Pedigree Finder: A web-based crop pedigree viewer for graph databases

Abstract

Accurate crop pedigree information is essential for breeding programs, especially to make better decisions on the breeding materials to be selected in crossings. As the available tools for facilitating pedigree analysis and visualization are insufficient, breeders use a limited pedigree chart to trace the relationships between crop varieties. To resolve this problem, we have developed a web-based pedigree viewer for graph databases, “Pedigree Finder” (https://pedigree.db.naro.go.jp/), that facilitates the effective utilization of pedigree data sets for breeding programs and crop data analysis. For data normalization, the ontologies and data formats used to describe pedigree information have been standardized. Pedigree, genomic, and phenotypic data can be integrated by assigning and applying unique identifiers to different crop varieties. The Resource Description Framework (RDF) was adopted as the data model to enhance commonality and persistence, and an RDF graph was constructed to visualize the pedigree network. This semantic web technology enables advanced search functions and allows for the blending of data sets from disparate sources using an RDF model. “Pedigree Finder” provides an integrated data-driven framework for the appropriate selection of breeding materials, understanding of genetic correlations between phenotypes and pedigrees in breeding programs, and promotion of crop genetics research.