of the population, and 27,454 SNPs were selected to construct a high-density genetic map. The selected SNPs were clustered into 19 linkage groups (LGs) spanning a genetic distance of 1442.638 cM. Berry color was evaluated by color grade, chromatic aberration, total anthocyanin content and anthocyanin composition. The Pearson correlation coefficients of these phenotypes in 2017 and 2018 were significant at the 0.01 level. The major color locus of MYBA1 and MYBA2 on LG2 was identified, explaining between 26 and 63.6% of all phenotypic variance. Furthermore, 9 additional QTLs with smaller effects were detected on Chr2, Chr4, Chr6, Chr11 and Chr17. Combined with the gene annotation and RNA-seq data, multiple new candidate genes were selected from the above QTLs. Conclusion These results indicated that grape berry color is a quantitative trait controlled by a major color locus and multiple minor loci. Though the major color locus was consistent with previous studies, several minor QTLs and candidate genes associated with grape berry color and anthocyanin accumulation were identified in this study. And the specific regulatory mechanism still needs to be further explored.

In this study, we present the molecular characterization of 61 Chinese grape landraces and 33 foreign cultivars by using nine microsatellite DNA markers. A total of 115 distinct alleles were amplified, and the average allele number was 12.78. The average observed and expected heterozygosity values were 0.797 and 0.839, respectively. The effective allele numbers ranged from 5.011 to 8.575. The average polymorphism information content (PIC) was 0.816. Eighty distinct genotypes were detected, and new synonyms and homonyms were found. The clustering dendrogram indicated that 94 Vitis materials could be divided into five major groups, and the cluster analysis showed that part of the Chinese grape landraces had a close relationship with the foreign cultivars. Assessment of the true cultivar identity, and the identification of synonyms and homonyms will be a contribution to improve the grape germplasm management and protect breeders’ intellectual rights.

The color of berry skin is an important economic trait of grape, which is determined by the composition and concentration of anthocyanins. The anthocyanin accumulation of grape berry skin is affected by light. In order to further explore the mechanisms of light regulation on anthocyanin accumulation in grape, we detected anthocyanin by UPLC-MS and performed transcriptomic analysis using red grape Vitis vinifera cv. 'Red Globe' as material. In our study, 6 kinds of anthocyanins were detected in the berry skin of 'Red Globe'. The high expression of F3'H genes and the low expression of F3'5'H genes led to the accumulation of dihydroxylated anthocyanins which account for 95% of total anthocyanins. After cluster bagging, the expression of key genes which were related to anthocyanin accumulation was down-regulated, and the concentration of total anthocyanins significantly decreased in 'Red Globe'. However, the anthocyanin composition was not changed. A series of candidate genes which were annotated as HY5, UVR8, PHY, CRY and COL may play important roles in the response and transmission of light signals in grape. And multiple transcription factors genes (1 MYB, 3 bHLH, 2 NAC and 1 ERF) were selected which may be involved in the regulation of light-induced anthocyanin accumulation in grape. The results demonstrated that 'Red Globe' is a typical light-depended grape variety whose anthocyanin synthesis in the berry skin is induced by light. Light-induced anthocyanin synthesis is a complex process involving multiple genes. This investigation provided useful insights into further studies on light-induced anthocyanin accumulation in grape berry skin.

With the rapid development of China’s grape industry and the improvement of breeding and cultivation management technology, great changes have taken place in Xinjiang grape planting. By the investigation of grape planting distribution in recent ten years in China, using geographic information technology (GIS) to analyze the changes of Xinjiang grape production layout and agglomeration characteristics, summed up the layout and development of Xinjiang grape industry, in order to provide reference for optimizing regional grape variety structure. The results showed that the grape industry in Xinjiang has entered a high-quality development stage, grape planting in the spatial distribution showed an expansion trend, the degree of concentration and imbalance was slightly reduced, the regional layout and variety structure were optimized to some extent, but the grape industry in Xinjiang was still in a high degree of centralized distribution

Anthocyanins are natural pigments that exhibit a wide range of protective effects with potential benefits for human health related to their antioxidant activities. Grape berries are rich anthocyanins, and these compounds have considerable influence on wine quality. However, these pigments are known to only be present in coloured grape berries. In the present study, we investigated three distinctive grapes, in which only a few reports of mutant strains on the skin colour of the grape berry were reported. Anthocyanin and non-anthocyanin phenolic profiles of grape berry skin, pulp, and seeds at different growth stages were analysed using high performance liquid chromatography of flight mass spectrometry (HPLC-ESI-MS/MS). Meanwhile, grape antioxidant properties were evaluated at growth stages, including the early stage, veraison, and mature stage. The results showed that some anthocyanins contents, such as malvidin 3-O-glucoside, are significantly different between white skin grapes and their corresponding coloured genotypes, with high content in coloured but not in white skin grapes. However, other anthocyanins, such as delphinidin 3-O-glucoside, showed no significant differences between white skin grapes and their corresponding coloured genotypes. Moreover, non-anthocyanin phenolic profiles and antioxidant properties, except cultivars Pinot Blanc and Pinot Noir, showed no significant differences between white skin grapes and their corresponding coloured genotypes at any growth stage, including the pulp and seeds. However, significant differences were noted between different cultivars, for example, white-ciputao and Pinot Noir, Pinot Blanc and Muscat Rouge, and coloured-ciputao and Muscat Blanc, showing that the antioxidant capacity was not always in correlation with skin colour of grape berries.

Chinese wild grapevine is an important germplasm source worldwide; thus, it is necessary to study its genetic diversity, population structure, and linkage disequilibrium (LD). In this study, 81 strains of Chinese wild grapevine were studied and constituted the core collection. These strains were genotyped according to 160 genome-wide SSR (simple sequence repeat) markers. All SSR markers were widely spread across the strains and revealed a total of 3469 alleles. After population structure analysis, all the Chinese wild grapevine strains were grouped into two subgroups that were well matched with the geographical distribution and the results published by our research team. Of all SSR pairs, 8.3% (P 2 value was 0.0229. The LD decay distance across Chinese wild grapevine was up to 14.13 cM, below the critical r 2 value of 0.1, following y = −0.0383 ln (x) + 0.2016. According to both the linear mixed model and general linear model, the associations of the 160 SSR markers with grape white rot resistance were calculated. Five associated markers were located, four of which had been previously associated with other resistance traits and one of which was new. Chinese wild grapevine association mapping was performed to anchor useful quantitative trait loci (QTLs), and the five markers identified can help us anchor additional resistance-associated genes.

Vitis amurensis is a species of wild grape with high ecological, medicinal, and economic values. Here, the complete chloroplast genome of this plant was assembled from whole-genome high-throughput sequencing data. The circular double-stranded DNA molecule is 160,953 bp in size, including a pair of inverted repeats (26,354 bp each) separated by large (89,187 bp) and small (19,058 bp) single-copy regions. The chloroplast genome contains 133 genes, including 88 protein-coding genes (80 PCG species), 37 transfer RNA genes (29 tRNA species) and eight ribosomal RNA genes (four rRNA species), 20 of which are duplicated, including eight protein-coding, eight tRNA, and four rRNA genes. The base composition is asymmetric (30.93 % A, 19.07 % C, 18.33 % G, 31.67 % T) with an overall A + T content of 62.60 %. A phylogenetic analysis based on complete chloroplast genome sequences showed that V. amurensis is closely related to V. vinifera, V. aestivalis, and V. rotundifolia.

Global climate warming will significantly impact grapevine growth and development, and thus grape and wine industries worldwide. Heat-tolerant germplasms are very valuable for grapevine breeding programs. In this study, we assessed the thermotolerance of 247 wild grape accessions by chlorophyll fluorescence parameter (Fv/Fm) under critical high temperature according to Xu et al. in 2016, 2017, and 2018. The results showed that 36 grape accessions showed strong heat tolerance. Therefore, these accessions can be used as parents for breeding heat-tolerant grape cultivars.

Understanding the Vitis species at the genomic level is important for cultivar improvement of grapevine. Here we report whole-genome genetic variation at single-base resolution of 472 Vitis accessions, which cover 48 out of 60 extant Vitis species from a wide geographic distribution. The variation helps to identify a recent dramatic expansion and contraction of effective population size in the domesticated grapevines and that cultivars from the pan-Black Sea region have a unique demographic history in comparison to the other domesticated cultivars. We also find selective sweeps for berry edibility and stress resistance improvement. Furthermore, we find associations between candidate genes and important agronomic traits, such as berry shape and aromatic compounds. These results demonstrate resource value of the resequencing data for illuminating the evolutionary biology of Vitis species and providing targets for grapevine genetic improvement.

International audience; Heat stress is a serious and widespread threat to the quality and yield of many crop species, including grape (Vitis vinifera L.), which is cultivated worldwide. Here, we conducted phosphoproteomic and acetylproteomic analyses of leaves of grape plants cultivated under four distinct temperature regimes. The phosphorylation or acetylation of a total of 1011 phosphoproteins with 1828 phosphorites and 96 acetyl proteins with 148 acetyl sites changed when plants were grown at 35 degrees C, 40 degrees C, and 45 degrees C in comparison with the proteome profiles of plants grown at 25 degrees C. The greatest number of changes was observed at the relatively high temperatures. Functional classification and enrichment analysis indicated that phosphorylation, rather than acetylation, of serine/arginine-rich splicing factors was involved in the response to high temperatures. This finding is congruent with previous observations by which alternative splicing events occurred more frequently in grapevine under high temperature. Changes in acetylation patterns were more common than changes in phosphorylation patterns in photosynthesis-related proteins at high temperatures, while heat-shock proteins were associated more with modifications involving phosphorylation than with those involving acetylation. Nineteen proteins were identified with changes associated with both phosphorylation and acetylation, which is consistent with crosstalk between these posttranslational modification types.

Deciphering the genetic control of grape berry traits is crucial for optimizing yield, fruit quality, and consumer acceptability. In this study, an association panel of 179 grape genotypes comprising a mixture of ancient cultivars, landraces, and modern varieties collected worldwide were genotyped with genotyping-by-sequencing using a genome-wide association approach based on 32,311 single-nucleotide polymorphism (SNP) markers. Genome-wide efficient mixed-model association was selected as the optimal statistical model based on the results of known control loci of grape berry color traits. Many of the associated SNPs identified in this study were in accordance with the previous QTL analyses using biparental mapping. The grape skin color locus was found to be associated with a mybA transcription factor on chromosome 2. Two strong and distinct association signals associated with berry development periods were found on chromosome 16. Most candidate genes of the interval were highlighted as receptor-like protein kinase. For berry weight, significant association loci were identified on chromosome 18, as previously known, and on chromosome 19 and chromosome 17, as newly mapped. Berry flesh texture was newly located on chromosome 16; candidate genes in the interval were related to calcium. Berry flavor was determined on chromosome 5. Genomic regions were further investigated to reveal candidate genes. In this work, we identified interesting genetic determinants of grape berry-related traits. The identification of the markers closely associated with these berry traits may be useful for grape molecular breeding., Grapes: The genetic basis of fruit traits Genetic analysis of 179 types of vine has revealed regions of the genome and associated genes and proteins that control many of the key traits in the grapes. These traits are crucial for determining fruit quality and yield, in addition to conferring flavors that are highly valued by consumers and wine makers. Researchers in China, led by Da-Long Guo at Henan University of Science and Technology, used DNA sequencing to analyze genetic markers in a mixture of ancient, traditionally cultivated and modern grape varieties. The analysis identified specific regions of the genome linked to grape fruit development, weight, texture, skin color and flavor. The molecular basis of the effects of the identified genetic regions were also explored. The findings will help generate new varieties of grapes for the food and wine industries.

Number of DEGs between V. davidii and V. vinifera in different KEGG pathways detected at different infection stages. (DOCX 25 kb)

Primer sequences used in this study. (DOCX 16 kb)

Understanding the Vitis species at the genomic level is important for cultivar improvement of grapevine. Here we report whole-genome genetic variation at single-base resolution of 472 Vitis accessions, which cover 48 out of 60 extant Vitis species from a wide geographic distribution. The variation helps to identify a recent dramatic expansion and contraction of effective population size in the domesticated grapevines and that cultivars from the pan-Black Sea region have a unique demographic history in comparison to the other domesticated cultivars. We also find selective sweeps for berry edibility and stress resistance improvement. Furthermore, we find associations between candidate genes and important agronomic traits, such as berry shape and aromatic compounds. These results demonstrate resource value of the resequencing data for illuminating the evolutionary biology of Vitis species and providing targets for grapevine genetic improvement., Despite the importance of grapevine cultivation in human history and the economic values of cultivar improvement, large-scale genomic variation data are lacking. Here the authors resequence 472 Vitis accessions and use the identified genetic variations for domestication history, demography, and GWAS analyses.

Grapevine (Vitis spp.) is an important crop worldwide, but its growth, fruit quality, and yield are frequently reduced by pathogens. Admixture of resistance genes is an effective method to breed new varieties. Wild grapevine populations are very important subjects for grapevine research, given their germplasmic resistance to various diseases, especially white rot disease caused by Coniella diplodiella. However, molecular and sequencing research is still required to fully understand the relationships among Vitis spp., particularly among Chinese Vitis species. We analyzed 88,877 single nucleotide polymorphisms (SNPs) from 386 grapevine genotypes through restriction site-associated DNA sequencing. Overall, Chinese Vitis spp. had considerably less linkage disequilibrium and exhibited stronger resistance to white rot disease than their European congeners. Association analysis revealed six SNPs associated with eight candidate genes linked to white rot resistance that were up-regulated by the pathogen. In resistant Vitis spp., genes XM_002272404.2 (WAT1-related protein At3g30340-like), XM_002278827.2 (receptor-like protein kinase HSL1), XM_002281911.3 (ethylene-responsive transcription factor ERF105-like), XM_002281568.4 (leucine rich repeat receptor-like serine/threonine-protein kinase At1g74360-like), and XM_003634259.2 (zinc finger RNA-binding protein) were more up-regulated by the pathogen than in susceptible Vitis species. The present results clarify the genetic basis of the geographical distribution, classification, and resistance traits of Chinese Vitis spp., thereby contributing to the use of wild Chinese Vitis spp. in breeding.

Grapevine is an important fruit crop grown worldwide, and its cultivars are mostly derived from the European speciesThe anatomical structure and disease symptoms of grapevine leaves were analyzed for two grapevine species, and the critical period of resistance of grapevine to pathogenic bacteria was determined to be 12 h post inoculation (hpi). Differentially expressed genes (DEGs) were identified from transcriptome analysis of leaf samples obtained at 12 and 36 hpi, and the transcripts in four pathways (cell wall genes, LRR receptor-like genes,The consistency of the results in

China is one of the major diversity centres of grape (Vitis spp.) and is therefore one of the most abundant sources of Vitis germplasm in the world. Grape wild relative species (GWRs) represent a potentially important source of valuable traits for the improvement of cultivated grape varieties and have significant characters for resistance to biotic and abiotic stress factors. We studied the ecogeographic diversity of GWRs, conservation gaps and impact of climate change on GWRs in China, based on a wide range of distribution data sourced from germplasm and herbarium specimens, field surveys and other literature. Results show that there are 39 species, 1 subspecies and 14 varieties of GWRs native to China and that 19 species and 9 varieties are the closest wild relatives to cultivated grape according to the Taxon Group Concept. GWRs are distributed in nearly all provinces in China except for Xinjiang, but they are particularly abundant in Jiangxi and Hunan provinces. The richest regions for GWRs are the Qinling, Daba, Wuling, Nanling and Wuyi mountains. Around 22% of GWR species are found in natural reserves (NRs) and are well protected, but 15 species are not found in NRs and require further strengthening of both protection and collection. The potential distribution of GWRs at the present and predicted future climate was compared using BIOCLIM. The results showed that simulated current distributions matched actual distribution ranges. Under the future climate scenario with doubled CO2 concentration, suitable areas for continued survival of 21 GWRs could be reduced. Our results will therefore be extremely valuable for the development of a complementary conservation strategy for Vitis in China.

The Chinese wild grapevine, Vitis davidii, is disease resistant, matures late, and is the only Vitis species with white-fruit type native to China, and is ideal for grape breeding programs. To uncover the molecular mechanisms responsible for the V. davidii white-fruit phenotype and the relationship between accessions with white and pigmented fruits, the SSR markers, DNA sequencing and qRT-PCR were used. We found a high coefficient of genetic similarity between the two phenotypes; 12 markers, in particular, revealed that the white-skinned V. davidii “Baiciputao” evolved from the pigmented “Hunanci”. The MybA1 gene sequence analysis results revealed that “Baiciputao” harbored only MybA1a at the MybA1 locus, and in “Hunanci”, both MybA1a and MybA1c alleles were detected. This was also linked to grape skin color of the control cultivars, which were Pinot blanc and Pinot noir, Muscat blanc and Muscat rouge. To verify our conclusions, the elementary composition of the anthocyanin profiles of V. davidii and V. vinifera were analyzed using high-performance liquid chromatography and electrospray ionization mass spectrometry (HPLC–ESI–MS/MS), revealing divergent chemical profiles. The main cyanidin derivative in V. davidii was 3-O-glucoside-5-O-glucoside, whereas it was 3-O-glucoside in V. vinifera. The qRT-PCR results indicated that the total anthocyanin content in V. davidii grape skins was not solely determined by UFGT or MYB-related expression levels. These data support the conclusion that the molecular mechanism leading to the white-skinned V. davidii phenotype is the MybA1 gene mutation.

This study investigated the genetics of seedlessness in grape (Vitis vinifera L.) by the application of specific locus amplified fragment sequencing (SLAF-seq) and genome-wide association mapping. SLAF-seq was used to provide dense genome-wide marker coverage for the 199 grape accessions to screen for genetic controls over seedlessness. After comparison of genome sequences with the reference genome, single nucleotide polymorphisms (SNPs) were developed. A phylogenetic tree of the 199 accessions was then constructed and investigated using principal component analysis (PCA). Linkage disequilibrium between the SNPs was estimated and a genome wide association study (GWAS) was performed to detect trait loci and candidate genes associated with seedlessness. In total, 414,223 SNPs were identified, and were used for the fine mapping of seed development genes. The r2 decay to half of its initial value was 11.57 kb. The phylogenetic tree showed that the 199 accessions were clustered into 12 branches; PCA indicated that most grape accessions were clustered. Analysis using a general linear model identified 294 SNPs significant correlation with seedlessness, while the compressed mixed linear model identified 82 SNPs. Candidate genes involved in seed development were identified at loci near the significant SNPs. These candidates included ubiquitin protein, abscisic aldehyde oxidase, ethylene responsive transcription factor, zinc finger protein, somatic embryogenesis receptor, and MADs-box genes. This study demonstrates that integrating SLAF-seq and GWAS are powerful complementary approaches for dissecting complex traits in the grape.

Berry firmness is one of the most important quality traits in table grapes. The underlying molecular and genetic mechanisms for berry firmness remain unclear. We constructed a high-density genetic map based on whole-genome resequencing to identify loci associated with berry firmness. The genetic map had 19 linkage groups, including 1662 bin markers (26,039 SNPs), covering 1463.38 cM, and the average inter-marker distance was 0.88 cM. An analysis of berry firmness in the F1 population and both parents for three consecutive years revealed continuous variability in F1, with a distribution close to the normal distribution. Based on the genetic map and phenotypic data, three potentially significant quantitative trait loci (QTLs) related to berry firmness were identified by composite interval mapping. The contribution rate of each QTL ranged from 21.5% to 28.6%. We identified four candidate genes associated with grape firmness, which are related to endoglucanase, abscisic acid (ABA), and transcription factors. A qRT-PCR analysis revealed that the expression of abscisic-aldehyde oxidase-like gene (VIT_18s0041g02410) and endoglucanase 3 gene (VIT_18s0089g00210) in Muscat Hamburg was higher than in Crimson Seedless at the veraison stage, which was consistent with that of parent berry firmness. These results confirmed that VIT_18s0041g02410 and VIT_18s0089g00210 are candidate genes associated with berry firmness.