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Related Experiment Videos

SNP high-throughput screening in grapevine using the SNPlex genotyping system.

Massimo Pindo1, Silvia Vezzulli, Giuseppina Coppola

  • 1IASMA Research Center, Via E, Mach, 1 - I 38010 - San Michele all'Adige, Italy. massimo.pindo@iasma.it

BMC Plant Biology
|January 30, 2008
PubMed
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The SNPlex genotyping system offers a high-throughput method for grapevine (Vitis vinifera L.) research, enabling the simultaneous analysis of hundreds of single nucleotide polymorphisms (SNPs) in numerous samples. This approach is valuable for genetic studies in well-equipped laboratories.

Area of Science:

  • Plant Genomics
  • Molecular Genetics
  • Bioinformatics

Background:

  • Traditional grapevine (Vitis vinifera L.) single nucleotide polymorphism (SNP) discovery and genotyping methods were low- to mid-throughput.
  • The availability of the highly heterozygous Pinot Noir genome sequence enabled the identification of millions of electronic SNPs (eSNPs).
  • eSNPs provide a resource for developing high-throughput genotyping methods in grapevine.

Purpose of the Study:

  • To report the first application of the SNPlex genotyping system in grapevine.
  • To anchor an eukaryotic genome using SNP-based markers.
  • To evaluate the efficiency of the SNPlex assay for high-throughput genotyping in grapevine.

Main Methods:

  • Development of 813 candidate eSNPs from non-repetitive contigs of the Pinot Noir genome.

Related Experiment Videos

  • Application of the SNPlex genotyping system to test these eSNPs in 90 progeny of a Syrah x Pinot Noir cross.
  • Utilized multiple displacement amplification (MDA) for genomic DNA preparation to enhance assay efficiency.

    • Main Results:

    • Successfully obtained and mapped 563 new SNP-based markers.
    • Achieved an initial efficiency rate of 69% for SNP detection.
    • Enhanced the efficiency rate to 80% by employing MDA methods for DNA preparation.

    Conclusions:

    • The SNPlex genotyping system provides a balanced approach for investigating hundreds of SNPs across numerous genotypes simultaneously.
    • This method is advantageous compared to those analyzing thousands of SNPs in few genotypes or few SNPs in many genotypes.
    • The combination of the SNPlex assay and whole genome amplification (WGA) is a viable solution for high-throughput grapevine genotyping in advanced laboratories.