David Douches, Michigan State University; Heather L. Merk, The Ohio State University
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.
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.
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.
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.
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.
During the sixth video, Dr. Douches reviews progress toward accomplishing SolCAP research objectives.
This video contains the full-length recording lasting 72 minutes.
- Solanaceae Coordinated Agricultural Project (SolCAP) [Online]. Michigan State University. Available at: http://www.solcap.msu.edu/ (verified 22 Aug 2011).
- JoinMap 4.1. [Online]. Kyazma B.V. Available at: http://www.kyazma.nl/ (verified 22 Aug 2011).
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.
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