Downstream Analysis of SNP Markers Using MSA, GGT, and STRUCTURE Software

Plant Breeding and Genomics April 08, 2013 Print Friendly and PDF

Authors:

Sung-Chur Sim, The Ohio State University; Heather L. Merk, The Ohio State University

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.

 

If you experience problems viewing this video connect to our YouTube channel or see the YouTube troubleshooting guide.

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.

If you experience problems viewing this video connect to our YouTube channel or see the YouTube troubleshooting guide.

Find all the presentations from the 2010 Tomato Disease Workshop

References Cited

  • 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 12 May 2012).

External Links

Additional Resources

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.

PBGworks 1005

Connect with us

  • Twitter
  • Facebook
  • YouTube

Welcome

This is where you can find research-based information from America's land-grant universities enabled by eXtension.org

LOCATE

USDA / NIFA

This work is supported by the USDA National Institute of Food and Agriculture, New Technologies for Ag Extension project.