High-Throughput SNP Genotyping in Grapevine
Author Information
Author(s): Pindo Massimo, Vezzulli Silvia, Coppola Giuseppina, Cartwright Dustin A, Zharkikh Andrey, Velasco Riccardo, Troggio Michela
Primary Institution: IASMA Research Center
Hypothesis
Can the SNPlex genotyping system be effectively applied to grapevine for high-throughput SNP discovery?
Conclusion
The SNPlex genotyping system is an effective method for investigating several hundred SNPs in a large number of grapevine samples simultaneously.
Supporting Evidence
- 813 candidate eSNPs were developed and tested.
- 563 new SNP-based markers were obtained and mapped.
- The efficiency rate improved from 69% to 80% with MDA methods.
Takeaway
This study shows a new way to quickly check many tiny differences in grapevine DNA, which can help scientists learn more about grapes.
Methodology
The study used the SNPlex genotyping system to analyze genomic DNA from 90 grapevine progeny and developed 563 new SNP markers.
Potential Biases
Potential bias due to SNPlex probe design based on preliminary contig assembly.
Limitations
The study noted a 10% rate of systematic failed assays and 21% false polymorphisms.
Participant Demographics
90 F1 progeny from a Syrah × Pinot Noir cross and two parental genotypes.
Digital Object Identifier (DOI)
Want to read the original?
Access the complete publication on the publisher's website