Allen Van Deynze, University of California, Davis; Heather L. Merk, The Ohio State University
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.
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.
Infinium_Genotyping.pdf (1.93 MB)