Addition of a breeding database in the Genome Database for Rosaceae

Kate Evans,Lisa Brutcher,Taein Lee,Sook Jung,Dorrie Main,Ilhyung Cho,Cameron Peace

doi:10.1093/database/bat078

Abstract

Breeding programs produce large datasets that require efficient management systems to keep track of performance, pedigree, geographical and image-based data. With the development of DNA-based screening technologies, more breeding programs perform genotyping in addition to phenotyping for performance evaluation. The integration of breeding data with other genomic and genetic data is instrumental for the refinement of marker-assisted breeding tools, enhances genetic understanding of important crop traits and maximizes access and utility by crop breeders and allied scientists. Development of new infrastructure in the Genome Database for Rosaceae (GDR) was designed and implemented to enable secure and efficient storage, management and analysis of large datasets from the Washington State University apple breeding program and subsequently expanded to fit datasets from other Rosaceae breeders. The infrastructure was built using the software Chado and Drupal, making use of the Natural Diversity module to accommodate large-scale phenotypic and genotypic data. Breeders can search accessions within the GDR to identify individuals with specific trait combinations. Results from Search by Parentage lists individuals with parents in common and results from Individual Variety pages link to all data available on each chosen individual including pedigree, phenotypic and genotypic information. Genotypic data are searchable by markers and alleles; results are linked to other pages in the GDR to enable the user to access tools such as GBrowse and CMap. This breeding database provides users with the opportunity to search datasets in a fully targeted manner and retrieve and compare performance data from multiple selections, years and sites, and to output the data needed for variety release publications and patent applications. The breeding database facilitates efficient program management. Storing publicly available breeding data in a database together with genomic and genetic data will further accelerate the cross-utilization of diverse data types by researchers from various disciplines.Database URL: http://www.rosaceae.org/breeders_toolbox

Highlights

Breeding programs generate large volumes of data and, with at least 18 years from seed to release being typical for a tree fruit crop like apple (Malus Â domestica Borkh.), an efficient management system for keeping track of the data collected each year is essential for a program to be successful
Developing the breeding database within the Genome Database for Rosaceae (GDR) provides an excellent opportunity for easy access to publicly available data that could be used to enhance breeders’ selection ability with newly developed genetic tests or expand breeders’ private analyzable datasets with public breeding data from projects such as RosBREED [3]
The database provides a secure area for storage and management of private breeding data

Summary

Background

Breeding programs generate large volumes of data and, with at least 18 years from seed to release being typical for a tree fruit crop like apple (Malus Â domestica Borkh.), an efficient management system for keeping track of the data collected each year is essential for a program to be successful. To store the breeding data, we have used the newly developed Natural Diversity (ND) module [11] along with other related modules, such as Stock, Phenotype and Genetic modules of Chado [12], the generic schema for biological databases The varieties, and their clones and samples, are stored in the stock table of the Stock module. Private varieties or breeding selections are tagged in the database and all of their data can be accessed only by those users who belong to the appropriate Organic Group. A search in the public WABP database might be for ‘Appearance’ = 3–5 (average to beautiful), ‘Overall score’ = 2–3 (promising and advance to phase 2), ‘Sweetness’ = 4–5 (sweet and very sweet), ‘Tartness’ = 3 (medium acid) and ‘Hardness’ = 4 (firm) Such a search currently results in a list of 31 individuals (Figure 2A), including both seedling and reference varieties.

Discussion

Conclusions