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ARS Home » Southeast Area » Stuttgart, Arkansas » Dale Bumpers National Rice Research Center » Research » Publications at this Location » Publication #392761

Research Project: Gene Discovery and Crop Design for Current and New Rice Management Practices and Market Opportunities

Location: Dale Bumpers National Rice Research Center

Title: Breedbase: a digital ecosystem for modern plant breeding

Author
item MORALES, NICOLAS - Boyce Thompson Institute
item OGBONNA, ALEX - Boyce Thompson Institute
item ELLERBROCK, BRYAN - Boyce Thompson Institute
item BAUCHET, GUILLAUME - Boyce Thompson Institute
item TANTIKANJANA, TITIMA - Boyce Thompson Institute
item TECLE, ISAAK - Boyce Thompson Institute
item POWELL, ADRIAN - Boyce Thompson Institute
item LYON, DAVID - Boyce Thompson Institute
item NAAMA, MENDA - Boyce Thompson Institute
item SIMOES, CHRISTIANO - Boyce Thompson Institute
item SAHA, SURYA - Boyce Thompson Institute
item HOSMANI, PRASHANT - Boyce Thompson Institute
item FLORES, MIRELLA - Boyce Thompson Institute
item PANITZ, NAFTALI - Boyce Thompson Institute
item PREBLE, RYAN - Boyce Thompson Institute
item AGBONA, AFOLABI - International Institute Of Tropical Agriculture (IITA)
item RABBI, ISMAIL - International Institute Of Tropical Agriculture (IITA)
item KULAKOW, PETER - International Institute Of Tropical Agriculture (IITA)
item PETETI, PRASAD - International Institute Of Tropical Agriculture (IITA)
item KAWUKI, ROBERT - National Crops Resources Research Institute
item ESUMA, WILLIAMS - National Crops Resources Research Institute
item KANAABI, MICHEAL - National Crops Resources Research Institute
item CHELAGANT, DOREEN - National Crops Resources Research Institute
item UBA, EZENWANYI - National Root Crops Research Institute (NRCRI)
item OLOJEDE, ADEYEMI - National Root Crops Research Institute (NRCRI)
item ONYEKA, JOSEPH - National Root Crops Research Institute (NRCRI)
item SHAH, TRUSHAR - International Institute Of Tropical Agriculture (IITA)
item KARANJA, MARGARET - International Institute Of Tropical Agriculture (IITA)
item EGESI, CHIEDOZIE - Cornell University - New York
item TUFAN, HALE - Cornell University - New York
item PATERNE, AGRE - International Institute Of Tropical Agriculture (IITA)
item ASFAW, ASRAT - International Institute Of Tropical Agriculture (IITA)
item Jannink, Jean-Luc
item WOLFE, MARNIN - Cornell University - New York
item Birkett, Clayton
item HERSHBERGER, JENNA - Cornell University - New York
item GORE, MICHAEL - Cornell University - New York
item ROBBINS, KELLY - Cornell University - New York
item RIFE, TREVOR - Kansas State University
item CHANEY, COURTNEY - Kansas State University
item POLAND, JESSE - Kansas State University
item ARNAUD, ELIZABETH - Bioversity International
item LAPORTE, MARIE-ANGELIQUE - Bioversity International
item WARING, DAVID - Cornell University - New York
item BROWN, ALLAN - International Institute Of Tropical Agriculture (IITA)
item BAYO, STANLEY - International Institute Of Tropical Agriculture (IITA)
item UWIMANA, BRIGITTE - International Institute Of Tropical Agriculture (IITA)
item AKECH, VIOLET - International Institute Of Tropical Agriculture (IITA)
item YENCHO, CRAIG - Ku Leuven
item DE BOECK, BERT - International Potato Center
item CAMPOS, HUGO - International Potato Center
item SWENNEN, RONY - Ku Leuven
item Edwards, Jeremy
item MUELLER, LUKAS - Boyce Thompson Institute
item KULEMBEKA, HENERIKO - Tanzania Agricultural Research Institute
item SALUM, KASELE - Tanzania Agricultural Research Institute
item MREMA, EMMANUEL - Tanzania Agricultural Research Institute

Submitted to: G3, Genes/Genomes/Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/14/2022
Publication Date: 4/6/2022
Citation: Morales, N., Ogbonna, A.C., Ellerbrock, B.J., Bauchet, G.J., Tantikanjana, T., Tecle, I.Y., Powell, A.F., Lyon, D., Naama, M., Simoes, C.C., Saha, S., Hosmani, P., Flores, M., Panitz, N., Preble, R.S., Agbona, A., Rabbi, I., Kulakow, P., Peteti, P., Kawuki, R., Esuma, W., Kanaabi, M., Chelagant, D.M., Uba, E., Olojede, A., Onyeka, J., Shah, T., Karanja, M., Egesi, C., Tufan, H., Paterne, A., Asfaw, A., Jannink, J., Wolfe, M., Birkett, C.L., Hershberger, J.M., Gore, M.A., Robbins, K.R., Rife, T., Chaney, C., Poland, J., Arnaud, E., Laporte, M., Waring, D.J., Brown, A., Bayo, S., Uwimana, B., Akech, V., Yencho, C., De Boeck, B., Campos, H., Swennen, R., Edwards, J., Mueller, L.A., Kulembeka, H., Salum, K., Mrema, E. 2022. Breedbase: a digital ecosystem for modern plant breeding. G3, Genes/Genomes/Genetics. https://doi.org/10.1093/g3journal/jkac078.
DOI: https://doi.org/10.1093/g3journal/jkac078

Interpretive Summary: Breedbase is a database system for plant breeding. It is designed to help breeders 1) track breeding materials, 2) store experimental evaluations, 3) record field data in a consistent way, 4) store genotypic information, and 5) provide analysis and decision-making tools, all within a fully integrated digital ecosystem. It provides the infrastructure to integrate and manage large genomic datasets alongside breeding data to enable genome-based breeding methods that can accelerate the breeding cycle and increase the rate of gain. Breedbase is a free, web-based and open-source so that it can be modified for the specific needs of any breeding application. For anyone with web-browsing experience, the interface should be intuitive and straightforward, and it is continuously improved based on user driven feedback. In Breedbase, processes are presented in an interactive workflow system, providing step-by-step guidance to breeders and users in accomplishing specific tasks. Breedbase was originally developed for Cassava and is presently used by dozens of different crops and projects including clonal crops such as banana, sweet potato, yam, rice, wheat, oat, kelp, potato, and maize.

Technical Abstract: Modern breeding methods integrate next-generation sequencing (NGS) and phenomics to identify plants with the best characteristics and greatest genetic merit for use as parents in subsequent breeding cycles to ultimately create improved cultivars able to sustain high adoption rates by farmers. This data-driven approach hinges on strong foundations in data management, quality control, and analytics. Of crucial importance is a central database able to 1) track breeding materials, 2) store experimental evaluations, 3) record phenotypic measurements using consistent ontologies, 4) store genotypic information, and 5) implement algorithms for analysis, prediction, and selection decisions. Because of the complexity of the breeding process, breeding databases also tend to be complex, difficult, and expensive to implement and maintain. Here, we present a breeding database system, Breedbase (https://breedbase.org/). Originally initiated as Cassavabase (https://cassavabase.org/) with the NextGen Cassava project (https://www.nextgencassava.org/), and later developed into a crop-agnostic system, it is presently used by dozens of different crops and projects. The system is web-based and is available as open source software. It is available on GitHub (https://github.com/solgenomics/) and packaged in a Docker image for deployment (https://dockerhub.com/breedbase/). The Breedbase system enables breeding programs to better manage and leverage their data for decision making within a fully integrated digital ecosystem.