Skip to main content
Log in

Untranslated leader region polymorphism of Tvv1, a retrotransposon family, is a novel marker useful for analyzing genetic diversity and relatedness in the genus Vitis

  • Original Paper
  • Published:
Theoretical and Applied Genetics Aims and scope Submit manuscript

Abstract

Grapevine retrotransposons belonging to the Tvv1 family share a single, highly conserved open reading frame but differ by their untranslated leader (UTL) region, which is highly variable in size. Amplification of the UTL region of Tvv1 elements from 94 Vitaceae accessions reveals that each of them shows a unique pattern of UTL-derived bands, which is inherited in progenies but conserved between clones vegetatively propagated. The overall organization of genetic diversity of the Vitaceae at the inter and intraspecific level and relatedness among accessions described by UTL-derived bands was compared to those obtained using 15 microsatellite loci. Both fingerprinting methods show a similar grouping of Vitis vinifera accessions but UTL-based fingerprinting more accurately isolates the muscadine grapes from the American and Asian Vitis. Finally, sequence analysis of seven UTL regions determines that their size variation is essentially caused by large deletions/insertions within the internal region, whereas flanking regions are more conserved. UTL-based fingerprinting could be considered as a novel marker system specific of the genus Vitis; moreover, as this multiband genotype is stable between clones it is suitable to be used as a “DNA barcode” for Vitis identification.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6

Similar content being viewed by others

References

  • Adam-Blondon A-F, Roux C, Claux D, Butterlin G, Merdinoglu D, This P (2004) Mapping 245 SSR markers on the Vitis vinifera genome: a tool for grape genetics. Theor Appl Genet 109:1017–1027

    Article  PubMed  CAS  Google Scholar 

  • Aradhya MK, Dangl GS, Prins BH, Boursiquot JM, Walker MA, Meredith CP, Simon CJ (2003) Genetic structure and differentiation in cultivated grape, Vitis vinifera L. Genet Res 81:179–191

    Article  PubMed  CAS  Google Scholar 

  • Arroyo-Garcia R, Ruiz-Garcia L, Boulling L, Ocete R, López MA, Arnold C, Ergul A, Söylemezo-lu G, Uzun IH, Cabello F, Ibáñez J, Aradhya MK, Atanassov A, Atanassov I, Balint S, Cenis JL, Constantini L, Gorislavets S, Grando S, Klein B, McGovern P, Merdinoglu D, Pejic I, Pelsy F, Primikirios N, Risovannaya V, Roubelakis-Angelakis K, Snoussi H, Sotiri P, Tamhankar S, This P, Troshin L, Malpica JM, Lefort F, Martinez-Zapater J (2006) Multiple origins of cultivated grapevine (Vitis vinifera L. ssp. sativa) based on chloroplast DNA polymorphisms. Mol Ecol 15:3707–3714

    Article  PubMed  CAS  Google Scholar 

  • Bailey LH (1934) The species of grapes peculiar to North America. Gentes Herb 3:154–244

    Google Scholar 

  • Bennetzen JL, SanMiguel P, Chen M, Tikhonov A, Francki M, Avramova Z (1998) Grass genomes. Proc Natl Acad Sci USA 95:1975–1978

    Article  PubMed  CAS  Google Scholar 

  • Bowers J, Meredith C (1997) The parentage of a classic wine grape, Cabernet Sauvignon. Nature Genet 16:84–87

    Article  PubMed  CAS  Google Scholar 

  • Bowers JE, Boursiquot JM, This P, Chu K, Johansson H, Meredith CP (1999a) Historical genetics: the parentage of Chardonnay, Gamay, and other wine grapes of northeastern France. Science 285:1562–1565

    Article  PubMed  CAS  Google Scholar 

  • Bowers JE, Dangl GS, Meredith CP (1999b) Development and characterization of additional microsatellite DNA markers for grape. Am J Enol Vitic 50:243–246

    CAS  Google Scholar 

  • Brookfield JFY (1996) A simple new method for estimating null allele frequency from heterozygote deficiency. Mol Ecol 5:453–455

    Article  PubMed  CAS  Google Scholar 

  • Casacuberta JM, Grandbastien M-A (1993) Characterisation of LTR sequences involved in the protoplast specific expression of the tobacco Tnt1 retrotransposon. Nucl Acids Res 21:2087–2093

    Article  PubMed  CAS  Google Scholar 

  • Casacuberta JM, Vernhettes S, Grandbastien M-A (1995) Sequence variability within the tobacco retrotransposon Tnt1 population. EMBO J 14:2670–2678

    PubMed  CAS  Google Scholar 

  • Di Gaspero G, Peterlunger E, Testolin R, Edwards KJ, Cipriani G (2000) Conservation of microsatellite loci within the genus Vitis. Theor Appl Genet 101:301–308

    Article  CAS  Google Scholar 

  • Di Gaspero G, Cipriani G, Marrazzo M, Andreetta D, Prado Castro M, Peterlunger E, Testolin R (2005) Isolation of (AC)n-microsatellites in Vitis vinifera L. and analysis of genetic background in grapevines under marker assisted selection. Mol Breeding 15:11–20

    Article  Google Scholar 

  • Doligez A, Adam-Blondon A-F, Cipriani G, Di Gaspero G, Laucou V, Merdinoglu D, Meredith CP, Riaz S, Roux C, This P (2006) An integrated SSR map of grapevine based on five mapping populations. Theor Appl Genet 113:369–382

    Article  PubMed  CAS  Google Scholar 

  • Fablet M, McDonald JF, Biemont C, Vieira C (2006) Ongoing loss of the tirant transposable element in natural populations of Drosophila simulans. Gene 375:54–62

    Article  PubMed  CAS  Google Scholar 

  • Flavell AJ, Dunbar E, Anderson R, Pearce SR, Hartley R, Kumar A (1992) Ty1-copia group retrotransposons are ubiquitous and heterogeneous in higher plants. Nucl Acids Res 20:3639–3644

    Article  PubMed  CAS  Google Scholar 

  • Flavell AJ, Knox MR, Pearce SR, Ellis THN (1998) Retrotransposon-based insertion polymorphisms (RBIP) for high throughput marker analysis. Plant J 16:643–650

    Article  PubMed  CAS  Google Scholar 

  • Franks T, Botta R, Thomas MR (2002) Chimerism in grapevines: implications for cultivar identity, ancestry and genetic improvement. Theor Appl Genet 104:192–199

    Article  PubMed  CAS  Google Scholar 

  • Galtier N, Gouy M, Gautier C (1996) SeaView and Phylo-win, two graphic tools for sequence alignment and molecular phylogeny. Comput Appl Biosci 12:543–548

    PubMed  CAS  Google Scholar 

  • Gerrath J, Lacroix C, Posluszny U (1998) Phyllotaxis in the Vitaceae. World Scientific, Singapore, pp 89–107

    Google Scholar 

  • Goldy RG, Onokpise OU (2001) Muscadine grapes. Genetics and breeding In: Basiouny FM, Himelrick DG (eds) ASHS crop production series. ASHS Press, Alexandria, pp 51–90

    Google Scholar 

  • Hocquigny S, Pelsy F, Dumas V, Kindt S, Héloir MC, Merdinoglu D (2004) Diversification within grapevine cultivars goes through chimeric states. Genome 47:579–589

    Article  PubMed  CAS  Google Scholar 

  • Ingrouille MJ, Chase MW, Fay MF, Bowman D, Bank Mvd, Bruijn ADE (2002) Systematics of Vitaceae from the viewpoint of plastid rbcL DNA sequence data. Bot J Linean Soc 138:421–432

    Article  Google Scholar 

  • Kumar A, Bennetzen JL (1999) Plant retrotransposons. Annu Rev Genet 33:479–532

    Article  PubMed  CAS  Google Scholar 

  • Lefort F, Pelsy F, Schehrer L, Scott KD, Merdinoglu D (2003) Assessment of two highly polymorphic microsatellite loci in 103 accessions of Vitis species. J Int Sci Vigne Vin 37:67–74

    CAS  Google Scholar 

  • Ma JX, Devos KM, Bennetzen JL (2004) Analyses of LTR-retrotransposon structures reveal recent and rapid genomic DNA loss in rice. Genome Res 14:860–869

    Article  PubMed  CAS  Google Scholar 

  • Manninen I, Schulman AH (1993) BARE-I, a copia-like retroelement in barley (Hordeum vulgare). Plant Mol Biol 22:829–864

    Article  PubMed  CAS  Google Scholar 

  • Marillonnet S, Wessler SR (1998) Extreme structural heterogeneity among the members of a maize retrotransposon family. Genetics 150:1245–1256

    PubMed  CAS  Google Scholar 

  • Merdinoglu D, Butterlin G, Bevilacqua L, Chiquet V, Adam-Blondon A-F, Decroocq S (2005) Development and characterization of a large set of microsatellite markers in grapevine (Vitis vinifera L.) suitable for multiplex PCR. Mol Breed 15:349–366

    Article  CAS  Google Scholar 

  • Meredith CP (2001) Grapevine genetics: probing the past and facing the future. Agric Conspec Sci 66:21–25

    Google Scholar 

  • Meyers BC, Scott V, Tingey, Morgante M (2001) Abundance, distribution, and transcriptional activity of repetitive elements in the maize genome. Genome Res 11:1660–1676

    Article  PubMed  CAS  Google Scholar 

  • Mugnier N, Biemont C, Vieira C (2005) New regulatory regions of Drosophila 412 retrotransposable element generated by recombination. Mol Biol Evol 22:747–757

    Article  PubMed  CAS  Google Scholar 

  • Nei M (1973) Analysis of gene diversity in subdivided populations. Proc Natl Acad Sci USA 70:3321–3332

    Article  PubMed  CAS  Google Scholar 

  • Peakall R, Smouse PE (2006) GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol Ecol Notes 6:288–295

    Article  Google Scholar 

  • Pelsy F, Merdinoglu D (2002) Complete sequence of Tvv1, a family of Ty1 copia-like retrotransposons of Vitis vinifera L., reconstituted by chromosome walking. Theor Appl Genet 105:614–621

    Article  PubMed  CAS  Google Scholar 

  • Pouteau S, Huttner E, Grandbastien MA, Caboche M (1991) Specific expression of the tobacco Tnt1 retrotransposon in protoplasts. EMBO J 10:1911–1918

    PubMed  CAS  Google Scholar 

  • Preston BD (1996) Error-prone retrotransposition: rime of the ancient mutators. Proc Natl Acad Sci USA 93:7427–7431

    Article  PubMed  CAS  Google Scholar 

  • Sefc KM, Regner F, Turetschek E, Glossl J, Steinkellner H (1999) Identification of microsatellite sequences in Vitis riparia and their applicability for genotyping of different Vitis species. Genome 42:367–373

    Article  PubMed  CAS  Google Scholar 

  • Sefc KM, Lefort F, Grando MS, Scott KD, Steinkellner H, Thomas MR (2001) Microsatellite markers for grapevine: A state of the art. Mol Biol Biotechnol Grapevine 463:433–463

    Google Scholar 

  • Soejima A, Wen J (2006) Phylogenetic analysis of the grape family (Vitaceae) based on three chloroplast markers. Am J Bot 93:278–287

    CAS  Google Scholar 

  • Suoniemi A, Tanskanen J, Schulman AH (1998) Gypsy-like retrotransposons are widespread in the plant kingdom. Plant J 13:699–705

    Article  PubMed  CAS  Google Scholar 

  • This P, Jung A, Boccacci P, Borrego J, Botta R, Costantini L, Crespan M, Dangl GS, Eisenheld C, Ferreira-Monteiro F, Grando S, Ibanez J, Lacombe T, Laucou V, Magalhaes R, Meredith CP, Milani N, Peterlunger E, Regner F, Zulini L, Maul E (2004) Development of a standard set of microsatellite reference alleles for identification of grape cultivars. Theor Appl Genet 109:1448–1458

    Article  PubMed  CAS  Google Scholar 

  • Thomas M, Scott N (1994) Microsatellite sequence tagged site markers: simplified technique for rapidly obtaining flanking sequences. Plant Mol Biol 12:58–64

    CAS  Google Scholar 

  • Vicient C, Kalendar R, Schulman A (2005) Variability, recombination, and mosaic evolution of the barley BARE-1 retrotransposon. J Mol Evol 61:275–291

    Article  PubMed  CAS  Google Scholar 

  • Voytas DF, Cumming MP, Konieczny A, Ausubel FM, Rodermel SR (1992) Copia-like retrotransposons are ubiquitous among plants. Proc Natl Acad Sci USA 89:7124–7128

    Article  PubMed  CAS  Google Scholar 

  • Waugh R, McLean K, Flavell AJ, Pearce SR, Kumar A, Thomas BBT, Powell W (1997) Genetic distribution of Bare-1-like retrotransposable elements in the barley genome revealed by sequence-specific amplification polymorphisms (S-SAP). Mol Gen Genet 253:687–694

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgments

The authors thank Lucie Bevilacqua-Schehrer for valuable technical assistance, Didier Merdinoglu for helpful comments and Pere Mestre for his careful revision of the English. All experiments described in this study comply with the current laws of France.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Frédérique Pelsy.

Additional information

Communicated by A. Schulman.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Pelsy, F. Untranslated leader region polymorphism of Tvv1, a retrotransposon family, is a novel marker useful for analyzing genetic diversity and relatedness in the genus Vitis . Theor Appl Genet 116, 15–27 (2007). https://doi.org/10.1007/s00122-007-0643-9

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00122-007-0643-9

Keywords

Navigation