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The aim of this study was to characterize the changes in berry anatomy during the development of grape (Vitis vinifera L., and Vitis vinifera × Vitis labrusca) with different shapes. Paraffin sectioning was used to examine the structural parameters of the cells. The results revealed that, with the development of berries, the transverse and longitudinal diameters of the flesh cells gradually increased, revealing certain regularity. However, the transverse and longitudinal diameters of the epidermal and sub-epidermal cells were different between varieties, reflecting the specificity of the varieties. The growth of the transverse and longitudinal diameters of the berries was found to be completed in the early stage of development. A combination of correlation analysis and size analysis for each cell layer revealed that, due to the small cross-sectional area of the epidermal and sub-epidermal cells, the influence of these cells on the transverse and the longitudinal diameters of the berries would be small. In conclusion, the longitudinal and transverse diameters of the grape berries were mainly determined by the longitudinal and transverse diameters of the flesh cells. The different shapes of the grape berries could mainly be attributed to the different growth rates of the flesh cells in the longitudinal and transverse directions. These different rates of growth led to different lengths and widths of the berry.

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.

The distal end of grape berries preferentially cracks during the soaking process in vitro, which may be related to preferential water uptake and cell anatomy. Thus, the relationship between water uptake and cell anatomical structure was assessed using 49 grape varieties. In vitro immersion experiments were performed on mature berries to measure the differences in berry-cracking properties. A whole-berry in vitro staining method was used to trace the water uptake of the vascular bundles, and paraffin sections were used to observe and analyze the structural parameters of the different tissues. The results showed that the berry-cracking rate and water uptake of the distal end of berries prone to cracking were significantly higher than that of the resistant berries. Compared with the berries that were resistant to cracking, the berries that were prone to cracking possessed a thin cuticle, epidermis and sub-epidermis. Dye accumulated in the distal end of the cracking-prone berries, which even exhibited cracking during the dyeing process. However, less dye accumulated on the surface of the cracking-resistant varieties and was only sporadically distributed on the surface. In addition, cracking of the distal end of the berry may also be related to other shape and size parameters of the cells in cell layer. Analysis of vascular bundle water transport and the differences in the cell structure characteristics of the different varieties, offered a preliminary explanation for why the distal end of the berry is prone to cracking, providing theoretical support for further research on the mechanisms of berry cracking.

Grape (Vitis vinifera L.), a commercial fruit crop, is profoundly sensitive to gibberellic acid (GA), however exogenous application can significantly induce seedless grape berries. Nevertheless, the underlying molecular mechanism of grape leafy cotyledon 1 (LEC1) on seedless induction remains intangible. Herein, the morphological changes of ‘Wink’ grape cultivar during berry development in response to GA treatments were recorded. To better comprehend the function of VvLEC1 in grape seedless berry induced by GA, the gene and protein sequence were determined by bioinformatics methods, of which motif elements analysis intimates the potential function in seed development. The expression level of VvLEC1 which was repressed by GA treatment, determined by RT PCR, exhibited highest up-regulation at four weeks after flowering in the seed. Furthermore, VvLEC1, a member of the nuclear factor Y subunit B (NF-YB-type) transcription factor, interacts with five proteins which belong to the NF-YC-type transcription factor by the prediction of protein interaction network, thus indicating their collective effects on the development of grape seed. Our research findings elucidate a novel molecular insight into the role of VvLEC1 responsive to GA in accentuating grapevine seed development, which is crucial for the molecular breeding of high-quality seedless grapes.

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.

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.

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.

Grape berry cracking refers to the phenomenon of peel cracking that occurs during berry growth and development. It is related to be berry structure and the characteristics of the berry tissue. To study the relationship between berry-cracking and berry anatomical structure, 53 grape germplasm resources were selected. The ripening berry was soaked and cracked in vitro, after which the berry-cracking rate was measured and paraffin sections were prepared to analyze the structural parameters of different berry tissues. Berry cracking was found to be influenced by the shape of cuticle, the arrangement of epidermal cells and,subepidermal cells, and the thickness of cell layers. With regard to cuticle shape, grapes with local suberization had the highest cracking rate (58.33%), and those with a flat cuticle shape had the lowest rate (30.67%). Grape berries with a compact epidermal cell arrangement had the highest berry cracking rate (57.00%). As for subepidermal cell arrangement, the highest berry-cracking rates were observed in varieties with a looser arrangement (83.33%); and the lowest rates were found in varieties with a more compact subepidermal cell arrangement (32.33%). Correlation analysis between the grape berry-cracking rate and cell layer thickness showed that berry-cracking rate was negatively correlated with the thickness of the cuticle, epidermis, and subepidermis. Moreover, the cell shape and size parameters in the different cell layers may also affect the occurrence of berry cracking. Using paraffin sections to analyze cell structure characteristics, we can predict the cracking of grape berries, which would then provide theoretical support for further screening of germplasm resources to identify cracking-resistant berries.

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.

Background The color of berry skin is an important economic trait for grape and is essentially determined by the components and content of anthocyanins. The fruit color of Chinese wild grapes is generally black, and the profile of anthocyanins in Chinese wild grapes is significantly different from that of Vitis vinifera. However, V. davidii is the only species that possesses white berry varieties among Chinese wild grape species. Thus, we performed a transcriptomic analysis to compare the difference of transcriptional level in black and white V. davidii, in order to find some key genes that are related to anthocyanins accumulation in V. davidii. Results The results of anthocyanins detection revealed that 3,5-O-diglucoside anthocyanins is the predominant anthocyanins in V. davidii. It showed obvious differences from V. vinifera in the profile of the composition of anthocyanins. The transcriptome sequencing by Illumina mRNA-Seq technology generated an average of 57 million 100-base pair clean reads from each sample. Differential gene expression analysis revealed thousands of differential expression genes (DEGs) in the pairwise comparison of different fruit developmental stages between and within black and white V. davidii. After the analysis of functional category enrichment and differential expression patterns of DEGs, 46 genes were selected as the candidate genes. Some genes have been reported as being related to anthocyanins accumulation, and some genes were newly found in our study as probably being related to anthocyanins accumulation. We inferred that 3AT (VIT_03s0017g00870) played an important role in anthocyanin acylation, GST4 (VIT_04s0079g00690) and AM2 (VIT_16s0050g00910) played important roles in anthocyanins transport in V. davidii. The expression of some selected DEGs was further confirmed by quantitative real-time PCR (qRT-PCR). Conclusions The present study investigated the transcriptomic profiles of berry skin from black and white spine grapes at three fruit developmental stages by Illumina mRNA-Seq technology. It revealed the variety specificity of anthocyanins accumulation in V. davidi at the transcriptional level. The data reported here will provide a valuable resource for understanding anthocyanins accumulation in grapes, especially in V. davidii. Electronic supplementary material The online version of this article (doi:10.1186/s41065-016-0021-1) contains supplementary material, which is available to authorized users.