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


Ontology type: schema:ScholarlyArticle     


Article Info

DATE

2004-12

AUTHORS

Marzia Salmaso, Giorgia Faes, Cinzia Segala, Marco Stefanini, Ilkhom Salakhutdinov, Eva Zyprian, Reinhard Toepfer, M. Stella Grando, Riccardo Velasco

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. More... »

PAGES

385-395

References to SciGraph publications

  • 2000-04. Targeted screening for induced mutations in NATURE BIOTECHNOLOGY
  • 2001-08. SNP frequency and allelic haplotype structure of Beta vulgaris expressed genes in MOLECULAR BREEDING
  • 1999-10. Genome-wide mapping with biallelic markers in Arabidopsis thaliana in NATURE GENETICS
  • 2000-04. Large-scale discovery and genotyping of single-nucleotide polymorphisms in the mouse in NATURE GENETICS
  • 1997. Genetics of Grapevine Breeding in PROGRESS IN BOTANY
  • 2001-07. Dwarf8 polymorphisms associate with variation in flowering time in NATURE GENETICS
  • 2002-10. Genetic mapping of grapevine (Vitis vinifera L.) applied to the detection of QTLs for seedlessness and berry weight in THEORETICAL AND APPLIED GENETICS
  • 2001-02. A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms in NATURE
  • 1993-04. Repetitive DNA of grapevine: classes present and sequences suitable for cultivar identification in THEORETICAL AND APPLIED GENETICS
  • 1998-07. Variation of Microsatellite Size Homoplasy Across Electromorphs, Loci, and Populations in Three Invertebrate Species in JOURNAL OF MOLECULAR EVOLUTION
  • 2002-03. Discovery and assay of single-nucleotide polymorphisms in barley (Hordeum vulgare) in PLANT MOLECULAR BIOLOGY
  • 1995-01. Nuclear DNA content of Vitis species, cultivars, and other genera of the Vitaceae in THEORETICAL AND APPLIED GENETICS
  • 1996-09. The comparison of RFLP, RAPD, AFLP and SSR (microsatellite) markers for germplasm analysis in MOLECULAR BREEDING
  • 1999-11. PCR-based cloning and segregation analysis of functional gene homologues in Beta vulgaris in MOLECULAR GENETICS AND GENOMICS
  • 2003-05. Molecular linkage maps of Vitis vinifera L. and Vitis riparia Mchx in THEORETICAL AND APPLIED GENETICS
  • Journal

    TITLE

    Molecular Breeding

    ISSUE

    4

    VOLUME

    14

    Author Affiliations

    Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1007/s11032-004-0261-z

    DOI

    http://dx.doi.org/10.1007/s11032-004-0261-z

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1002210556


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