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PedigreeNet: a web-based pedigree viewer for biological databases.

Bremen L Braun1, David A Schott1,2, John L Portwood1

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Plant breeders now have PedigreeNet, a web-based tool for visualizing plant genetic relationships. This tool aids in making informed selections for improved crop varieties and stress tolerance.

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Area of Science:

  • Plant genetics and breeding
  • Bioinformatics and computational biology
  • Genomics and crop improvement

Background:

  • Plant breeding requires understanding genetic makeup for stress tolerance.
  • Current genotyping data is abundant, but pedigree analysis tools are limited.
  • Classical pedigree diagrams are insufficient for complex genetic relationships.

Purpose of the Study:

  • To develop a web-based tool for creating and visualizing customizable plant pedigree relationships.
  • To address the need for advanced pedigree analysis and visualization in plant breeding.
  • To facilitate informed plant selections through enhanced genetic relationship mapping.

Main Methods:

  • Developed PedigreeNet, a web-based tool implemented at MaizeGDB.
  • Utilized a JavaScript wrapper around Cytoscape Web for visualization.
  • Integrated the tool on MaizeGDB Stock Pages for direct access.

Main Results:

  • Created a dynamic pedigree network of 4706 maize lines and 5487 relationships.
  • The tool allows filtering, custom relationship uploads, and ancestor identification.
  • PedigreeNet provides a stand-alone and integrated solution for breeders.

Conclusions:

  • PedigreeNet effectively visualizes and customizes plant pedigree relationships in a network context.
  • The tool enhances breeders' ability to understand genetic connections for improved germplasm.
  • Accessible online and open-source, PedigreeNet supports advanced plant breeding strategies.