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Open Access Methodology article

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

Massimo Pindo1*, Silvia Vezzulli1, Giuseppina Coppola1, Dustin A Cartwright2, Andrey Zharkikh2, Riccardo Velasco1 and Michela Troggio1

Author Affiliations

1 IASMA Research Center, Via E. Mach, 1 – I 38010 – San Michele all'Adige, Italy

2 Myriad Genetics Inc, Wakara Way, 320 – UT 84108 – Salt Lake City, USA

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BMC Plant Biology 2008, 8:12  doi:10.1186/1471-2229-8-12

Published: 28 January 2008

Abstract

Background

Until recently, only a small number of low- and mid-throughput methods have been used for single nucleotide polymorphism (SNP) discovery and genotyping in grapevine (Vitis vinifera L.). However, following completion of the sequence of the highly heterozygous genome of Pinot Noir, it has been possible to identify millions of electronic SNPs (eSNPs) thus providing a valuable source for high-throughput genotyping methods.

Results

Herein we report the first application of the SNPlex™ genotyping system in grapevine aiming at the anchoring of an eukaryotic genome. This approach combines robust SNP detection with automated assay readout and data analysis. 813 candidate eSNPs were developed from non-repetitive contigs of the assembled genome of Pinot Noir and tested in 90 progeny of Syrah × Pinot Noir cross. 563 new SNP-based markers were obtained and mapped. The efficiency rate of 69% was enhanced to 80% when multiple displacement amplification (MDA) methods were used for preparation of genomic DNA for the SNPlex assay.

Conclusion

Unlike other SNP genotyping methods used to investigate thousands of SNPs in a few genotypes, or a few SNPs in around a thousand genotypes, the SNPlex genotyping system represents a good compromise to investigate several hundred SNPs in a hundred or more samples simultaneously. Therefore, the use of the SNPlex assay, coupled with whole genome amplification (WGA), is a good solution for future applications in well-equipped laboratories.