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      Variation in DNA methylation patterns of grapevine somaclones ( Vitis vinifera L.)

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          Abstract

          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.

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          Most cited references38

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          AFLP: a new technique for DNA fingerprinting.

          A novel DNA fingerprinting technique called AFLP is described. The AFLP technique is based on the selective PCR amplification of restriction fragments from a total digest of genomic DNA. The technique involves three steps: (i) restriction of the DNA and ligation of oligonucleotide adapters, (ii) selective amplification of sets of restriction fragments, and (iii) gel analysis of the amplified fragments. PCR amplification of restriction fragments is achieved by using the adapter and restriction site sequence as target sites for primer annealing. The selective amplification is achieved by the use of primers that extend into the restriction fragments, amplifying only those fragments in which the primer extensions match the nucleotides flanking the restriction sites. Using this method, sets of restriction fragments may be visualized by PCR without knowledge of nucleotide sequence. The method allows the specific co-amplification of high numbers of restriction fragments. The number of fragments that can be analyzed simultaneously, however, is dependent on the resolution of the detection system. Typically 50-100 restriction fragments are amplified and detected on denaturing polyacrylamide gels. The AFLP technique provides a novel and very powerful DNA fingerprinting technique for DNAs of any origin or complexity.
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            Somaclonal variation - a novel source of variability from cell cultures for plant improvement.

            It is concluded from a review of the literature that plant cell culture itself generates genetic variability (somaclonal variation). Extensive examples are discussed of such variation in culture subclones and in regenerated plants (somaclones). A number of possible mechanisms for the origin of this phenomenon are considered. It is argued that this variation already is proving to be of significance for plant improvement. In particular the phenomenon may be employed to enhance the exchange required in sexual hybrids for the introgression of desirable alien genes into a crop species. It may also be used to generate variants of a commercial cultivar in high frequency without hybridizing to other genotypes.
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              Association of dwarfism and floral induction with a grape 'green revolution' mutation.

              The transition from vegetative to reproductive growth is an essential process in the life cycle of plants. Plant floral induction pathways respond to both environmental and endogenous cues and much has been learnt about these genetic pathways by studying mutants of Arabidopsis. Gibberellins (GAs) are plant growth regulators important in many aspects of plant growth and in Arabidopsis they promote flowering. Here we provide genetic evidence that GAs inhibit flowering in grapevine. A grapevine dwarf mutant derived from the L1 cell layer of the champagne cultivar Pinot Meunier produces inflorescences along the length of the shoot where tendrils are normally formed. The mutated gene associated with the phenotype is a homologue of the wheat 'green revolution' gene Reduced height-1 (ref. 6) and the Arabidopsis gene GA insensitive (GAI). The conversion of tendrils to inflorescences in the mutant demonstrates that the grapevine tendril is a modified inflorescence inhibited from completing floral development by GAs.
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                Author and article information

                Journal
                BMC Plant Biol
                BMC Plant Biology
                BioMed Central
                1471-2229
                2008
                15 July 2008
                : 8
                : 78
                Affiliations
                [1 ]Université de Haute Alsace, Laboratoire Vigne Biotechnologies & Environnement, 33 rue de Herrlisheim, BP 50568, F-68008 Colmar, France
                [2 ]Technische Universität München, Lehrstuhl für Pflanzenzüchtung, Am Hochanger 2, D-85350 Freising-Weihenstephan, Germany
                [3 ]Bavarian State Research Centre for Agriculture, Institute for Crop Science and Plant Breeding, Am Gereuth 8, D-85354 Freising, Germany
                Article
                1471-2229-8-78
                10.1186/1471-2229-8-78
                2491626
                18627604
                cc907dc4-e134-4307-9fbe-67461cb2881f
                Copyright © 2008 Schellenbaum et al; licensee BioMed Central Ltd.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 4 December 2007
                : 15 July 2008
                Categories
                Research Article

                Plant science & Botany
                Plant science & Botany

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