Inter‐varietal structural variation in grapevine genomes

Grapevine (Vitis vinifera L.) is one of the world's most important crop plants, which is of large economic value for fruit and wine production. There is much interest in identifying genomic variations and their functional effects on inter‐varietal, phenotypic differences. Using an approach developed for the analysis of human and mammalian genomes, which combines high‐throughput sequencing, array comparative genomic hybridization, fluorescent in situ hybridization and quantitative PCR, we created an inter‐varietal atlas of structural variations and single nucleotide variants (SNVs) for the grapevine genome analyzing four economically and genetically relevant table grapevine varieties. We found 4.8 million SNVs and detected 8% of the grapevine genome to be affected by genomic variations. We identified more than 700 copy number variation (CNV) regions and more than 2000 genes subjected to CNV as potential candidates for phenotypic differences between varieties.     

Transport and accumulation of flavonoids in grapevine (Vitis vinifera L.)

Flavonoids are a group of secondary metabolites widely distributed in plants that represent a huge portion of the soluble phenolics present in grapevine (Vitis vinifera L.). These compounds play different physiological roles and are often involved in protection against biotic and abiotic stress. Even if the flavonoid biosynthetic pathways have been largely characterized, the mechanisms of their transport and accumulation in cell wall and vacuole are still not completely understood. This review analyses the known mechanisms of flavonoid uptake and accumulation in grapevine, with reference to the transport models and membrane carrier proteins described in other plant species. The effect of different environmental factors on flavonoid biosynthesis and transporters is also discussed.Key words: ABC proteins, active transport, bilitranslocase, biotic and abiotic stress, flavonoid, secondary metabolites     

Vitis vinifera in the Iberian Peninsula: A review

The origin of the Eurasian grapevine, Vitis vinifera L. and the different steps in the development of viticulture from the wild grapevine to the modern varietal situation in the Iberian Peninsula are reviewed here. The ancestors of Vitis vinifera subs. sylvestris, the only representative of the Vitis genus in natural Eurasian and North African ecosystems, appeared in the late Miocene. In the Iberian Peninsula, human action has significantly reduced the habitat of this species, whose oldest palaeobotanical remains go back to the late Pleistocene. The introduction of viticulture in Iberia is connected with the relationships between the indigenous population and the trading colonies founded by Phoenicians and Greeks. In this way, there is evidence of wine production and consumption, even as a ritual and prestige item, going back to the third millennium BP. Chloroplast genome studies carried out in wild and cultivated plants indicate that a secondary domestication process occurred in the Iberian Peninsula and this is reflected in the “A” chlorotype, which contrasts with the predominance of the “B” and “C” chlorotypes in wild and domesticated vines in the Transcaucasian region, where domesticated grapes at sites of the Shulaveri Culture (Georgia) are evidence of early viticulture around 8000 BP.     

Botrytis cinerea: Activité Antifongique dans les Jeunes Grappes de Vitis vinifera, Varieté Gamay

Botrytis cinerea: fungicidal activity in young grape berries of Vitis vinifera (Gamay) Extracts of young grape berries of Vitis vinifera (Gamay) inhibit the germination of conidia of Botrytis cinerea. This inhibitory activity is present in extracts obtained from clusters at bloom stage and is maintained until a developmental stage close to the maturity. These extracts ruptured the cellular membranes.     

3-oxo-α-ionol,vomifoliol and roseoside in Vitis vinifera fruit

3-Oxo-β-ionol, vomifoliol and dehydrovomifoliol were identified for the first time in fruit from Vitis vinifera. The last named compound was mainly present free in the juice while the others existed predominantly as conjugates. In the case of vomifoliol, the conjugation was with glucose, i.e. as roseoside. Hydrolytic studies on 3-oxo-α-ionol and vomifoliol gave a range of compounds which have been recognized as fruit and plant products.     

Expression analysis of UDP-glucose:flavonoid 3-O-glucosyltransferase (UFGT) gene in an interspecific hybrid grape between Vitis ficifolia var. ganebu and Vitis vinifera cv. Muscat of Alexandria

Kadainou R-1, an interspecific hybrid grape derived from red (Vitis ficifolia var. ganebu) and white (V. vinifera cv. Muscat of Alexandria) grapes, accumulates high concentrations of anthocyanin in the berry skin. Hence, the expression of uridine 5′-diphosphate (UDP)-glucose:flavonoid 3-O-glucosyltransferase (UFGT), the key enzyme of the anthocyanin pathway, was examined in the berry skin of Kadainou R-1. As information on gene sequences of V. ficifolia var. ganebu and other wild grape species was unavailable, we performed GeneChip hybridization using biotin-labeled genomic deoxyribonucleic acid (DNA) to investigate how the genomic sequences of V. vinifera varieties and that of V. ficifolia var. ganebu differ. The study showed a lower correlation coefficient between V. vinifera cultivars and V. ficifolia var. ganebu than that among V. vinifera cultivars. The sequences of the UFGT gene derived from both parents of the red and white cultivars were sequenced in Kadainou R1 and revealed that both were expressed irrespective of the fact that it was not expressed in the white grape (male parent).     

ULTRASTRUCTURE OF DIFFERENTIATED CELLS IN HIGHER PLANTS

Esau , Katherine . (U. California, Santa Barbara.) Ultrastructure of differentiated cells in higher plants. Amer. Jour. Bot. 50(5): 495–506. Illus. 1903.—This paper reviews the rather meager information on differences between meristematic and fully differentiated cells of higher plants at the ultrastructural level. It includes personal observations on differentiated cells in Cucurbita maxima and Vitis vinifera, particularly those of the phloem tissue. The structures considered and illustrated by means of electron micrographs are vacuoles, the nucleus, mitochondria, the endoplasmic reticulum, dictyosomes, plasmodesmata, and, briefly, plastids.     

Remarks on mixotrophic and autotrophic carbon nutrition of Vitis plantlets cultured in vitro

Two Vitis species were cultured in vitro under photoautrophic (sucrose-free culture medium) and photomixotrophic (sucrose 15 g l^-1) conditions during the period following microcutting rooting (day 34 to day 120). Several parameters were measured at the end of the culture: growth, plant dry weight, carbohydrate uptake from the medium and rates of photosynthesis and dark respiration. The two species behaved very differently. Under photoautotrophic conditions, dark respiration, net photosynthesis and daily CO₂ fixation were higher in Vitis vinifera than in Vitis rupestris. Culture under mixotrophic conditions caused increase in growth, respiration and photosynthesis in Vitis rupestris. In contrast, photosynthesis decreased in Vitis vinifera under the same conditions.     

Phylogeographical structure and conservation genetics of wild grapevine

The distribution of Vitis vinifera subsp. silvestris, the wild grapevine subspecies of Vitis vinifera L., has been dramatically reduced in its major sites of diffusion, at first by the spread, over the last 150 years, of pathogens from North America and, more recently, with fragmentation of habitat and disbranching by humans. In this work, 418 wild grapevine samples, belonging to 78 populations, were collected in their main Mediterranean distribution areas, including the Caucasus area, and the extent of their genetic variability evaluated by analysing plastid microsatellite DNA polymorphism. Results show low haplotype diversity value, with five haplotypes detected within the analysed populations. The highest within-population haplotypic diversity, with the presence of all five detected haplotypes, was found in the Caucasus regions and in the central regions of Italy. The distribution of all detected haplotypes suggests the Caucasian region as the possible center of origin of Vitis vinifera subsp. silvestris. A principal plastid lineage was found to be fixed in several locations, in the Northernmost European countries and in the Southern island of Sardinia. These results draw attention to two different refugium sites in the Mediterranean basin and suggest that conservation priority should be given to grapevine populations still preserved in hotspots of these regions.     

Characterization of new microsatellite loci from Vitis vinifera and their conservation in some Vitis species and hybrids

We present here characterization data for seven new microsatellite markers designed from new microsatellite loci isolated from a microsatellite‐enriched DNA library from Vitis vinifera. The observed heterozygosity varied from 0.73 up to 0.93 and the number of alleles per locus ranged from 12 to 26. This high polymorphism makes these new markers interesting for use in genotyping studies and completing the set of microsatellite markers already available for V. vinifera. Additionally these seven new markers appear to be conserved in four other Vitis species and 15 Vitis hybrids used as rootstocks for V. vinifera cultivation.     

Bacterial Endophytes from Vitis vinifera L. – Metabolomics Characterization of Plant-Endophyte Crosstalk

Bacterial endophytes are known to protect Vitis vinifera L. against various harmful effects of the environment and support its growth. However, for the most part, biochemical responses of such co-existence have not yet been fully elucidated. In this work, we aimed to characterize the activities of endophytic consortia in a plant-endophyte extract by measuring five indicators of colonization (overall endophyte metabolic activity, microbial ACC deaminase activity, ability to solubilize phosphorus, ability to convert atmospheric nitrogen to ammonia ions, and ability to produce growth promoting indole acetic acid), and find relationships between these activities and metabolome. The V. vinifera canes for the metabolomics fingerprinting were extracted successively with water and methanol, and analysed by ultra-high performance liquid chromatography coupled with high resolution mass spectrometry. For data processing, the MS-DIAL – MS-CleanR – MS-FINDER software platform was used, and the data matrix was processed by PCA and PLS-DA multivariate statistical methods. The metabolites that were upregulated with the heavy endophyte colonization were mainly chlorins, phenolics, flavonoid and terpenoid glycosides, tannins, dihydropyranones, sesquiterpene lactones, and long-chain unsaturated fatty acids.     

Large-scale parentage analysis in an extended set of grapevine cultivars (Vitis vinifera L.)

Inheritance of nuclear microsatellite markers (nSSR) has been proved to be a powerful tool to verify or uncover the parentage of grapevine cultivars. The aim of the present study was to undertake an extended parentage analysis using a large sample of Vitis vinifera cultivars held in the INRA “Domaine de Vassal” Grape Germplasm Repository (France). A dataset of 2,344 unique genotypes (i.e. cultivars without synonyms, clones or mutants) identified using 20 nSSR was analysed with FAMOZ software. Parentages showing a logarithm of odds score higher than 18 were validated in relation to the historical data available. The analysis first revealed the full parentage of 828 cultivars resulting in: (1) 315 original full parentages uncovered for traditional cultivars, (2) 100 full parentages confirming results established with molecular markers in prior papers and 32 full parentages that invalidated prior results, (3) 255 full parentages confirming pedigrees as disclosed by the breeders and (4) 126 full parentages that invalidated breeders’ data. Second, incomplete parentages were determined in 1,087 cultivars due to the absence of complementary parents in our cultivar sample. Last, a group of 276 genotypes showed no direct relationship with any other cultivar in the collection. Compiling these results from the largest set of parentage data published so far both enlarges and clarifies our knowledge of the genetic constitution of cultivated V. vinifera germplasm. It also allows the identification of the main genitors involved in varietal assortment evolution and grapevine breeding.     

Historical isolation and Quaternary range expansion of divergent lineages in wild grapevine

Vitis vinifera subsp. silvestris, the wild subspecies of Vitis vinifera L., is a unique and valuable genetic resource for cultivated grapevines. At present, this wild form is rare and is spread from the Southern Atlantic coast of Europe to the Western Himalayas. In the present study, six nuclear microsatellite DNAs were analysed in 301 wild grape samples, using factorial correspondence analysis and the Bayesian model. The aim was to detect the distribution of genetic variability and admixture proportions and thus to identify the main routes of recolonization after the quaternary glaciation, as well as signals of secondary contacts in Europe. The results obtained show that some Caucasus and Italian areas played key roles as refugial areas. Moreover, the data suggest the existence of two main migration routes through central Europe during the post‐glacial or the inter‐glacial periods. The first started from Southern Italy and moved northward, whereas the second originated from refugia possibly located in eastern areas and migrated westwards. This scenario is most likely associated with the population expansion that followed the European Quaternary glaciations. In accordance with this assumption, central Europe is proposed as an admixture confluence of migration routes radiating from separate grapevine refugia. © 2008 The Linnean Society of London, Biological Journal of the Linnean Society, 2008, 95 , 611–619.     

Chalcone isomerase in grape vine: gene expression and localization in the developing fruit

Chalcone isomerase (CHI, EC 5.5.1.6) is an entrance enzyme in the flavonoid biosynthesis, which catalyzes the conversion of chalcones to flavanones. In this study, the full-length CHI cDNA from grape vine (Vitis vinifera L.) was cloned, the recombinant protein was purified and the polyclonal antibody was prepared. Using these tools, the expression and tissue localization of CHI in developing grape berry was analyzed by RT-PCR, gel blot hybridization and immunohistochemical techniques. The expression of CHI was dependent on developmental stage, and CHI protein was mainly distributed in vascular bundles throughout all the stages of berry development, which suggested that flavonoids in the berry might have been partially synthesized in situ.     

Silybum marianum cell cultures stably transformed with Vitis vinifera stilbene synthase accumulate t‐resveratrol in the extracellular medium after elicitation with methyl jasmonate or methylated β‐cyclodextrins

The growing demand for t‐resveratrol for industrial uses has generated considerable interest in its production. Heterologous resveratrol production in plant cell suspensions, apart from requiring the introduction of only one or two genes, has the advantage of high biomass yield and a short cultivation time, and thus could be an option for large‐scale production. Silybum marianum is the source of the flavonolignan silymarin. Phenylpropanoid synthesis in cultures of this species can be activated by elicitation with methyl jasmonate and methylated β‐cyclodextrins, with products of the pathway (coniferyl alcohol and some isomers of the silymarin complex) being released into the medium. Given that stilbene synthase shares the same key precursors involved in flavonoid and /or monolignol biosynthesis, we explored the potential of metabolically engineered S. marianum cultures for t‐resveratrol production. Cell suspensions were stably transformed with Vitis vinifera stilbene synthase 3 and the expression of the transgene led to extracellular t‐resveratrol accumulation at the level of milligrams per litre under elicitation. Resveratrol synthesis occurred at the expense of coniferyl alcohol. Production of silymarin was less affected in the transgenic cultures, since the flavonoid pathway is limiting for its synthesis, due to the preferred supply of precursors for the monolignol branch. The fact that the expressed STS gene took excessively produced precursors of non‐bioactive compounds (coniferyl alcohol), while keeping the metabolic flow for target secondary compounds (i.e. silymarin) unaltered, opens a way to extend the applications of plant cell cultures for the simultaneous production of both constitutive and foreign valuable metabolites.     

The calcium nutrition of bambara groundnut (Vigna subterranea (L.) Verdc.)

Iron chlorosis induced by Fe-deficiency is a widespread nutritional disorder in many woody plants and in particular in grapevine. This phenomenon results from different environmental, nutritional and varietal factors. Strategy I plants respond to Fe-deficiency by inducing physiological and biochemical modifications in order to increase Fe uptake. Among these, acidification of the rhizosphere, membrane redox activities and synthesis of organic acids are greatly enhanced during Fe-deficiency. Grapevine is a strategy I plant but the knowledge on the physiological and biochemical responses to this iron stress deficiency in this plant is still very poor. In this work four different genotypes of grapevine were assayed for these parameters. It was found that there is a good correlation between genotypes which are known to be chlorosis-resistant and increase in both rhizosphere acidification and Fe^III reductase activity. In particular, when grown in the absence of iron, Vitis berlandieri and Vitis vinifera cv Cabernet sauvignon and cv Pinot blanc show a higher capacity to acidify the culture medium (pH was decreased by 2 units), a higher concentration of organic acids, a higher resting transmembrane electrical potential and a greater capacity to reduce Fe^III-chelates. On the contrary, Vitis riparia, well known for its susceptibility to iron chlorosis, fails to decrease the pH of the medium and shows a lower concentration in organic acids, lower capacity to reduce Fe^III and no difference in the resting transmembrane electrical potential. H Marschner Section editor     

Stilbene biosynthesis and gene expression in response to methyl jasmonate and continuous light treatment in Vitis vinifera cv. Malvasia del Lazio and Vitis rupestris Du Lot cell cultures

Vitis rupestris is used as rootstock or to obtain hybrids with Vitis vinifera, due to its resistance to certain pathogens. Its resistance mechanisms are poorly understood, while it is known that stilbene neo‐synthesis is a central defense strategy in V. vinifera. In the present study, the response to methyl jasmonate (MeJa) and light treatment in terms of stilbene biosynthesis and the expression of genes involved in polyphenol biosynthesis was investigated in V. vinifera and V. rupestris cells. The two species exhibited a similar constitutive stilbene content [2.50–2.80 mg g^?1 dry weight (DW)], which greatly increased in response to elicitation (8.97–11.90 mg g^?1 DW). In V. vinifera, continuous light treatment amplified the effect of MeJa, with a stilbene production that had never previously been obtained (26.49 mg g^?1 DW). By contrast, it suppressed the effect of MeJa in V. rupestris. Gene expression was consistent with stilbene production in V. vinifera, whereas discrepancies were recorded in V. rupestris that could be explained by the synthesis of stilbenes that had never before been analyzed in this species.     

Characterization of genome-wide long terminal repeat retrotransposons provide insights into trait evolution of four grapevine species

Grapevine is one of the most economically important crops in the world. Although long terminal repeat (LTR) retrotransposons are thought to have played an important role in plants, its distribution in grapevine is not clear. Here, we identified genome-wide intact LTR retrotransposons in a total of six high-quality grapevine genomes from Vitis vinifera L., Vitis sylvestris C.C. Gmel., Vitis riparia Michx. and Vitis amurensis Rupr. with an average of 2938 per genome. Among them, the Copia superfamily (particularly for Ale) is a major component of the LTR retrotransposon in grapevine. Insertion time and copy number analysis revealed that the expansion of 70% LTR retrotransposons concentrating on approximately 2.5 Ma was able to drive genome size variation. Phylogenetic tree and syntenic analyses showed that most LTR retrotransposons in these genomes formed and evolved after species divergence. Furthermore, the function and expression of genes inserted by LTR retrotransposons in V. vinifera (Pinot noir) and V. riparia were explored. The length and expression of genes related to starch metabolism and quinone synthesis pathway in Pinot noir and environmental adaptation pathway in V. riparia were significantly affected by LTR retrotransposon insertion. The results improve the understanding of LTR retrotransposons in grapevine genomes and provide insights for its potential contribution to grapevine trait evolution.