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1.  Characterisation of the Vitis vinifera PR10 multigene family 
BMC Plant Biology  2010;10:184.
Background
Genes belonging to the pathogenesis related 10 (PR10) group have been studied in several plant species, where they form multigene families. Until now, such an analysis has not been performed in Vitis vinifera, although three different PR10 genes were found to be expressed under pathogen attack or abiotic stress, and during somatic embryogenesis induction. We used the complete genome sequence for characterising the whole V. vinifera PR10 gene family. The expression of candidate genes was studied in various non-treated tissues and following somatic embryogenesis induction by the auxin 2,4-D.
Results
In addition to the three V. vinifera PR10 genes already described, namely VvPR10.1, VvPR10.2 and VvPR10.3, fourteen different PR10 related sequences were identified. Showing high similarity, they form a single cluster on the chromosome 5 comprising three pseudogenes. The expression of nine different genes was detected in various tissues. Although differentially expressed in non-treated plant organs, several genes were up-regulated in tissues treated with 2,4-D, as expected for PR genes.
Conclusions
PR10 genes form a multigene family in V. vinifera, as found in birch, apple or peach. Seventeen closely related PR10 sequences are arranged in a tandem array on the chromosome 5, probably reflecting small-scale duplications during evolution. Various expression patterns were found for nine studied genes, highlighting functional diversification. A phylogenetic comparison of deduced proteins with PR10 proteins of other plants showed a characteristic low intraspecific variability. Particularly, a group of seven close tandem duplicates including VvPR10.1, VvPR10.2 and VvPR10.3 showed a very high similarity, suggesting concerted evolution or/and recent duplications.
doi:10.1186/1471-2229-10-184
PMCID: PMC3095314  PMID: 20727162
2.  Low level of polymorphism in two putative NPR1 homologs in the Vitaceae family 
Biology Direct  2010;5:9.
Background
Grapevine is subjected to numerous pests and diseases resulting in the use of phytochemicals in large quantities. The will to decrease the use of phytochemicals leads to attempts to find alternative strategies, implying knowledge of defence mechanisms. Numerous studies have led to the identification of signalling pathways and regulatory elements involved in defence in various plant species. Nonexpressor of Pathogenesis Related 1 (NPR1) is an important regulatory component of systemic acquired resistance (SAR) in Arabidopsis thaliana.
Results
Two putative homologs of NPR1 gene were found in the two sequenced grapevine genomes available in the Genoscope database for line 40024 and in the IASMA database for Pinot noir ENTAV 115. We named these two NPR1 genes of Vitis vinifera : VvNPR1.1 and VvNPR1.2. A PCR-based strategy with primers designed on exons was used to successfully amplify NPR1 gene fragments from different Vitaceae accessions. Sequence analyses show that NPR1.1 and NPR1.2 are highly conserved among the different accessions not only V. vinifera cultivars but also other species. We report nucleotide polymorphisms in NPR1.1 and NPR1.2 from fifteen accessions belonging to the Vitaceae family. The ratio of nonsynonymous to synonymous nucleotide substitutions determines the evolutionary pressures acting on the Vitaceae NPR1 genes. These genes appear to be experiencing purifying selection. In some of the species we have analysed one of the two alleles of NPR1.1 contains a premature stop codon. The deduced amino acid sequences share structural features with known NPR1-like proteins: ankyrin repeats, BTB/POZ domains, nuclear localization signature and cysteines. Phylogenetic analyses of deduced amino acid sequences show that VvNPR1.1 belongs to a first group of NPR1 proteins known as positive regulators of SAR and VvNPR1.2 belongs to a second group of NPR1 proteins whose principal members are AtNPR3 and AtNPR4 defined as negative regulators of SAR.
Conclusion
Our study shows that NPR1.1 and NPR1.2 are highly conserved among different accessions in the Vitaceae family. VvNPR1.1 and VvNPR1.2 are phylogenetically closer to the group of positive or negative SAR regulators respectively.
Reviewers
This article was reviewed by Fyodor Kondrashov, Purificación López-García and George V. Shpakovski.
doi:10.1186/1745-6150-5-9
PMCID: PMC2832633  PMID: 20137081
3.  Characterization of Vitis vinifera NPR1 homologs involved in the regulation of Pathogenesis-Related gene expression 
BMC Plant Biology  2009;9:54.
Background
Grapevine protection against diseases needs alternative strategies to the use of phytochemicals, implying a thorough knowledge of innate defense mechanisms. However, signalling pathways and regulatory elements leading to induction of defense responses have yet to be characterized in this species. In order to study defense response signalling to pathogens in Vitis vinifera, we took advantage of its recently completed genome sequence to characterize two putative orthologs of NPR1, a key player in salicylic acid (SA)-mediated resistance to biotrophic pathogens in Arabidopsis thaliana.
Results
Two cDNAs named VvNPR1.1 and VvNPR1.2 were isolated from Vitis vinifera cv Chardonnay, encoding proteins showing 55% and 40% identity to Arabidopsis NPR1 respectively. Constitutive expression of VvNPR1.1 and VvNPR1.2 monitored in leaves of V. vinifera cv Chardonnay was found to be enhanced by treatment with benzothiadiazole, a SA analog. In contrast, VvNPR1.1 and VvNPR1.2 transcript levels were not affected during infection of resistant Vitis riparia or susceptible V. vinifera with Plasmopara viticola, the causal agent of downy mildew, suggesting regulation of VvNPR1 activity at the protein level. VvNPR1.1-GFP and VvNPR1.2-GFP fusion proteins were transiently expressed by agroinfiltration in Nicotiana benthamiana leaves, where they localized predominantly to the nucleus. In this system, VvNPR1.1 and VvNPR1.2 expression was sufficient to trigger the accumulation of acidic SA-dependent Pathogenesis-Related proteins PR1 and PR2, but not of basic chitinases (PR3) in the absence of pathogen infection. Interestingly, when VvNPR1.1 or AtNPR1 were transiently overexpressed in Vitis vinifera leaves, the induction of grapevine PR1 was significantly enhanced in response to P. viticola.
Conclusion
In conclusion, our data identified grapevine homologs of NPR1, and their functional analysis showed that VvNPR1.1 and VvNPR1.2 likely control the expression of SA-dependent defense genes. Overexpression of VvNPR1 has thus the potential to enhance grapevine defensive capabilities upon fungal infection. As a consequence, manipulating VvNPR1 and other signalling elements could open ways to strengthen disease resistance mechanisms in this crop species.
doi:10.1186/1471-2229-9-54
PMCID: PMC2686700  PMID: 19432948
4.  Variation in DNA methylation patterns of grapevine somaclones (Vitis vinifera L.) 
BMC Plant Biology  2008;8:78.
Background
In traditional vine areas, the production should present a typicity that partly depends on the grapevine variety. Therefore, vine improvement is considered difficult because of the limited choice in the natural variability of the cultivars within the limits of their characteristics. A possibility to circumvent this problem is the use of somatic variability. In vitro somatic embryogenesis and organogenesis can lead to genotypic and phenotypic variations, described as somaclonal variation, that could be useful for the selection of improved grapevine genotypes.
Results
In order to study tissue culture-induced variation of grapevine, we have analysed 78 somaclones obtained from somatic embryos of two distinct cultivars using molecular marker techniques. SSRs were only useful to verify the conservation of the microsatellite genotype between the somaclones and the respective mother clones. AFLP polymorphism between mother clones and somaclones was 1.3–2.8 times higher to that found between clones. However, a majority of the somaclones (45/78) exhibited only few changes. Seven and five somaclones of 'Chardonnay 96' and 'Syrah 174', respectively, which covered at least all polymorphic loci found in AFLP analysis were used for MSAP study. All of the 120 polymorphic fragments were found only in the somaclones. The percentage of full methylation at CCGG recognition sites was slightly higher in somaclones due to more polymorphic bands generated after cleavage by EcoRI/HpaII. Different digestion patterns revealed different methylation status, especially different levels of de-methylation, that are the consequence of the in vitro culture.
Conclusion
MSAP highlights DNA methylation variation in somaclones compared to mother clones and, therefore, is a powerful tool for genotypic characterisation of somatic embryo-derived grapevines. The detection of the same polymorphic bands in numerous somaclones of different cultivars suggests the possibility of hot spots of DNA methylation variation. SSR profiles of the 'Chardonnay' and 'Syrah' somaclones were the same as of the respective mother clones. The somaclones exhibited a higher AFLP variation than clones obtained via traditional clonal selection in the field. Therefore, somatic embryogenesis through in vitro culture technique could be useful for the selection of improved cultivars with subtle changes but conserving their main characteristics.
doi:10.1186/1471-2229-8-78
PMCID: PMC2491626  PMID: 18627604
5.  Genetic chimerism of Vitis vinifera cv. Chardonnay 96 is maintained through organogenesis but not somatic embryogenesis 
BMC Plant Biology  2005;5:20.
Background
Grapevine can be a periclinal chimera plant which is composed at least of two distinct cell layers (L1, L2). When the cell layers of this plant are separated by passage through somatic embryogenesis, regenerated plants could show distinct DNA profiles and a novel phenotype which proved different from that of the parent plant.
Results
Genetically Chardonnay clone 96 is a periclinal chimera plant in which is L1 and L2 cell layers are distinct. Plants obtained via organogenesis through meristematic bulks are shown to be composed of both cell layers. However, plants regenerated through somatic embryogenesis starting from anthers or nodal explants are composed only of L1 cells. These somaclones do not show phenotypic differences to the parental clone up to three years after regeneration. Interestingly, the only somaclone showing an atypical phenotype (asymmetric leave) shows a genotypic modification.
Conclusion
These results suggest that the phenotype of Chardonnay 96 does not result from an interaction between the two distinct cell layers L1 and L2. If phenotype conformity is further confirmed, somatic embryogenesis will result in true-to-type somaclones of Chardonnay 96 and would be well suitable for gene transfer.
doi:10.1186/1471-2229-5-20
PMCID: PMC1285365  PMID: 16194273

Results 1-5 (5)