Genetic variations of acidity in grape berries are controlled by the interplay between organic acids and potassium

Basic leucine zipper gene VvbZIP61 is expressed at a quantitative trait locus for high monoterpene content in grape berries

The widely appreciated muscat flavor of grapes and wine is mainly attributable to the monoterpenes that accumulate in ripe grape berries. To identify quantitative trait loci (QTL) for grape berry monoterpene content, an F1 mapping population was constructed by a cross between two grapevine genotypes, one with neutral aroma berries (cv. 'Beifeng') and the other with a pronounced muscat aroma (elite Vitis vinifera line '3-34'). A high-density genetic linkage map spanning 1563.7 cM was constructed using 3332 SNP markers that were assigned to 19 linkage groups. Monoterpenes were extracted from the berry of the F1 progeny, then identified and quantified by gas chromatography-mass spectrometry. Twelve stable QTLs associated with the amounts of 11 monoterpenes in berries were thus identified. In parallel, the levels of RNA in berries from 34 diverse cultivars were estimated by RNA sequencing and compared to the monoterpene content of the berries. The expression of five genes mapping to stable QTLs correlated well with the monoterpene content of berries. These genes, including the basic leucine zipper VvbZIP61 gene on chromosome 12, are therefore considered as potentially being involved in monoterpene metabolism. Overexpression of VvbZIP61 in Vitis amurensis callus through Agrobacterium-mediated transformation significantly increased the accumulation of several monoterpenes in the callus, including nerol, linalool, geranial, geraniol, β-myrcene, and D-limonene. It is hypothesized that VvbZIP61 expression acts to increase muscat flavor in grapes. These results advance our understanding of the genetic control of monoterpene biosynthesis in grapes and provide important information for the marker-assisted selection of aroma compounds in grape breeding.

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.

A high-density integrated map for grapevine based on three mapping populations genotyped by the Vitis18K SNP chip

We present a high-density integrated map for grapevine, allowing refinement and improved understanding of the grapevine genome, while demonstrating the applicability of the Vitis18K SNP chip for linkage mapping. The improvement of grapevine through biotechnology requires identification of the molecular bases of target traits by studying marker-trait associations. The Vitis18K SNP chip provides a useful genotyping tool for genome-wide marker analysis. Most linkage maps are based on single mapping populations, but an integrated map can increase marker density and show order conservation. Here we present an integrated map based on three mapping populations. The parents consist of the well-known wine cultivars 'Cabernet Sauvignon', 'Corvina' and 'Rhine Riesling', the lesser-known wine variety 'Deckrot', and a table grape selection, G1-7720. Three high-density population maps with an average inter-locus gap ranging from 0.74 to 0.99 cM were developed. These maps show high correlations (0.9965-0.9971) with the reference assembly, containing only 93 markers with large order discrepancies compared to expected physical positions, of which a third is consistent across multiple populations. Moreover, the genetic data aid the further refinement of the grapevine genome assembly, by anchoring 104 yet unanchored scaffolds. From these population maps, an integrated map was constructed which includes 6697 molecular markers and reduces the inter-locus gap distance to 0.60 cM, resulting in the densest integrated map for grapevine thus far. A small number of discrepancies, mainly of short distance, involve 88 markers that remain conflictual across maps. The integrated map shows similar collinearity to the reference assembly (0.9974) as the single maps. This high-density map increases our understanding of the grapevine genome and provides a useful tool for its further characterization and the dissection of complex traits.

A genome-wide association and prediction study in grapevine deciphers the genetic architecture of multiple traits and identifies genes under many new QTLs

To cope with the challenges facing agriculture, speeding-up breeding programs is a worthy endeavor, especially for perennial species such as grapevine, but requires understanding the genetic architecture of target traits. To go beyond the mapping of quantitative trait loci in bi-parental crosses, we exploited a diversity panel of 279 Vitis vinifera L. cultivars planted in 5 blocks in the vineyard. This panel was phenotyped over several years for 127 traits including yield components, organic acids, aroma precursors, polyphenols, and a water stress indicator. The panel was genotyped for 63k single nucleotide polymorphisms by combining an 18K microarray and genotyping-by-sequencing. The experimental design allowed to reliably assess the genotypic values for most traits. Marker densification via genotyping-by-sequencing markedly increased the proportion of genetic variance explained by single nucleotide polymorphisms, and 2 multi-single nucleotide polymorphism models identified quantitative trait loci not found by a single nucleotide polymorphism-by-single nucleotide polymorphism model. Overall, 489 reliable quantitative trait loci were detected for 41% more response variables than by a single nucleotide polymorphism-by-single nucleotide polymorphism model with microarray-only single nucleotide polymorphisms, many new ones compared with the results from bi-parental crosses. A prediction accuracy higher than 0.42 was obtained for 50% of the response variables. Our overall approach as well as quantitative trait locus and prediction results provide insights into the genetic architecture of target traits. New candidate genes and the application into breeding are discussed.

Berry Anthocyanin, Acid, and Volatile Trait Analyses in a Grapevine-Interspecific F2 Population Using an Integrated GBS and rhAmpSeq Genetic Map

Increased map density and transferability of markers are essential for the genetic analysis of fruit quality and stress tolerance in interspecific grapevine populations. We used 1449 GBS and 2000 rhAmpSeq markers to develop a dense map for an interspecific F₂ population (VRS-F₂) that was derived by selfing a single F₁ from a Vitis riparia x ‘Seyval blanc’ cross. The resultant map contained 2519 markers spanning 1131.3 cM and was highly collinear with the Vitis vinifera ‘PN40024’ genome. Quantitative trait loci (QTL) for berry skin color and flower type were used to validate the map. Four rhAmpSeq transferable markers were identified that can be used in pairs (one pistillate and one hermaphroditic) to predict pistillate and hermaphrodite flower type with ≥99.7% accuracy. Total and individual anthocyanin diglucoside QTL mapped to chromosome 9 near a 5-O-GLUCOSYLTRANSFERASE candidate gene. Malic acid QTL were observed on chromosome 1 and 6 with two MALATE DEHYRDROGENASE CYTOPLASMIC 1 and ALUMINUM-ACTIVATED MALATE TRANSPORTER 2-LIKE (ALMT) candidate genes, respectively. Modeling malic acid identified a potential QTL on chromosome 8 with peak position in proximity of another ALMT. A first-ever reported QTL for the grassy smelling volatile (E)-2-hexenal was found on chromosome 2 with a PHOSPHOLIPID HYDROPEROXIDE GLUTATHIONE PEROXIDASE candidate gene near peak markers.

Stable QTL for malate levels in ripe fruit and their transferability across Vitis species

Malate is a major contributor to the sourness of grape berries (Vitis spp.) and their products, such as wine. Excessive malate at maturity, commonly observed in wild Vitis grapes, is detrimental to grape and wine quality and complicates the introgression of valuable disease resistance and cold hardy genes through breeding. This study investigated an interspecific Vitis family that exhibited strong and stable variation in malate at ripeness for five years and tested the separate contribution of accumulation, degradation, and dilution to malate concentration in ripe fruit in the last year of study. Genotyping was performed using transferable rhAmpSeq haplotype markers, based on the Vitis collinear core genome. Three significant QTL for ripe fruit malate on chromosomes 1, 7, and 17, accounted for over two-fold and 6.9 g/L differences, and explained 40.6% of the phenotypic variation. QTL on chromosomes 7 and 17 were stable in all and in three out of five years, respectively. Variation in pre-veraison malate was the major contributor to variation in ripe fruit malate (39%), and based on two and five years of data, respectively, their associated QTL overlapped on chromosome 7, indicating a common genetic basis. However, use of transferable markers on a closely related Vitis family did not yield a common QTL across families. This suggests that diverse physiological mechanisms regulate the levels of this key metabolite in the Vitis genus, a conclusion supported by a review of over a dozen publications from the past decade, showing malate-associated genetic loci on all 19 chromosomes.

Contribution of Piriformospora indica on improving the nutritional quality of greenhouse tomato and its resistance against cu toxicity after humic acid addition to soil

Protected cultivation has a significant contribution in vegetable production. We investigated whether humic acid addition to soil and Piriformospora indica can improve the nutritional quality of greenhouse tomato. We conducted a pot experiment, in which the effects of P. indica inoculation, humic acid addition, and Cu spiking to soil (0, 120, 240, and 500 ppm Cu) were tested. Humic acid addition to soil spiked with 500 ppm Cu decreased the Cu concentration in the fruits of plants inoculated with P. indica from 0.65 to 0.40 mg 100 g Fw^-1, which is still above the maximum allowed limits of Cu in tomato by World Health Organization (WHO). The lycopene and ascorbic acid content of tomato fruits were consistently improved by humic acid addition and P. indica inoculation. The antioxidant enzymes' activity changed in response to humic acid addition, Cu spiking to soil, and P. indica inoculation. With increasing Cu level up to 240 ppm, the activity of superoxide dismutase (SOD) and peroxidase (POD) increased significantly. However, with spiking more Cu to soil, the activity of antioxidant enzymes reduced and the MDA content increased significantly. Addition of humic acid to soil and/or presence of P. indica increased the activity of antioxidant enzymes when the soil spiked with 500 ppm Cu. This study indicated that addition of P. indica and humic acid to the soil can enhance the nutritional quality of greenhouse tomato by reduction of Cu toxicity as a common pollutant in the greenhouse media and increasing the antioxidant content of fruits.

Alternative splicing regulation appears to play a crucial role in grape berry development and is also potentially involved in adaptation responses to the environment

BACKGROUND

Alternative splicing (AS) produces transcript variants playing potential roles in proteome diversification and gene expression regulation. AS modulation is thus essential to respond to developmental and environmental stimuli. In grapevine, a better understanding of berry development is crucial for implementing breeding and viticultural strategies allowing adaptation to climate changes. Although profound changes in gene transcription have been shown to occur in the course of berry ripening, no detailed study on splicing modifications during this period has been published so far. We report here on the regulation of gene AS in developing berries of two grapevine (Vitis vinifera L.) varieties, Gewurztraminer (Gw) and Riesling (Ri), showing distinctive phenotypic characteristics. Using the software rMATS, the transcriptomes of berries at four developmental steps, from the green stage to mid-ripening, were analysed in pairwise comparisons between stages and varieties.

RESULTS

A total of 305 differential AS (DAS) events, affecting 258 genes, were identified. Interestingly, 22% of these AS events had not been reported before. Among the 80 genes that underwent the most significant variations during ripening, 22 showed a similar splicing profile in Gw and Ri, which suggests their involvement in berry development. Conversely, 23 genes were subjected to splicing regulation in only one variety. In addition, the ratios of alternative isoforms were different in Gw and Ri for 35 other genes, without any change during ripening. This last result indicates substantial AS differences between the two varieties. Remarkably, 8 AS events were specific to one variety, due to the lack of a splice site in the other variety. Furthermore, the transcription rates of the genes affected by stage-dependent splicing regulation were mostly unchanged, identifying AS modulation as an independent way of shaping the transcriptome.

CONCLUSIONS

The analysis of AS profiles in grapevine varieties with contrasting phenotypes revealed some similarity in the regulation of several genes with developmental functions, suggesting their involvement in berry ripening. Additionally, many splicing differences were discovered between the two varieties, that could be linked to phenotypic specificities and distinct adaptive capacities. Together, these findings open perspectives for a better understanding of berry development and for the selection of grapevine genotypes adapted to climate change.

Adjustment of K+ Fluxes and Grapevine Defense in the Face of Climate Change

Grapevine is one of the most economically important fruit crops due to the high value of its fruit and its importance in winemaking. The current decrease in grape berry quality and production can be seen as the consequence of various abiotic constraints imposed by climate changes. Specifically, produced wines have become too sweet, with a stronger impression of alcohol and fewer aromatic qualities. Potassium is known to play a major role in grapevine growth, as well as grape composition and wine quality. Importantly, potassium ions (K+) are involved in the initiation and maintenance of the berry loading process during ripening. Moreover, K+ has also been implicated in various defense mechanisms against abiotic stress. The first part of this review discusses the main negative consequences of the current climate, how they disturb the quality of grape berries at harvest and thus ultimately compromise the potential to obtain a great wine. In the second part, the essential electrical and osmotic functions of K+, which are intimately dependent on K+ transport systems, membrane energization, and cell K+ homeostasis, are presented. This knowledge will help to select crops that are better adapted to adverse environmental conditions.

Early Defoliation Techniques Enhance Yield Components, Grape and Wine Composition of cv. Trnjak (Vitis vinifera L.) in Dalmatian Hinterland Wine Region

Defoliation and cluster thinning are of practical importance in a control of the grapevine source-sink balance, cluster architecture, microclimate and berry composition. Nevertheless, their effectiveness on wine composition is unexplored. In this work, the impacts of preflowering (T1), after berry set (T2), and veraison defoliation (T3) and cluster thinning (T4), on yield components, grape and wine composition of cv. Trnjak are given. Implemented techniques significantly reduced yield and affected grape and wine components in comparison to untreated control (C). Despite lowest number of clusters ensured by cluster thinning, defoliation at veraison had lowest yield. Defoliations improved cluster architecture parameters. Highest berry per se was in preflowering T1 and lowest at veraison T3 defoliation. Berries of T1 had lowest sugar content (19.47 °Brix) while T3 had highest (22.3 °Brix), and the reverse is seen in total acidity highest in T1 (6.12 g/L) and lowest in T3 (5.01 g/L). Wines of early defoliations (T1 and T2) had lowest alcohol and highest anthocyanin concentration. Both techniques applied at veraison produced wines with lower anthocyanins and flavonols than those obtained without any intervention (C). In conclusion, the early defoliations (T1 and T2) improve yield and wine composition of cv. Trnjak in the Mediterranean region of Croatia.

Biosynthesis and Cellular Functions of Tartaric Acid in Grapevines

Tartaric acid (TA) is an obscure end point to the catabolism of ascorbic acid (Asc). Here, it is proposed as a "specialized primary metabolite", originating from carbohydrate metabolism but with restricted distribution within the plant kingdom and lack of known function in primary metabolic pathways. Grapes fall into the list of high TA-accumulators, with biosynthesis occurring in both leaf and berry. Very little is known of the TA biosynthetic pathway enzymes in any plant species, although recently some progress has been made in this space. New technologies in grapevine research such as the development of global co-expression network analysis tools and genome-wide association studies, should enable more rapid progress. There is also a lack of information regarding roles for this organic acid in plant metabolism. Therefore this review aims to briefly summarize current knowledge about the key intermediates and enzymes of TA biosynthesis in grapes and the regulation of its precursor, ascorbate, followed by speculative discussion around the potential roles of TA based on current knowledge of Asc metabolism, TA biosynthetic enzymes and other aspects of fruit metabolism.

Molecular Tools for Adapting Viticulture to Climate Change

Adaptation of viticulture to climate change includes exploration of new geographical areas, new training systems, new management practices, or new varieties, both for rootstocks and scions. Molecular tools can be defined as molecular approaches used to study DNAs, RNAs, and proteins in all living organisms. We present here the current knowledge about molecular tools and their potential usefulness in three aspects of grapevine adaptation to the ongoing climate change. (i) Molecular tools for understanding grapevine response to environmental stresses. A fine description of the regulation of gene expression is a powerful tool to understand the physiological mechanisms set up by the grapevine to respond to abiotic stress such as high temperatures or drought. The current knowledge on gene expression is continuously evolving with increasing evidence of the role of alternative splicing, small RNAs, long non-coding RNAs, DNA methylation, or chromatin activity. (ii) Genetics and genomics of grapevine stress tolerance. The description of the grapevine genome is more and more precise. The genetic variations among genotypes are now revealed with new technologies with the sequencing of very long DNA molecules. High throughput technologies for DNA sequencing also allow now the genetic characterization at the same time of hundreds of genotypes for thousands of points in the genome, which provides unprecedented datasets for genotype-phenotype associations studies. We review the current knowledge on the genetic determinism of traits for the adaptation to climate change. We focus on quantitative trait loci and molecular markers available for developmental stages, tolerance to water stress/water use efficiency, sugar content, acidity, and secondary metabolism of the berries. (iii) Controlling the genome and its expression to allow breeding of better-adapted genotypes. High-density DNA genotyping can be used to select genotypes with specific interesting alleles but genomic selection is also a powerful method able to take into account the genetic information along the whole genome to predict a phenotype. Modern technologies are also able to generate mutations that are possibly interesting for generating new phenotypes but the most promising one is the direct editing of the genome at a precise location.

Vitis vinifera L. Diversity for Cations and Acidity Is Suitable for Breeding Fruits Coping With Climate Warming

The selection of grapevine varieties is considered to be the smartest strategy for adapting the viticulture to climate warming. Present knowledge of the diversity of grape solutes known to be influenced by temperature is too limited to perform genetic improvement strategies. This study aimed to characterize the diversity for major cations (K⁺, Mg²⁺, Ca²⁺, NH₄ ⁺) of the Vitis vinifera fruit and their effect on acidity. Two developmental stages were targeted: the end of green growth, when organic acids reach a maximum, and the physiological ripe stage defined by the stopping of solutes and water import at the maximum volume of the berry. Twelve varieties and 21 microvines from the same segregating population were selected from preliminary phenotyping. The concentration of cations depended on the stage of fruit development, the genotype and the environment with GxE effects. In the ripe grape, K⁺ concentration varied from 28 to 57 mmol.L^-1 with other cations being less concentrated. Combined with the variation in organic acids, cation concentration diversity resulted in titratable acidity of the ripe fruit ranging from 38 to 215 meq.L^-1. These results open new perspectives for the selection of varieties to mitigate the adverse effects of climate warming on grape quality.