Downstream Analysis of SNPs from the SolCAP Tomato Infinium Array

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; John McQueen, Oregon State University

During this webinar, delivered to a live audience at the 2011 Tomato Disease Workshop at Cornell University in Ithaca, New York, Dr. Sung-Chur Sim from The Ohio State University discusses working with the tomato Infinium and genomic data.

The workshop webinar , Downstream Analysis of SNPs from the SolCAP Tomato Infinium Array, discusses the use of Infinium array data to improve tomato varieities. The SolCAP Cluster File v1 for the tomato Infinium array will be released to the public in the workshop. An emphasis will be placed on steps that can be taken to develop a subset of SNPs  as a cost-effective genotyping approach for mapping populations. The workshop is intended to be practical by providing demonstration with "hands on" examples.

At the end of the module, participants should be able to retrieve the SolCAP Cluster File, identify polymorphic SNPs in a specific mapping population, find the physical map locations of SNPs via BLAST, and select non-redundant and informative SNPs.

SolCAP Cluster File

Please read before accessing the pre-publication tomato cluster file.

The Solanaceae Coordinated Agricultural Project (SolCAP) is pleased to share a pre-publication tomato cluster file for use by research teams representing public and private interests as a resource to facilitate high-throughput genotyping.

The cluster file is based on genotyping the SolCAP tomato collection (solcap.msu.edu/tomato_germplasm_data.shtml). We caution that the cluster file is limited by the germplasm analyzed to date. The SolCAP collection is heavily biased toward inbred lines. Thus heterozygous calls were underrepresented in the data used to create this version. We encourage you to independently verify the genotype calls based on this file.

This cluster file is made available pre-publication with the understanding that users will respect the rights of those who developed the array and cluster file for publication. Consistent with current practices for release of sequence data (www.genome.gov/page.cfm?pageID=10506537), we are making this cluster file available to the community to use for research purposes. By downloading the file, you agree to not publish a global analysis or description of the SolCAP Infinium array prior to its publication by SoLCAP in a peer reviewed journal. Any use of the cluster file should acknowledge and credit the "Solanaceae Coordinated Agricultural Project". SolCAP is in the process of writing a manuscript on the array.
–The SolCAP team

I AGREE (click to download file)

External Links

  • Reaffirmation and Extension of NHGRI Rapid Data Release Policies:
    Large-scale Sequencing and Other Community Resource Projects [Online]. National Human Genome Research Institute, National Institutes of Health. Available at: www.genome.gov/page.cfm (verified 4 Oct 2011).
  • Solanaceae Coordinated Agricultural Project (SolCAP) [Online]. Michigan State University. Available at: http://www.solcap.msu.edu/ (verified 4 Oct 2011).

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.    

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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.