DeltaBreed: A BrAPI-centric breeding data information system

Shawn Yarnes, Nick Palladino, Dave Meidlinger, David Philips, Heather Sweeney, Shahana Mustafa, Matthew Mandych, Sam Bouabane, Tim Parsons, Tyler Slonecki, Dongyan Zhao, Trevor Rife, Bryan Ellerbrock, Chaney Courtney, Peter Selby, Lukas Mueller, Mirella Flores-Gonzalez, johan Aparicio, Khaled Al-Shamaa, Sebastian Raubach, Jean-Luc Jannink, Edward S. Buckler, Craig Beil, Moira Sheehan. (12/12/2025). DeltaBreed: A BrAPI-centric breeding data information system. PLoS ONE, 20 (12).

Abstract

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.