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Spine grape (Vitis davidii Foëx), an important wild grape species in South China, has gained attention because of its health-promoting effects and use in the wine industry. Fruit quality plays an important role in determining the quality of wine; however, a suitable evaluation system to monitor its fruit quality has not been established. The fruit quality characteristics (phenolics and aromas) of 15 spine grapes grown in China were evaluated using a combination of principal component and cluster analyses. The total sugar, organic acid, and phenolic content ranged from 81.80 to 154.89 mg·g−1, 8.02 to 15.48 mg·g−1, and 5.58 to 20.12 mg·g−1, respectively. The comprehensive assessment by principal component analysis revealed that ‘Red xiangzhenzhu’ had the highest quality and ‘Hongjiangci10’ and ‘Ziluolan’ the lowest quality. Cluster analysis using k-means grouped the cultivars into three clusters based on their quality: Cluster 1 grouped those with inferior quality (‘Hongjiangci09’, ‘Hongjiangci10’, ‘Hongjiangci11’, and ‘Hongjiangci07’, etc.), Cluster2 grouped those with average quality (‘Ciputao3#,’ ‘Ziluolan’, and ‘Xiangci4#’), and Cluster3 grouped those with superior quality (‘Red xiangzhenzhu’ and ‘Green xiangzhenzhu’). A combination of principal component analysis and cluster analysis provides a comprehensive and objective evaluation system for determining the quality of grape cultivars. This study is important for the systematic evaluation and utilization of spine grape resources.

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.

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.

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.

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.

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 measured the anthocyanin composition and content in the ‘Kyoho’ grape cultivar and its derivatives via ultra-performance liquid chromatography–mass spectrometry and characterized the MybA-related genes at the color locus via capillary electrophoresis and quantitative real-time polymerase chain reaction. A total of 30 anthocyanins (15 monoglucoside and 15 diglucoside) were detected. Peonidin-3-O-(t-6''-O-coumaroyl)-glucoside-5-O-glucoside was the most abundant component, and the content of malvidin-3-O-(c-6''-O-coumaroyl)-glucoside-5-O-glucoside was low in all cultivars. All 49 cultivars contained VvmybA1, VvmybA2, and VvmybA3, whereas only the black-skinned cultivars contained VlmybA2. The anthocyanin content in the cultivars that contained VlmybA2 was significantly higher than other cultivars. These results could provide information for future color breeding programs in grapes.

DNA-binding one zinc finger (DOF) proteins play a key role in plant resistance to drought conditions. In this paper, a DOF gene (VyDOF8) identified from Chinese wild grapevine Vitis yeshanensis 'Yanshan', was significantly increased by salt, drought, and cold stresses. The VyDOF8 protein was localized to the nucleus and functioned as a transcription factor. VyDOF8-overexpressing (VyDOF8-OE) tobacco (Nicotiana benthamiana) exhibited a smaller percent water loss and advanced root development, and accumulated more chlorophyll and proline under drought conditions compared with the control, which suggested that overexpression of VyDOF8 might confer enhanced drought tolerance by increasing the abscisic acid content and promoting stress-responsive gene expression. Meanwhile, VyDOF8-OE plants also showed reduced malondialdehyde (MDA) and H2O2 contents by boosting key enzymatic antioxidant activities under drought conditions. These findings provide valuable information for functional analysis of DOF genes in grape.

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.

Metformin improved vascular function in obese type 2 diabetic patients. 8-oxoguanine glycosylase (OGG1), a main DNA glycosylase, was involved in vascular complications in diverse diseases. However, whether metformin suppressed endothelial ROS via OGG1 pathway was unclear. Human umbilical vein endothelial cells (HUVECs) were exposed to HG (high glucose) or HG with metformin. OGG1 and AMPfα levels were measured after metformin treatment while HG-caused ROS was measured by DHE prober. Diabetic mice were induced by daily intraperitoneal injections of streptozotocin (STZ). Metformin reduced Endothelial ROS caused by HG via upregulating OGG1. Additionally, OGG1 protein expression was dependent on its mRNA stability, which was reversed by genetic inhibition of AMPKα and Lin-28. The role of OGG1 on ROS stimulated by HG was partially dependent on NFKB/NOX4 pathway in HUVECs. These results suggested that metformin contacted HG-induced endothelial ROS via AMPKα/Lin-28/OGG1 pathway.

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.

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)

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.

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.

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.

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.

Chinese wild grapes are almost exclusively dioecious and black-fruited, with rare reports of white and hermaphrodite types in V. davidii. To reveal the molecular mechanisms of these phenotypic variations, specific primers were designed to detect the genotypes of mybA-related genes in Vitis species, including the Chinese wild Vitis species, V. riparia, V. rupestris, cultivars of Vitis vinifera and its hybrids. We report here that three mybA-related genes, VvmybA1a, VvmybA2 and VvmybA3, were only detected in cultivars of V. vinifera and its hybrids, but not in V. riparia, V. rupestris or Chinese wild Vitis species, indicating that these genes could be used to test the genetic relationship to V. vinifera. On the other hand, the genes were not detected in the dioecious varieties of V. davidii, but were in the hermaphrodites. In particular, the white-fruited varieties were homozygous for VvmybA1a and showed a low expression of mybA-related genes and UFGT during the entire maturation period. Simple sequence repeat analysis showed that the hermaphrodite varieties of V. davidii, including the white-fruited varieties, were more closely related to V. vinifera cv. Pinot Noir and V. labruscana cv. Kyoho. These results suggested that the white-fruited and hermaphrodite varieties of V. davidii could be the result of its crossing with V. vinifera. It provides a new approach to identify truly Chinese wild varieties and to search for possible hybridization events.

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.

Simple Sequence Repeats (SSR) and Sequence-Related Amplified Polymorphism (SRAP) were used to analyze the genetic diversity of 26 genotypes from 15 Chinese wild grape species and one interspecific ...