Webinar at Extension:

Video Tutorial of Downstream Analysis with SNP Markers Using MSA, GGT, and STRUCTURE software

This webinar tutorial and the accompanying pdf and zip files were presented at the 2010 Tomato Disease Workshop. These materials outline the utility of MSA, GGT, and STRUCTURE software for downstream analysis with single nucleotide polymorphism (SNP) markers. In addition, a case study demonstrates the use of STRUCTURE for association mapping of bacterial spot resistance in tomato.

The pdf at the bottom of the page (Downstream_SNP_Analysis) is a copy of Dr. Sim's presentation. The accompanying zip files (Downstream_Supplemental_Files) at the bottom of the page include a sample data set, an Excel file with best K analysis, and SAS code for association analysis that incorporates the Q matrix.

In the first video, Dr. Sung-Chur Sim, The Ohio State University, outlines the utility of MSA, GGT, and STRUCTURE software for downstream analysis with single nucelotide polymorphism (SNP) markers. Dr. Sim also explains where and how to download the software and how to format input data.

In the second video, Dr. Sim demonstrates the use of STRUCTURE for association mapping of bacterial spot resistance in tomato. Dr. Sim introduces association analysis models and emphasizes the use of the Q matrix to correct for population structure in association mapping. In addition, Dr. Sim explains the detailed steps in STRUCTURE to infer the best "K" (number of populations), which is required to obtain the Q matrix.

References Cited

1. Evanno, G., S. Regnaut, and J. Goudet. 2005. Detecting the number of clusters of individuals using the software STRUCTURE: A simulation study. Molecular Ecology 14: 2611–2620. (Available online at: http://dx.doi.org/10.1111/j.1365-294X.2005.02553.x) (verified 4 Jan 2011).

External Links

• Microsatellite analyzer [Online]. University of Veterinary Medicine, Vienna (Vetmeduni Vienna). Available at: http://i122server.vu-wien.ac.at/MSA/MSA_download.html (verified 4 Jan 2011).
• Pritchard, J. Structure [Online]. Pritchard Lab. University of Chicago Division of Biological Sciences. Available at: http://pritch.bsd.uchicago.edu/structure.html (verified 4 Jan 2011).
• Wageningen UR. GGT2.0: Graphical genotypes [Online]. Wageningen UR Plant Breeding. Available at: http://www.plantbreeding.wur.nl/UK/software_ggt.html (verified 4 Jan 2011).

Attachments:

Downstream_SNP_Analysis.pdf (2.21 MB)

Downstream_Supplemental_Files.zip (14.8 MB)