Association analysis of grapevine bunch traits using a comprehensive approach

Dynamic temporal transcriptome analysis reveals grape VlMYB59-VlCKX4 regulatory module controls fruit set

Fruit set is a key stage in determining yield potential and guaranteeing quality formation and regulation. N-(2-chloro-4-pyridyl)-N'-phenylurea (CPPU) has been widely applied in grape production, the most iconic of which is the promotion of grape fruit set. However, current studies still lack the molecular mechanism of CPPU-induced grape fruit set. Here, the dynamic, high-resolution stage-specific transcriptome profiles were generated based on two different treatments and five developmental periods during fruit set in 'Kyoho' grape (Vitis vinifera L. × V. labrusca L.). Pairwise comparison and functional category analysis showed that phytohormone action cytokinin was significantly enriched during the CPPU-induced grape fruit set, but not the natural one. Value differentially expressed gene (VDEG) was a newly proposed analysis strategy for mining genes related to the grape fruit set. Notably, the cytokinin metabolic process was significantly enriched among up-regulated VDEGs. Of importance, a key VDEG VlCKX4 related to the cytokinin metabolic process was identified as related to the grape fruit set. Overexpression of VlCKX4 gene promoted the Arabidopsis plants that produce more and heavier siliques. The transcription factor VlMYB59 directly bound to the promoter of VlCKX4 and activated its expression. Moreover, overexpression of VlMYB59 gene also promoted the Arabidopsis fruit set. Overall, VlMYB59 responded to CPPU treatment and directly activated the expression of VlCKX4, thus promoting the fruit set. A regulatory pathway of the VlMYB59-VlCKX4 module in the fruit set was uncovered, which provides important insights into the molecular mechanisms of the fruit set and good genetic resources for high fruit set rate breeding.

Biography of Vitis genomics: recent advances and prospective

The grape genome is the basis for grape studies and breeding, and is also important for grape industries. In the last two decades, more than 44 grape genomes have been sequenced. Based on these genomes, researchers have made substantial progress in understanding the mechanism of biotic and abiotic resistance, berry quality formation, and breeding strategies. In addition, this work has provided essential data for future pangenome analyses. Apart from de novo assembled genomes, more than six whole-genome sequencing projects have provided datasets comprising almost 5000 accessions. Based on these datasets, researchers have explored the domestication and origins of the grape and clarified the gene flow that occurred during its dispersed history. Moreover, genome-wide association studies and other methods have been used to identify more than 900 genes related to resistance, quality, and developmental phases of grape. These findings have benefited grape studies and provide some basis for smart genomic selection breeding. Moreover, the grape genome has played a great role in grape studies and the grape industry, and the importance of genomics will increase sharply in the future.

Review: Status and prospects of association mapping in grapevine

Thanks to current advances in sequencing technologies, novel bioinformatics tools, and efficient modeling solutions, association mapping has become a widely accepted approach to unravel the link between genotype and phenotype diversity in numerous crops. In grapevine, this strategy has been used in the last decades to understand the genetic basis of traits of agronomic interest (fruit quality, crop yield, biotic and abiotic resistance), of special relevance nowadays to improve crop resilience to cope with future climate scenarios. Genome-wide association studies have identified many putative causative loci for different traits, some of them overlapping well-known causal genes identified by conventional quantitative trait loci studies in biparental progenies, and/or validated by functional approaches. In addition, candidate-gene association studies have been useful to pinpoint the causal mutation underlying phenotypic variation for several traits of high interest in breeding programs (like berry color, seedlessness, and muscat flavor), information that has been used to develop highly informative and useful markers already in use in marker-assisted selection processes. Thus, association mapping has proved to represent a valuable step towards high quality and sustainable grape production. This review summarizes current applications of association mapping in grapevine research and discusses future prospects in view of current viticulture challenges.

Lateral shoots removal has little effect on berry growth of grapevine (Vitis vinifera L.) ‘Riesling’ in cool climate

Bunch compactness is an important trait that affects the sanitary status and quality of wine grapes. Many studies have demonstrated that canopy managements, such as leaf removal, shoot trimming, and postponed first shoot topping, can effectively reduce compactness. However, few studies have determined the effects of canopy management measures on bunch compactness. Shoot wrapping has been previously shown to elongate the rachis length and reduce bunch compactness. Here, we tested whether the presence of laterals affects cluster growth in Vitis vinifera L. ‘Riesling’ through a field experiment with four treatments over two consecutive seasons: shoot wrapping with laterals, shoot wrapping without laterals, hedging with laterals, and hedging without laterals. Laterals were removed weekly. Lateral removal had little effect on cluster compactness; the effect was shown temporarily and not consistent the growing seasons. The effect of laterals on cluster compactness and rachis length slightly varied with years. The short-term and variable effect of laterals may be explained by the fact that they experienced little competition with clusters.

Toward the identification of molecular markers associated with phytochemical traits in the Iranian sumac (Rhus coriaria L.) population

Sumac (Rhus coriaria L.) is one of the important forest species dispersed in the northwest of Iran. It is one of the important spice in Iran and the Middle East because of active components containing organic acids, phenolic acids, flavonoids, anthocyanins, tannins and terpenoids. This study aimed to investigate population structure and linkage disequilibrium (LD) extent within Rhus coriaria L. genotypes using ISSR markers and identify molecular markers associated with phytochemical traits using association analysis. In the molecular part of the experiment, the genetic diversity of 75 sumac genotypes from five different areas of northwest Iran was assessed by 18 ISSR primers. In the phenotypic assessment, the fruits of the sumac genotypes were analyzed using HPLC-LC/MSMS for determining phytochemical components including maleic acid, ellagic acid, maleic acid hexoside, gallic acid, coumaric acid, quercetin, caftaric acid, and linoleic acid. The phenotypic data analysis revealed the great phenotypic diversity among and within Iranian sumac populations for the studied phytochemical traits. The studied sumac genotypes were divided into two subpopulations based on molecular marker-based structure analysis. A significant level of LD was observed in 11.64% of the ISSR marker pairs (p < .05). The mixed linear model procedure showed that 12 loci had a significant association with investigated traits. The ISSR loci identified in this study can be potentially used in marker-assisted selection in sumac breeding programs.

Genetic variation and association analyses identify genes linked to fruit set-related traits in grapevine

Grapevine is one of the most valuable fruit crops in the world. Adverse environmental conditions reduce fruit quality and crop yield, so understanding the genetic and molecular mechanisms determining crop yield components is essential to optimize grape production. The analysis of a diverse collection of grapevine cultivars allowed us to evaluate the relationship between fruit set-related components of yield, including the incidence of reproductive disorders such as coulure and millerandage. The collection displayed a great phenotypic variation that we surveyed in a genetics association study using 15,309 single nucleotide polymorphisms (SNPs) detected in the sequence of 289 candidate genes scattered across the 19 grapevine linkage groups. After correcting statistical models for population structure and linkage disequilibrium effects, 164 SNPs from 34 of these genes were found to associate with fruit set-related traits, supporting a complex polygenic determinism. Many of them were found in the sequence of different putative MADS-box transcription factors, a gene family related with plant reproductive development control. In addition, we observed an additive effect of some of the associated SNPs on the phenotype, suggesting that advantageous alleles from different loci could be pyramided to generate superior cultivars with optimized fruit production.

Candidate genes and SNPs associated with stomatal conductance under drought stress in Vitis

BACKGROUND

Understanding the complexity of the vine plant's response to water deficit represents a major challenge for sustainable winegrowing. Regulation of water use requires a coordinated action between scions and rootstocks on which cultivars are generally grafted to cope with phylloxera infestations. In this regard, a genome-wide association study (GWAS) approach was applied on an 'ad hoc' association mapping panel including different Vitis species, in order to dissect the genetic basis of transpiration-related traits and to identify genomic regions of grape rootstocks associated with drought tolerance mechanisms. The panel was genotyped with the GrapeReSeq Illumina 20 K SNP array and SSR markers, and infrared thermography was applied to estimate stomatal conductance values during progressive water deficit.

RESULTS

In the association panel the level of genetic diversity was substantially lower for SNPs loci (0.32) than for SSR (0.87). GWAS detected 24 significant marker-trait associations along the various stages of drought-stress experiment and 13 candidate genes with a feasible role in drought response were identified. Gene expression analysis proved that three of these genes (VIT_13s0019g03040, VIT_17s0000g08960, VIT_18s0001g15390) were actually induced by drought stress. Genetic variation of VIT_17s0000g08960 coding for a raffinose synthase was further investigated by resequencing the gene of 85 individuals since a SNP located in the region (chr17_10,497,222_C_T) was significantly associated with stomatal conductance.

CONCLUSIONS

Our results represent a step forward towards the dissection of genetic basis that modulate the response to water deprivation in grape rootstocks. The knowledge derived from this study may be useful to exploit genotypic and phenotypic diversity in practical applications and to assist further investigations.

Differential expression of transcription factor- and further growth-related genes correlates with contrasting cluster architecture in Vitis vinifera 'Pinot Noir' and Vitis spp. genotypes

Grapevine (Vitis vinifera L.) is an economically important crop that needs to comply with high quality standards for fruit, juice and wine production. Intense plant protection is required to avoid fungal damage. Grapevine cultivars with loose cluster architecture enable reducing protective treatments due to their enhanced resilience against fungal infections, such as Botrytis cinerea-induced gray mold. A recent study identified transcription factor gene VvGRF4 as determinant of pedicel length, an important component of cluster architecture, in samples of two loose and two compact quasi-isogenic 'Pinot Noir' clones. Here, we extended the analysis to 12 differently clustered 'Pinot Noir' clones from five diverse clonal selection programs. Differential gene expression of these clones was studied in three different locations over three seasons. Two phenotypically opposite clones were grown at all three locations and served for standardization. Data were correlated with the phenotypic variation of cluster architecture sub-traits. A set of 14 genes with consistent expression differences between loosely and compactly clustered clones-independent from season and location-was newly identified. These genes have annotations related to cellular growth, cell division and auxin metabolism and include two more transcription factor genes, PRE6 and SEP1-like. The differential expression of VvGRF4 in relation to loose clusters was exclusively found in 'Pinot Noir' clones. Gene expression studies were further broadened to phenotypically contrasting F1 individuals of an interspecific cross and OIV reference varieties of loose cluster architecture. This investigation confirmed PRE6 and six growth-related genes to show differential expression related to cluster architecture over genetically divergent backgrounds.

Crosstalk Pathway between Trehalose Metabolism and Cytokinin Degradation for the Determination of the Number of Berries per Bunch in Grapes

In grapes, the number of flowers per inflorescence determines the compactness of grape bunches. Grape cultivars with tight bunches and thin-skinned berries easily undergo berry splitting, especially in growing areas with heavy rainfall during the grapevine growing season, such as Japan. We report herein that grape cytokinin oxidase/dehydrogenase 5 (VvCKX5) determines the number of berries per inflorescence in grapes. The number of berries per bunch was inversely proportional to the VvCKX5 expression level in juvenile inflorescences among the cultivars tested. VvCKX5 overexpression drastically decreased the number of flower buds per inflorescence in Arabidopsis plants, suggesting that VvCKX5 might be one of the negative regulators of the number of flowers per inflorescence in grapes. Similarly, the overexpression of grape sister of ramose 3 (VvSRA), which encodes trehalose 6-phosphate phosphatase that catalyzes the conversion of trehalose-6-phosphate into trehalose, upregulated AtCKX7 expression in Arabidopsis plants, leading to a decrease in the number of flower buds per Arabidopsis inflorescence. VvCKX5 gene expression was upregulated in grapevine cultured cells and juvenile grape inflorescences treated with trehalose. Finally, injecting trehalose into swelling buds nearing bud break using a microsyringe decreased the number of berries per bunch by half. VvCKX5 overexpression in Arabidopsis plants had no effect on the number of secondary inflorescences from the main inflorescence, and similarly trehalose did not affect pedicel branching on grapevine inflorescences, suggesting that VvCKX5, as well as VvSRA-mediated trehalose metabolism, regulates flower formation but not inflorescence branching. These findings may provide new information on the crosstalk between VvSRA-mediated trehalose metabolism and VvCKX-mediated cytokinin degradation for determining the number of berries per bunch. Furthermore, this study is expected to contribute to the development of innovative cultivation techniques for loosening tight bunches.

Population genetic analysis in old Montenegrin vineyards reveals ancient ways currently active to generate diversity in Vitis vinifera

Global viticulture has evolved following market trends, causing loss of cultivar diversity and traditional practices. In Montenegro, modern viticulture co-exists with a traditional viticulture that still maintains ancient practices and exploits local cultivars. As a result, this region provides a unique opportunity to explore processes increasing genetic diversity. To evaluate the diversity of Montenegrin grapevines and the processes involved in their diversification, we collected and analyzed 419 samples in situ across the country (cultivated plants from old orchards and vines growing in the wild), and 57 local varieties preserved in a grapevine collection. We obtained 144 different genetic profiles, more than 100 corresponding to cultivated grapevines, representing a surprising diversity for one of the smallest European countries. Part of this high diversity reflects historical records indicating multiple and intense introduction events from diverse viticultural regions at different times. Another important gene pool includes many autochthonous varieties, some on the edge of extinction, linked in a complex parentage network where two varieties (Razaklija and Kratošija) played a leading role on the generation of indigenous varieties. Finally, analyses of genetic structure unveiled several putative proto-varieties, likely representing the first steps involved in the generation of new cultivars or even secondary domestication events.

Identification of SNPs and InDels associated with berry size in table grapes integrating genetic and transcriptomic approaches

BACKGROUND

Berry size is considered as one of the main selection criteria in table grapes breeding programs, due to the consumer preferences. However, berry size is a complex quantitive trait under polygenic control, and its genetic determination of berry weight is not yet fully understood. The aim of this work was to perform marker discovery using a transcriptomic approach, in order to identify and characterize SNP and InDel markers associated with berry size in table grapes. We used an integrative analysis based on RNA-Seq, SNP/InDel search and validation on table grape segregants and varieties with different genetic backgrounds.

RESULTS

Thirty SNPs and eight InDels were identified using a transcriptomic approach (RNA-Seq). These markers were selected from SNP/InDel found among segregants from a Ruby x Sultanina population with contrasting phenotypes for berry size. The set of 38 SNP and InDel markers was distributed in eight chromosomes. Genotype-phenotype association analyses were performed using a set of 13 RxS segregants and 41 table grapes varieties with different genetic backgrounds during three seasons. The results showed several degrees of association of these markers with berry size (10.2 to 30.7%) as other berry-related traits such as length and width. The co-localization of SNP and /or InDel markers and previously reported QTLs and candidate genes associated with berry size were analysed.

CONCLUSIONS

We identified a set of informative and transferable SNP and InDel markers associated with berry size. Our results suggest the suitability of SNPs and InDels as candidate markers for berry weight in seedless table grape breeding. The identification of genomic regions associated with berry weight in chromosomes 8, 15 and 17 was achieved with supporting evidence derived from a transcriptome experiment focused on SNP/InDel search, as well as from a QTL-linkage mapping approach. New regions possibly associated with berry weight in chromosomes 3, 6, 9 and 14 were identified.

VviUCC1 Nucleotide Diversity, Linkage Disequilibrium and Association with Rachis Architecture Traits in Grapevine

Cluster compactness is a trait with high agronomic relevance, affecting crop yield and grape composition. Rachis architecture is a major component of cluster compactness determinism, and is a target trait toward the breeding of grapevine varieties less susceptible to pests and diseases. Although its genetic basis is scarcely understood, a preliminary result indicated a possible involvement of the VviUCC1 gene. The aim of this study was to characterize the VviUCC1 gene in grapevine and to test the association between the natural variation observed for a series of rachis architecture traits and the polymorphisms detected in the VviUCC1 sequence. This gene encodes an uclacyanin plant-specific cell-wall protein involved in fiber formation and/or lignification processes. A high nucleotide diversity in the VviUCC1 gene promoter and coding regions was observed, but no critical effects were predicted in the protein domains, indicating a high level of conservation of its function in the cultivated grapevine. After correcting statistical models for genetic stratification and linkage disequilibrium effects, marker-trait association results revealed a series of single nucleotide polymorphisms (SNPs) significantly associated with cluster compactness and rachis traits variation. Two of them (Y-984 and K-88) affected two common cis-transcriptional regulatory elements, suggesting an effect on phenotype via gene expression regulation. This work reinforces the interest of further studies aiming to reveal the functional effect of the detected VviUCC1 variants on grapevine rachis architecture.

A novel high-density grapevine (Vitis vinifera L.) integrated linkage map using GBS in a half-diallel population

A half-diallel population involving five elite grapevine cultivars was generated and genotyped by GBS, and highly-informative segregation data was used to construct a high-density genetic map for Vitis vinifera L. Grapevine is one of the most relevant fruit crops in the world. Deeper genetic knowledge could assist modern grapevine breeding programs to develop new wine grape varieties able to face climate change effects. To assist in the rapid identification of markers for crop yield components, grape quality traits and adaptation potential, we generated a large Vitis vinifera L. population (N = 624) by crossing five red wine cultivars in a half-diallel scheme, which was subsequently sequenced by an efficient GBS procedure. A high number of fully informative genetic variants was detected using a novel mapping approach capable of reconstructing local haplotypes from adjacent biallelic SNPs, which were subsequently used to construct the densest consensus genetic map available for the cultivated grapevine to date. This 1378.3-cM map integrates 10 bi-parental consensus maps and orders 4437 markers in 3353 unique positions on 19 chromosomes. Markers are well distributed all along the grapevine reference genome, covering up to 98.8% of its genomic sequence. Additionally, a good agreement was observed between genetic and physical orders, adding confidence in the quality of this map. Collectively, our results pave the way for future genetic studies (such as fine QTL mapping) aimed to understand the complex relationship between genotypic and phenotypic variation in the cultivated grapevine. In addition, the method used (which efficiently delivers a high number of fully informative markers) could be of interest to other outbred organisms, notably perennial fruit crops.

Identification of co-located QTLs and genomic regions affecting grapevine cluster architecture

Loose cluster architecture is an important aim in grapevine breeding since it has high impact on the phytosanitary status of grapes. This investigation analyzed the contributions of individual cluster sub-traits to the overall trait of cluster architecture. Six sub-traits showed large impact on cluster architecture as major determinants. They explained 57% of the OIV204 descriptor for cluster compactness rating in a highly diverse cross-population of 149 genotypes. Genetic analysis revealed several genomic regions involved in the expression of this trait. Based on the linkage of phenotypic features to molecular markers, QTL calculations shed new light on the genetic determinants of cluster architecture. Eight QTL clusters harbor overlapping confidence intervals of up to four co-located QTLs. A physical projection of the QTL clusters by confidence interval-flanking markers onto the PN40024 reference genome sequence revealed genes enriched in these regions.

Genome-wide association study of berry-related traits in grape [Vitis vinifera L.] based on genotyping-by-sequencing markers

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.

GA3 application in grapes (Vitis vinifera L.) modulates different sets of genes at cluster emergence, full bloom, and berry stage as revealed by RNA sequence-based transcriptome analysis

In grapes (Vitis vinifera L.), exogenous gibberellic acid (GA₃) is applied at different stages of bunch development to achieve desirable bunch shape and berry size in seedless grapes used for table purpose. RNA sequence-based transcriptome analysis was used to understand the mechanism of GA₃ action at cluster emergence, full bloom, and berry stage in table grape variety Thompson Seedless. At cluster emergence, rachis samples were collected at 6 and 24 h after application of GA₃, whereas flower clusters and berry samples were collected at 6, 24, and 48 h after application at full bloom and 3-4 mm berry stages. Seven hundred thirty-three genes were differentially expressed in GA₃-treated samples. At rachis and flower cluster stage respectively, 126 and 264 genes were found to be significantly differentially expressed within 6 h of GA₃ application. The number of DEG reduced considerably at 24 h. However, at berry stage, major changes occurred even at 24 h and a number of DEGs at 6 and 24 h were 174 and 191, respectively. As compared to upregulated genes, larger numbers of genes were downregulated. Stage-specific response to the GA₃ application was observed as evident from the unique set of DEGs at each stage and only a few common genes among three stages. Among the DEGs, 67 were transcription factors. Functional categorization and enrichment analysis revealed that several transcripts involved in sucrose and hexose metabolism, hormone and secondary metabolism, and abiotic and biotic stimuli were enriched in response to application of GA₃. A high correlation was recorded for real-time PCR and transcriptome data for selected DEGs, thus indicating the robustness of transcriptome data obtained in this study for understanding the GA₃ response at different stages of berry development in grape. Chromosomal localization of DEGs and identification of polymorphic microsatellite markers in selected genes have potential for their use in breeding for varieties with improved bunch architecture.

SNP markers tightly linked to root knot nematode resistance in grapevine (Vitis cinerea) identified by a genotyping-by-sequencing approach followed by Sequenom MassARRAY validation

Plant parasitic nematodes, including root knot nematode Meloidogyne species, cause extensive damage to agriculture and horticultural crops. As Vitis vinifera cultivars are susceptible to root knot nematode parasitism, rootstocks resistant to these soil pests provide a sustainable approach to maintain grapevine production. Currently, most of the commercially available root knot nematode resistant rootstocks are highly vigorous and take up excess potassium, which reduces wine quality. As a result, there is a pressing need to breed new root knot nematode resistant rootstocks, which have no impact on wine quality. To develop molecular markers that predict root knot nematode resistance for marker assisted breeding, a genetic approach was employed to identify a root knot nematode resistance locus in grapevine. To this end, a Meloidogyne javanica resistant Vitis cinerea accession was crossed to a susceptible Vitis vinifera cultivar Riesling and results from screening the F1 individuals support a model that root knot nematode resistance, is conferred by a single dominant allele, referred as MELOIDOGYNE JAVANICA RESISTANCE1 (MJR1). Further, MJR1 resistance appears to be mediated by a hypersensitive response that occurs in the root apical meristem. Single nucleotide polymorphisms (SNPs) were identified using genotyping-by-sequencing and results from association and genetic mapping identified the MJR1 locus, which is located on chromosome 18 in the Vitis cinerea accession. Validation of the SNPs linked to the MJR1 locus using a Sequenom MassARRAY platform found that only 50% could be validated. The validated SNPs that flank and co-segregate with the MJR1 locus can be used for marker-assisted selection for Meloidogyne javanica resistance in grapevine.

Differences in Flower Transcriptome between Grapevine Clones Are Related to Their Cluster Compactness, Fruitfulness, and Berry Size

Grapevine cluster compactness has a clear impact on fruit quality and health status, as clusters with greater compactness are more susceptible to pests and diseases and ripen more asynchronously. Different parameters related to inflorescence and cluster architecture (length, width, branching, etc.), fruitfulness (number of berries, number of seeds) and berry size (length, width) contribute to the final level of compactness. From a collection of 501 clones of cultivar Garnacha Tinta, two compact and two loose clones with stable differences for cluster compactness-related traits were selected and phenotyped. Key organs and developmental stages were selected for sampling and transcriptomic analyses. Comparison of global gene expression patterns in flowers at the end of bloom allowed identification of potential gene networks with a role in determining the final berry number, berry size and ultimately cluster compactness. A large portion of the differentially expressed genes were found in networks related to cell division (carbohydrates uptake, cell wall metabolism, cell cycle, nucleic acids metabolism, cell division, DNA repair). Their greater expression level in flowers of compact clones indicated that the number of berries and the berry size at ripening appear related to the rate of cell replication in flowers during the early growth stages after pollination. In addition, fluctuations in auxin and gibberellin signaling and transport related gene expression support that they play a central role in fruit set and impact berry number and size. Other hormones, such as ethylene and jasmonate may differentially regulate indirect effects, such as defense mechanisms activation or polyphenols production. This is the first transcriptomic based analysis focused on the discovery of the underlying gene networks involved in grapevine traits of grapevine cluster compactness, berry number and berry size.