Breedbase: a digital ecosystem for modern plant breeding

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