DeltaBreed: A BrAPI-centric breeding data information system
DeltaBreed is a unified breeding data management system designed by Breeding Insight (BI, Cornell University) to serve the wide diversity of USDA-ARS specialty crop and livestock breeding programs. DeltaBreed has a RESTful microservice architecture that utilizes the BrAPI v2.1 Java Test Server as its primary database. The system is interoperable with many BrAPI-compliant applications (BrApps), including Field Book v6.1.0, and is continually aligned with the most recent BrAPI specifications (BrAPI v2.1). Here we describe the features of DeltaBreed v1.0, a minimum viable product, and how we aligned data capture and validation with community standards. We highlight the modules for management of germplasm, observation variables, experiments and observations, genotypic sample submission, and a prototype genomic database that supports polyploid and multiallelic genomic data, as well as SNP data. Several test cases are illustrated to demonstrate the successes and challenges of interoperability with other open-source BrAPI-enabled software packages. We also discuss expansion and enhancement plans for future DeltaBreed versions, as well as outline possible solutions to known limitations. To our knowledge, DeltaBreed is the first species-agnostic, fully BrAPI-compliant breeding data management system built for transactional use.
Authors
- Bryan J. Ellerbrock (ORCID: https://orcid.org/0009-0008-7937-0181)
- Dongyan Zhao (ORCID: https://orcid.org/0000-0002-2080-8416)
- Lukas A. Mueller (ORCID: https://orcid.org/0000-0001-8640-1750)
- Shawn C. Yarnes (ORCID: https://orcid.org/0000-0002-1090-0403)
- Edward S. Buckler (ORCID: https://orcid.org/0000-0002-3100-371X)
- Soma Mustafa
- Chaney Courtney
- Sebastian Raubach (ORCID: https://orcid.org/0000-0001-5659-247X)
- Jean‐Luc Jannink (ORCID: https://orcid.org/0000-0003-4849-628X)
- Khaled Al-Shamaa (ORCID: https://orcid.org/0000-0002-7668-3798)
- Tyler J. Slonecki (ORCID: https://orcid.org/0000-0002-4762-3518)
- Trevor W. Rife (ORCID: https://orcid.org/0000-0002-5974-6523)
- Heather M. Sweeney
- Moira J. Sheehan (ORCID: https://orcid.org/0000-0002-3400-2165)
- Johan Steven Aparicio (ORCID: https://orcid.org/0000-0003-3580-5354)
- Craig T. Beil (ORCID: https://orcid.org/0000-0002-1756-9987)
- Mirella Flores-Gonzalez (ORCID: https://orcid.org/0000-0002-7759-1617)
- Peter Selby (ORCID: https://orcid.org/0000-0001-7151-4445)
- David Philips
- Nick Palladino (ORCID: https://orcid.org/0009-0009-1645-297X)
- Matthew L. Mandych
- Timothy E Parsons (ORCID: https://orcid.org/0000-0001-6209-2455)
- Dave J. Meidlinger
- Sam Bouabane
Institutions
- University of Wisconsin–Madison (US)
- James Hutton Institute (GB)
- International Center for Agricultural Research in the Dry Areas (LB)
- Cornell University (US)
- Robert W. Holley Center for Agriculture & Health (US)
- Clemson University (US)
Publication Details
- Journal
- PLoS ONE
- Published
- 2025-12-12
- DOI
- https://doi.org/10.1371/journal.pone.0324104
- Citations
- 1
- Primary Topic
- Genetic Mapping and Diversity in Plants and Animals
- Type
- article
- Field-Weighted Citation Impact
- 1.82