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Application 2.2.4 Tool 6.3 - Genotyping Data Manager

Objective: Develop and deploy an Integrated Breeding Genotypic Data Management System Application

This activity started in April 2011 after planning meetings in January and February for the development of the Configurable Workflow System. The previous focus on LIMS development was stopped (Activity 2.1.3) and those resources merged with activity 2.2.4 with a new focus on tools to support low to medium throughput genotyping data. It is expected that the IBP will shift to use tools being developed by the international community for high and ultra-high throughput genotyping data when they become available.

Activities have been focused on adapting the ICRIS system (genotyping module) to fit the requirements and needs of the IBP project. The database schema was reviewed and revised with the help of collaborators from IRRI and the GCP who were involved in the earlier efforts of designing a gentoyping system.

The Genotyping Data Management System has been developed in Java using a browser-based front end. Since April efforts have been made to package the system so that it is available as a stand-alone system for users who do not have sufficient Internet access.

A prototype of the system (using medium-throughput SNP markers) was demonstrated at the Tropical Legumes 1 Annual Project Meeting in Madrid as well as the IBP annual meeting in Wagenigen. During the IBP meeting discussions were also initiated on how this would link with the phenotyping and germplasm information database through the fieldbook. The system is already able to retrieve genotyping information based on germplasmIDs (GID).

  • Genotyping Data Management System (GDMS)] schema developed from the old ICIRIS schema
  • Prototype Genotype Data Management System (GDMS) developed from ICRIS and made available. Live demonstrations were carried out at the TL1 annual meeting and at the IBP annual meeting.
  • GIDs have been incorporated in the schema to link GDMS with ICIS and the flapjack format has been adopted for retrieval and export of data.
  • Legume SNP data, map data and marker details have been loaded as a test case.
  • The concept of a gene catalogue is being re-evaluated, legacy sample management tools are being used and GCP and Flapjack templates ore being supported for input and output of genotyping data.
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