Skip to main content
SpringerLink
Log in

Genome diversity and gene haplotypes in the grapevine (Vitis vinifera L.), as revealed by single nucleotide polymorphisms

  • Published:
Molecular Breeding Aims and scope Submit manuscript

Abstract

EST (expressed sequence tags) sequencing, SNP (single nucleotide polymorphisms) development and haplotype assessment are powerful tools for the support of marker-assisted selection. The grapevine genome is currently being scavenged in our laboratory using an EST-SNP approach. Nine parental genotypes, used to create five inter- or intra-specific hybrids, have been tested to evaluate the degree of polymorphism between Vitis vinifera, Vitis riparia and a further intraspecific hybrid, measuring their nucleotide diversity. The SNPs were analysed on cDNA sequences of 4 functional classes of genes based on homology with genes present in a public database: sugar metabolism, cell signalling, anthocyanin metabolism and defence related. Primer pairs were deduced and used to amplify corresponding genomic sequences. Almost 12,000 bp of DNA have been scanned revealing differences among genotypes of up to 247 SNPs, with the highest rate of one SNP occurring every 78 bp when clones of different Vitis species are compared. Re-sequencing allowed the definition of haplotypes in the nine genotypes studied and these were confirmed by analysing segregating populations. The efficiency of SSCP, in comparison with re-sequencing, was considered for 25 gene fragments of the same 9 genotypes.

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

Access this article

Log in via an institution

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

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  • Alleweldt G. 1997. Genetics of grapevine breeding. Progress in Botany 58: 441-454.

    Google Scholar 

  • Bohn M., Utz F. and Melchinger A.E. 1999. Genetic similarities among winter wheat cultivars determined on the basis of RFLPs, AFLPs and SSRs and their use for predicting progeny variance. Crop Sci. 39: 228-237.

    Google Scholar 

  • Bonfield J.K., Rada C. and Staden R. 1998. Automated detection of point mutations using fluorescent sequence trace subtraction. Nucleic Acids Res. 26: 3404-3409.

    Google Scholar 

  • Botstein D., White R.L., Skolnick M. and Davis R.W. 1980. Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am. J. Hum. Genet. 32: 314-331.

    Google Scholar 

  • Cho R.J., Mindrinos M., Richards D.R., Sapolsky R.J., Anderson M., Drenkard E., Dewdney J., Reuber T.L., Stammers M., Federspiel N., Theologies A., Yang W.H., Hubbell E., Au M., Chung E.Y., Lashkary D., Lemieux B., Dean C., Lipshutz R.J., Ausubel F.M., Davis R.W. and Oefner P.J. 1999. Genome-wide mapping with biallelic markers in Arabidopsis thaliana. Nature Genet. 23: 203-207.

    Google Scholar 

  • Clark A.G. 1990. Inference of haplotypes from PCR-amplified samples of diploid populations. Mol. Biol. Evol. 7: 111-122.

    Google Scholar 

  • Clark A.G., Weiss K.M., Nickerson D.A., Taylor S.L., Buchanan A., Stengård J., Salomaa V., Vartiainen E., Perola M., Boerwinkle E. and Sing C.F. 1998. Haplotype structure and population genetic inferences from nucleotide-sequence variation in human lipoprotein lipase. Am. J. Hum. Genet. 63: 595-612.

    Google Scholar 

  • Collins F.S., Brooks L.D. and Chakravarti A. 1998. A DNA polymorphism discovery resource for research on human genetic variation. Genome Res. 8: 1229-1231.

    Google Scholar 

  • Dalbo' M.A., Ye G.N., Weeden N.F., Steinkellner H., Sefe K.M. and Reisch B.I. 2000. Gene controlling sex in grapevine placed on a molecular marker-based genetic map. Genome 43(2): 333-340.

    Google Scholar 

  • Doligez A., Bouquet A., Danglot Y., Lahogue F., Riaz S., Meredith C.P., Edwards K.J. and This P. 2002. Genetic mapping of grapevine (Vitis vinifera L.) applied to the detection of QTLs for seedlessness and berry weight. Theor. Appl. Genet. 105: 780-795.

    Google Scholar 

  • Doyle J.J. and Doyle J.L. 1990. Isolation of plant DNA from fresh tissue. Focus Biotech. 12: 13-15.

    Google Scholar 

  • Fischer B.M., Salakhutdinov I., Akkurt M., Eibach R., Edwards K.J., Topfer R. and Zyprian E.M. 2003. Quantitative trait locus analysis of fungal disease resistance factors on a molecular map of grapevine. Theor. Appl. Genet. Oct. 22: 000.

    Google Scholar 

  • Fullerton S.M., Clark A.G., Weiss K.M., Nickerson D.A., Taylor S.L., Stengard J.H., Salomaa V., Vartiainen E., Perola M., Boerwinkle E. and Sing C.F. 2000. Apolipoprotein E variation at the sequence haplotype level: implications for the origin and maintenance of a major human polymorphism. Am. J. Hum. Genet. 67: 881-900.

    Google Scholar 

  • Grando M.S., Bellin D., Edwards K.J., Pozzi C., Stefanini M. and Velasco R. 2003. Molecular linkage maps of Vitis vinifera and Vitis riparia. Theor. Appl. Gen. 106: 1213-1224.

    Google Scholar 

  • Hayashi K. 1999. Recent enhancements in SSCP. Genetic Analysis: Biomolecular Engineering 14: 193-196.

    Google Scholar 

  • Kanazin V., Talbert H., See D., DeCamp P., Nevo E. and Blake T. 2002. Discovery and assay of single-nucleotide polymorphisms in barley (Hordeum vulgare). Plant Mol. Biol. 48: 529-537.

    Google Scholar 

  • Landgreen U., Nilsson M. and Kwok P.Y. 1998. Reading bits of genetic information. Methods for single nucleotide polymorphism analysis. Genome Res. 8: 769-776.

    Google Scholar 

  • Li W.H. and Sadler L.A. 1991. Low nucleotide diversity in man. Genetics 129: 513-523.

    Google Scholar 

  • Lindblad-Toh K., Wibchester E., Daly M.J., Wang D.G., Hirchhorn J.N., Laviolette J.P., Ardlie K., Reich D.E., Robinson E., Sklar P., Shah N., Thomas D., Fan J.B., Gigeras T., Warrington J., Patil N., Hudson T.J. and Lander E.S. 2000. Large-scale discovery and genotyping of single-nucleotide polymorphisms in the mouse. Nature Genet. 24: 381-386.

    Google Scholar 

  • Lodhi M.A. and Reisch B.I. 1995. Nuclear DNA content of Vitis species, cultivars, and other genera of the Vitaceae. Theor. Appl. Genet. 90: 11-16.

    Google Scholar 

  • McCallum C.M., Comai L., Greene E.A. and Henikoff S. 2000. Targeted screening for induced mutations. Nature Biotech. 18: 455-457.

    Google Scholar 

  • Nei M. and Li W.H. 1979. Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc. Natl. Acad. Sci. USA 76: 5269-5273.

    Google Scholar 

  • Nei M. and Tajima F. 1981. DNA polymorphism detectable by restriction endonucleases. Genetics 97: 145-163.

    Google Scholar 

  • Orita M., Iwahana H., Kanazawa H., Hayashi K. and Sekiya T. 1989. Detection of polymorphisms of human DNA by gel electrophoresis as single strand conformational polymorphisms. Proc. Natl. Acad. Sci. USA 86: 2766-2770.

    Google Scholar 

  • Powell W., Morgante M., Andre C., Hanafey M., Vogel J., Tingey S.D. and Rafalsky A. 1996. The comparison of RFLP, RAPD, 394.AFLP and SSR (microsatellite) markers for germplasm analysis. Mol. Breed. 2: 225-238.

    Google Scholar 

  • Rafalski A. 2002. Application of single nucleotide polymorphisms in crop genetics. Curr. Op. Plant Biol. 5: 94-100.

    Google Scholar 

  • Riaz S., Dangl G.S., Edwards K.J. and Meredith C.P. 2003. A microsatellite based framework linkage map of Vitis vinifera L. Theor. Appl. Genet. Nov 6: 000.

    Google Scholar 

  • Rozen S. and Skaletsky H.J. 2000. Primer3 on the WWW for general users and for biologist programmers. In: Krawetz S., Misener S. (eds), Bioinformatics Methods and Protocols: Methods in Molecular Biology. Humana Press, Totowa, New Jersey, pp. 365-386.

    Google Scholar 

  • Sanguinetti C.J., Dias Neto E. and Simpson A.J. 1994. Rapid silver staining and recovery of PCR products separated on poly-acrylamide gels. Biotechniques 17: 914-21.

    Google Scholar 

  • Sachidanandam R., Weissman D., Schmidt S.C., Kakol J.M., Stein L.D., Marth G., Sherry S., Mulikin J.C., Mortimore B.J. and Willey D.L. 2001. A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature 409: 928-933.

    Google Scholar 

  • Sheffield V.C., Beck J.S., Kwitek A.E., Sandstrom D.W. and Stone E.M. 1993. The sensitivity of single strand conformational polymorphism analysis for the detection of single base substitutions. Genomics 16: 325-332.

    Google Scholar 

  • Schneider K., Borchardt D., Schaefer-Pregl R., Nagl N., Glass C., Jeppson A., Gebhardt C. and Salamini F. 1999. PCR-based cloning and segregation analysis of functional gene homologues in Beta vulgaris. Mol. Gen. Genet. 262: 515-524.

    Google Scholar 

  • Schneider K., Weisshaar B., Borchardt D.C. and Salamini F. 2001. SNPs frequency and allelic haplotype structure of Beta vulgaris expressed genes. Mol. Breed. 8: 63-74.

    Google Scholar 

  • Stephens J.C., Schneider J.A., Tanguay D.A., Choi J., Acharya T., Stanley S.E., Jiang R., Messer C.J., Chew A., Han J.H., Duan J., Carr J.L., Lee M.S., Koshy B., Kumar A.M., Zhang G., Newell W.R., Windemuth A., Xu C., Kalbfleisch T.S., Shaner S.L., Arnold K., Schulz V., Drysdale C.M., Nandabalan K., Judson R.S., Ruano G. and Vovis G.F. 2001. Haplotype variation and linkage disequilibrium in 313 human genes. Science 293: 489-493.

    Google Scholar 

  • Taramino T. and Tingey S.D. 1996. Simple sequence repeats for germplasm analysis and mapping in maize. Genome 39: 277-287.

    Google Scholar 

  • Thomas M.R., Matsumoto S., Cain P. and Scott N.S. 1993. Repetitive DNA of grapevine: classes present and sequences suitable for cultivar identification. Theor. Appl. Genet. 86: 286-289.

    Google Scholar 

  • Thornsberry J.M., Goodman M.M., Doebley J., Kresovich S., Nielsen D. and Buckler E.S. 2001. Dwarf8 polymorphisms associate with variation in flowering time. Nat. Genet. 28: 286-289.

    Google Scholar 

  • Tenaillon M.I., Sawkins M.C., Long A.D., Gaut R.L., Doebley J.F. and Gaut B.S. 2001. Patterns of DNA sequence polymorphism along chromosome 1 of maize (Zea mays ssp. Mays L). Proc. Natl. Acad. Sci. USA 98: 9161-9166.

    Google Scholar 

  • Viard F., Frank P., Dubois M.P., Estoup A. and Jarne P. 1998. Variation of microsatellite size homoplasy across electromorphs, loci, and populations in three invertebrate species. J. Mol. Evol. 47: 42-51.

    Google Scholar 

  • White M.B., Carvalho M., Derse D., O'Brien S.J. and Dean M. 1992. Detecting single base substitutions as heteroduplex ploymorphisms. Genomics 12: 301-305.

    Google Scholar 

  • Zhu Y.L., Song Q.J., Hyten D.L., Van Tassel C.P., Matukumalli L.K., Grimm D.R., Hyatt S.M., Fickus E.W., Young N.D., Cregan P.B. 2003. Single-Nucleotide Polymorphisms in Soy-bean. Genetics 168: 1123-1134.

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Istituto Agrario San Michele all'Adige, via Mach 1, I-38010, San Michele a/A (TN)

    Marzia Salmaso, Giorgia Faes, Cinzia Segala, Marco Stefanini, M. Stella Grando & Riccardo Velasco

  2. Federal Centre of Breeding Research on Cultivated Plants, Institute for Grapevine Breeding Geilweilerhof, D-76833, Siebeldingen

    Ilkhom Salakhutdinov, Eva Zyprian & Reinhard Toepfer

  3. Dept. of Environmental Agronomy and Crop Production, Agripolis, University of Padova, I-35020, Legnaro (PD)

    Marzia Salmaso

  4. Dept. of Plant Production, University of Udine, via delle Scienze 208, I-33100, Udine

    Giorgia Faes

Authors
  1. Marzia Salmaso
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Giorgia Faes
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Cinzia Segala
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Marco Stefanini
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Ilkhom Salakhutdinov
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Eva Zyprian
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Reinhard Toepfer
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. M. Stella Grando
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Riccardo Velasco
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Riccardo Velasco.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Salmaso, M., Faes, G., Segala, C. et al. Genome diversity and gene haplotypes in the grapevine (Vitis vinifera L.), as revealed by single nucleotide polymorphisms. Molecular Breeding 14, 385–395 (2004). https://doi.org/10.1007/s11032-004-0261-z

Download citation

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11032-004-0261-z

Search

Navigation