DeltaBreed: A BrAPI-centric breeding data information system

Shawn C. Yarnes; Nick Palladino; Dave J. Meidlinger; David R. Philips; Heather M. Sweeney; Shahana A. Mustafa; Matthew L. Mandych; Sam Bouabane; Tim E. Parsons; Tyler J. Slonecki; Dongyan Zhao; Trevor W. Rife; Bryan J. Ellerbrock; Chaney Courtney; Peter Selby; Lukas A. Mueller; Mirella Flores-Gonzalez; Johan S. Aparicio; Khaled Al-Sham’aa; Sebastian Raubach; Jean-Luc Jannink; Edward S. Buckler; Craig T. Beil; Moira J. Sheehan

doi:10.1371/journal.pone.0324104

DeltaBreed: A BrAPI-centric breeding data information system

Shawn C. Yarnes
, Nick Palladino
, Dave J. Meidlinger
, David R. Philips
, Heather M. Sweeney
, Shahana A. Mustafa
, Matthew L. Mandych
, Sam Bouabane
, Tim E. Parsons
, Tyler J. Slonecki
, Dongyan Zhao
, Trevor W. Rife
, Bryan J. Ellerbrock
, Chaney Courtney
, Peter Selby
, Lukas A. Mueller
, Mirella Flores-Gonzalez
, Johan S. Aparicio
, Khaled Al-Sham’aa
, Sebastian Raubach

Jean-Luc Jannink, Edward S. Buckler, Craig T. Beil, Moira J. Sheehan

Bioinformatics

Cornell University
Clemson University
University of Wisconsin-Madison
ICARDA (Egypt)
United States of America Department of Agriculture-Agricultural Research Service (New York)

Research output: Contribution to journal › Article › peer-review

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.

Original language	English
Article number	0324104
Number of pages	22
Journal	PLoS ONE
Volume	20
Issue number	12
DOIs	https://doi.org/10.1371/journal.pone.0324104
Publication status	Published - 12 Dec 2025

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10.1371/journal.pone.0324104Licence: CC BY

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Yarnes, S. C., Palladino, N., Meidlinger, D. J., Philips, D. R., Sweeney, H. M., Mustafa, S. A., Mandych, M. L., Bouabane, S., Parsons, T. E., Slonecki, T. J., Zhao, D., Rife, T. W., Ellerbrock, B. J., Courtney, C., Selby, P., Mueller, L. A., Flores-Gonzalez, M., Aparicio, J. S., Al-Sham’aa, K., ... Sheehan, M. J. (2025). DeltaBreed: A BrAPI-centric breeding data information system. PLoS ONE, 20(12), Article 0324104. https://doi.org/10.1371/journal.pone.0324104

@article{fdfb5b1eb09347b6b81271f84e3907e7,

title = "DeltaBreed: A BrAPI-centric breeding data information system",

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.",

author = "Yarnes, \{Shawn C.\} and Nick Palladino and Meidlinger, \{Dave J.\} and Philips, \{David R.\} and Sweeney, \{Heather M.\} and Mustafa, \{Shahana A.\} and Mandych, \{Matthew L.\} and Sam Bouabane and Parsons, \{Tim E.\} and Slonecki, \{Tyler J.\} and Dongyan Zhao and Rife, \{Trevor W.\} and Ellerbrock, \{Bryan J.\} and Chaney Courtney and Peter Selby and Mueller, \{Lukas A.\} and Mirella Flores-Gonzalez and Aparicio, \{Johan S.\} and Khaled Al-Sham{\textquoteright}aa and Sebastian Raubach and Jean-Luc Jannink and Buckler, \{Edward S.\} and Beil, \{Craig T.\} and Sheehan, \{Moira J.\}",

year = "2025",

month = dec,

day = "12",

doi = "10.1371/journal.pone.0324104",

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Yarnes, SC, Palladino, N, Meidlinger, DJ, Philips, DR, Sweeney, HM, Mustafa, SA, Mandych, ML, Bouabane, S, Parsons, TE, Slonecki, TJ, Zhao, D, Rife, TW, Ellerbrock, BJ, Courtney, C, Selby, P, Mueller, LA, Flores-Gonzalez, M, Aparicio, JS, Al-Sham’aa, K, Raubach, S, Jannink, J-L, Buckler, ES, Beil, CT & Sheehan, MJ 2025, 'DeltaBreed: A BrAPI-centric breeding data information system', PLoS ONE, vol. 20, no. 12, 0324104. https://doi.org/10.1371/journal.pone.0324104

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AU - Yarnes, Shawn C.

AU - Palladino, Nick

AU - Meidlinger, Dave J.

AU - Philips, David R.

AU - Sweeney, Heather M.

AU - Mustafa, Shahana A.

AU - Mandych, Matthew L.

AU - Bouabane, Sam

AU - Parsons, Tim E.

AU - Slonecki, Tyler J.

AU - Zhao, Dongyan

AU - Rife, Trevor W.

AU - Ellerbrock, Bryan J.

AU - Courtney, Chaney

AU - Selby, Peter

AU - Mueller, Lukas A.

AU - Flores-Gonzalez, Mirella

AU - Aparicio, Johan S.

AU - Al-Sham’aa, Khaled

AU - Raubach, Sebastian

AU - Jannink, Jean-Luc

AU - Buckler, Edward S.

AU - Beil, Craig T.

AU - Sheehan, Moira J.

PY - 2025/12/12

Y1 - 2025/12/12

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M3 - Article

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JO - PLoS ONE

JF - PLoS ONE

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DeltaBreed: A BrAPI-centric breeding data information system

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