SNP-Based Genetic Linkage Maps for Potato

Plant Breeding and Genomics October 24, 2012 Print Friendly and PDF

Authors:

David Douches, Michigan State University; Heather L. Merk, The Ohio State University

This webinar was presented at the 2011 Potato Association of America conference by Dr. David Douches of Michigan State University. Dr. Douches discusses the development of linkage maps using large-scale SNP genotypes in diploid and tetraploid potato populations relevant to the Solanaceae Coordinated Agricultural Project (SolCAP).

Introduction

The Solanaceae Coordinated Agricultural Project (SolCAP) potato germplasm panel includes over 200 potato cultivars and breeding lines. The panel was phenotyped and genotyped with over 8,300 SNP markers. Several mapping populations have also been genotyped using these SNPs. During this webinar, Dr. David Douches presents the series of steps, an analytical pipeline, used for linkage mapping with these reference populations.

During the first video, Dr. Douches introduces the SNP genotyping project.

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

During the second video, Dr. Douches introduces SNP genotyping for mapping populations, population development, the Illumina genotyping platform, SNP quality control, and design of the SolCAP SNP chip. Dr. Douches details the requirements for genotyping a mapping population using the Illumina Infinium potato SNP chip.

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

During the third video, Dr. Douches describes the output files in Genome Studio and explains how to export Genome Studio data to Microsoft Excel. Furthermore, Dr. Douches details quality control and filtering procedures for SNP data.

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

During the fourth video, Dr. Douches describes linkage mapping procedures. The initial steps include preparing and formatting data and importing data. Dr. Douches walks through map generation procedures for diploids using JoinMap and post mapping quality control.

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

During the fifth video, Dr. Douches introduces SNP analysis specific to tetraploids, including the calling of five clusters representing the AAAA, AAAB, AABB, ABBB, BBBB classes expected with tetraploid segregation.

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

During the sixth video, Dr. Douches reviews progress toward accomplishing SolCAP research objectives.

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

This video contains the full-length recording lasting 72 minutes.

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

Watch Other Webinars from the SolCAP Workshop at the 2011 Potato Association of America Meeting

Linkage Analysis and QTL Mapping in Tetraploids Webinar

Working with Infinium Genotype Data Webinar

External Link

  • Solanaceae Coordinated Agricultural Project (SolCAP) [Online]. Michigan State University. Available at: http://www.solcap.msu.edu/ (verified 22 Aug 2011).

Additional Resources

Funding Statement

Development of this page 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.

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USDA / NIFA

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