PedigreeNet: A web-based pedigree viewer for biological databases

Authors: BRAUN, BREMEN - Former ARS Employee; SCHOTT, DAVID - Iowa State University; Portwood, John; Andorf, Carson; Sen, Taner

Submitted to: Bioinformatics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/17/2019
Publication Date: 3/23/2019
Citation: Braun, B.L., Schott, D.A., Portwood Ii, J.L., Andorf, C.M., Sen, T.Z. 2019. PedigreeNet: A web-based pedigree viewer for biological databases. Bioinformatics. 1-3. https://doi.org/10.1093/bioinformatics/btz208.
DOI: https://doi.org/10.1093/bioinformatics/btz208

Interpretive Summary: Plant breeding aims to improve the yields of crops grown in varying and often suboptimal environments. To accomplish this goal, breeders rely on developing an understanding of the genetic makeup and relationships among different accessions to make informed decisions about which plants would make the best parents in genetic crosses. Rapid advances in genotyping technology have generated a large amount of data for breeders, but tools for pedigree visualization are scarce, and breeders usually use classical, but inherently limited, hierarchical pedigree diagrams available for only a handful of accessions. To answer this need, we developed a simple web-based tool, called PedNet, that can be easily implemented at biological databases to visualize pedigree relationships in a network context, displaying both previously known family relationships and those that users have deduced from genotype data. To demonstrate the tool's versatility, we implemented PedNet at MaizeGDB, the publicly accessible database for maize genetic information. PedNet fills a great need for breeders to have access to an online tool for customized representation and visualization of pedigree relationships.

Technical Abstract: Plant breeding aims to improve the yields of current germplasm grown under different conditions in the presence of biotic and abiotic stresses. To accomplish this goal, breeders rely on developing an understanding of genetic makeup and relationships among accessions for informed plant selections. Rapid advances in genotyping technology generated a large amount of data for breeders, along with several tools for data storage and analysis, but tools for pedigree visualization are scarce, and breeders usually use classical, but inherently limited, hierarchical pedigree diagrams available for only a handful of accessions. To answer this need, we developed a simple web-based tool, called PedNet, that can be easily implemented at biological databases to visualize pedigree relationships in a network context, displaying pre- and user-uploaded pedigree relationships in the csv format. As a proof-of-concept, we implemented PedNet at the model organism database for maize, MaizeGDB. The PedNet viewer at MaizeGDB has a dynamically-generated pedigree network of 4,706 maize lines that are currently available on the MaizeGDB Stock Pages and 5,487 relationships among them. The tool allows the user to apply a number of filters, select or upload their own breeding relationships, center a pedigree network around an accession, identify the common ancestor between two accessions, and display the shortest path(s) between two accessions on the pedigree network. The PedNet code layer is written in javascript wrapped around Cytoscape.js. PedNet fills a great need for breeders to have access to an online tool to represent and visually customize pedigree relationships.