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Working with Tomato Infinium Genotyping Data Webinar

Last Updated: January 31, 2012

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Authors:

Allen Van Deynze, University of California, Davis

Heather L. Merk, The Ohio State University

This webinar and the accompanying pdf (located at the bottom of the page), presented at the 2010 Tomato Disease Workshop, provide an introduction to Infinium genotyping data and demonstrate the utility of Illumina Genome Studio software. The discussion of Illumina Genome Studio software covers data manipulation, data quality analysis, and data exporting.

In the first video, Dr. Van Deynze, University of California, Davis, discusses the Illumina genotyping platform that SolCAP used for SNP genotyping in tomato and potato.

In the second video, Dr. Van Deynze discusses the germplasm that was sequenced to develop single nucleotide polymorphism (SNP) markers for the SolCAP SNP array. In addition, Dr. Van Deynze discusses the technical and biological considerations when the candidate SNPs were developed.

In the third video, Dr. Van Deynze describes validation and polymorphism rates for the SolCAP tomato SNP array. In addition, Dr. Van Deynze describes how the BeadXpress genotyping platform works.

In the fourth video, Dr. Van Deynze describes the design of the SolCAP community tomato SNP array.

In the fifth video, Dr. Van Deynze provides an introduction to Illumina's Genome Studio software. Genome Studio can be used to analyze SNP genotyping data.

In the sixth video, Dr. Van Deynze demonstrates how to manually define clusters in Genome Studio. In addition, Dr. Van Deynze demonstrates how a cluster file calls SNPs and how to import and export cluster files.

In the seventh video, Dr. Van Deynze highlights some of the tools available in Genome Studio for working with samples and SNPs individually and as a group. Dr. Van Deynze also discusses the importance of selecting appropriate germplasm for genotyping with the SolCAP tomato SNP array.

In the eighth video, Dr. Van Deynze discusses SNP data quality analysis using the GenTrain score in Genome Studio.

In the ninth video, Dr. Van Deynze demonstrates how to export statistical data and genotype data from Genome Studio, and he discusses relevant data that users may want to export.

Find all the presentations from the 2010 Tomato Disease Workshop

Additional Resources

Molecular Markers as Size and Sequence Variants

Funding Statement

Development of this lesson was supported in part by the National Institute of Food and Agriculture (NIFA) Solanaceae Coordinated Agricultural Project, agreement 2009-85606-05673, administered by Michigan State University. Any opinions, findings, conclusions, or recommendations expressed in this publication are those of the author(s) and do not necessarily reflect the view of the United States Department of Agriculture.

Mention of specific companies is not intended for promotional purposes.

Attachments:

Infinium_Genotyping.pdf (1.93 MB)

PBGworks 1004

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