Breedbase: a digital ecosystem for modern plant breeding
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 d...
| Autores principales: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
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| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
Oxford University Press
2022
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| Materias: | |
| Acceso en línea: | https://hdl.handle.net/10568/119327 |
| _version_ | 1855523492710055936 |
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| author | Morales, Nicolas Ogbonna, Alex C. Ellerbrock, Bryan J. Bauchet, Guillaume J. Tantikanjana, Titima Tecle, Isaak Y. Powell, Adrian F. Lyon, David Menda, Naama Simoes, Christiano C. Saha, Surya Hosmani, Prashant Flores, Mirella Panitz, Naftali Preble, Ryan S. Agbona, Afolabi Rabbi, Ismail Kulakow, Peter A. Peteti, Prasad Kawuki, Robert Esuma, Williams Kanaabi, Micheal Chelangat, Doreen M. Uba, Ezenwanyi Olojede, Adeyemi Onyeka, Joseph Shah, Trushar Karanja, Margaret Egesi, Chiedozie N. Tufan, Hale Ann Paterne, Agre Asfaw, Asrat Jannink, Jean-Luc Wolfe, Marnin Birkett, Clay L. Waring, David J. Hershberger, Jenna M. Gore, Michael A. Robbins, Kelly R. Rife, Trevor Courtney, Chaney Poland, Jesse A. Arnaud, Elizabeth Laporte, Marie-Angélique Kulembeka, Heneriko Salum, Kasele Mrema, Emmanuel Brown, Allan Bayo, Stanley Uwimana, Brigitte Akech, Violet Yencho, Craig Boeck, Bert de Campos, Hugo Swennen, Rony L. Edwards, Jeremy D. Mueller, Lukas A. |
| author_browse | Agbona, Afolabi Akech, Violet Arnaud, Elizabeth Asfaw, Asrat Bauchet, Guillaume J. Bayo, Stanley Birkett, Clay L. Boeck, Bert de Brown, Allan Campos, Hugo Chelangat, Doreen M. Courtney, Chaney Edwards, Jeremy D. Egesi, Chiedozie N. Ellerbrock, Bryan J. Esuma, Williams Flores, Mirella Gore, Michael A. Hershberger, Jenna M. Hosmani, Prashant Jannink, Jean-Luc Kanaabi, Micheal Karanja, Margaret Kawuki, Robert Kulakow, Peter A. Kulembeka, Heneriko Laporte, Marie-Angélique Lyon, David Menda, Naama Morales, Nicolas Mrema, Emmanuel Mueller, Lukas A. Ogbonna, Alex C. Olojede, Adeyemi Onyeka, Joseph Panitz, Naftali Paterne, Agre Peteti, Prasad Poland, Jesse A. Powell, Adrian F. Preble, Ryan S. Rabbi, Ismail Rife, Trevor Robbins, Kelly R. Saha, Surya Salum, Kasele Shah, Trushar Simoes, Christiano C. Swennen, Rony L. Tantikanjana, Titima Tecle, Isaak Y. Tufan, Hale Ann Uba, Ezenwanyi Uwimana, Brigitte Waring, David J. Wolfe, Marnin Yencho, Craig |
| author_facet | Morales, Nicolas Ogbonna, Alex C. Ellerbrock, Bryan J. Bauchet, Guillaume J. Tantikanjana, Titima Tecle, Isaak Y. Powell, Adrian F. Lyon, David Menda, Naama Simoes, Christiano C. Saha, Surya Hosmani, Prashant Flores, Mirella Panitz, Naftali Preble, Ryan S. Agbona, Afolabi Rabbi, Ismail Kulakow, Peter A. Peteti, Prasad Kawuki, Robert Esuma, Williams Kanaabi, Micheal Chelangat, Doreen M. Uba, Ezenwanyi Olojede, Adeyemi Onyeka, Joseph Shah, Trushar Karanja, Margaret Egesi, Chiedozie N. Tufan, Hale Ann Paterne, Agre Asfaw, Asrat Jannink, Jean-Luc Wolfe, Marnin Birkett, Clay L. Waring, David J. Hershberger, Jenna M. Gore, Michael A. Robbins, Kelly R. Rife, Trevor Courtney, Chaney Poland, Jesse A. Arnaud, Elizabeth Laporte, Marie-Angélique Kulembeka, Heneriko Salum, Kasele Mrema, Emmanuel Brown, Allan Bayo, Stanley Uwimana, Brigitte Akech, Violet Yencho, Craig Boeck, Bert de Campos, Hugo Swennen, Rony L. Edwards, Jeremy D. Mueller, Lukas A. |
| author_sort | Morales, Nicolas |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | 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. |
| format | Journal Article |
| id | CGSpace119327 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2022 |
| publishDateRange | 2022 |
| publishDateSort | 2022 |
| publisher | Oxford University Press |
| publisherStr | Oxford University Press |
| record_format | dspace |
| spelling | CGSpace1193272025-12-08T09:54:28Z Breedbase: a digital ecosystem for modern plant breeding Morales, Nicolas Ogbonna, Alex C. Ellerbrock, Bryan J. Bauchet, Guillaume J. Tantikanjana, Titima Tecle, Isaak Y. Powell, Adrian F. Lyon, David Menda, Naama Simoes, Christiano C. Saha, Surya Hosmani, Prashant Flores, Mirella Panitz, Naftali Preble, Ryan S. Agbona, Afolabi Rabbi, Ismail Kulakow, Peter A. Peteti, Prasad Kawuki, Robert Esuma, Williams Kanaabi, Micheal Chelangat, Doreen M. Uba, Ezenwanyi Olojede, Adeyemi Onyeka, Joseph Shah, Trushar Karanja, Margaret Egesi, Chiedozie N. Tufan, Hale Ann Paterne, Agre Asfaw, Asrat Jannink, Jean-Luc Wolfe, Marnin Birkett, Clay L. Waring, David J. Hershberger, Jenna M. Gore, Michael A. Robbins, Kelly R. Rife, Trevor Courtney, Chaney Poland, Jesse A. Arnaud, Elizabeth Laporte, Marie-Angélique Kulembeka, Heneriko Salum, Kasele Mrema, Emmanuel Brown, Allan Bayo, Stanley Uwimana, Brigitte Akech, Violet Yencho, Craig Boeck, Bert de Campos, Hugo Swennen, Rony L. Edwards, Jeremy D. Mueller, Lukas A. data databases breeding phenotypes genotyping marker-assisted selection digital technology mejora fenotipos 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. 2022-07-06 2022-04-14T13:36:22Z 2022-04-14T13:36:22Z Journal Article https://hdl.handle.net/10568/119327 en Open Access application/pdf Oxford University Press Morales, N.; Ogbonna, A.C.; Ellerbrock, .J.; Bauchet, G.J.; Tantikanjana, T.; Tecle, I.Y.; Powell, A.F.; Lyon, D.; Menda, N.; 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.; Chelangat, D.M.; Uba, E.; Olojede, A.; Onyeka, J.; Shah, T.; Karanja, M.; Egesi, C.; Tufan, H.; Paterne, A.; Asfaw, A.; Jannink, J.-L.; Wolfe, M.; Birkett, C.L.; Waring, D.J.; Hershberger, J.M.; Gore, M.A.; Robbins, K.R.; Rife, T.; Courtney, C.; Poland, J.; Arnaud, E.; Laporte, M.-A.; Kulembeka, H.; Salum, K.; Mrema, E.; Brown, A.; Bayo, S.; Uwimana, B.; Akech, V.; Yencho, C.; De Boeck, B.; Campos, H.; Swennen, R.; Edwards, J.D.; Mueller, L.A. Breedbase: a digital ecosystem for modern plant breeding. G3-Genes Genomes Genetics ISSN: 2160-1836 |
| spellingShingle | data databases breeding phenotypes genotyping marker-assisted selection digital technology mejora fenotipos Morales, Nicolas Ogbonna, Alex C. Ellerbrock, Bryan J. Bauchet, Guillaume J. Tantikanjana, Titima Tecle, Isaak Y. Powell, Adrian F. Lyon, David Menda, Naama Simoes, Christiano C. Saha, Surya Hosmani, Prashant Flores, Mirella Panitz, Naftali Preble, Ryan S. Agbona, Afolabi Rabbi, Ismail Kulakow, Peter A. Peteti, Prasad Kawuki, Robert Esuma, Williams Kanaabi, Micheal Chelangat, Doreen M. Uba, Ezenwanyi Olojede, Adeyemi Onyeka, Joseph Shah, Trushar Karanja, Margaret Egesi, Chiedozie N. Tufan, Hale Ann Paterne, Agre Asfaw, Asrat Jannink, Jean-Luc Wolfe, Marnin Birkett, Clay L. Waring, David J. Hershberger, Jenna M. Gore, Michael A. Robbins, Kelly R. Rife, Trevor Courtney, Chaney Poland, Jesse A. Arnaud, Elizabeth Laporte, Marie-Angélique Kulembeka, Heneriko Salum, Kasele Mrema, Emmanuel Brown, Allan Bayo, Stanley Uwimana, Brigitte Akech, Violet Yencho, Craig Boeck, Bert de Campos, Hugo Swennen, Rony L. Edwards, Jeremy D. Mueller, Lukas A. Breedbase: a digital ecosystem for modern plant breeding |
| title | Breedbase: a digital ecosystem for modern plant breeding |
| title_full | Breedbase: a digital ecosystem for modern plant breeding |
| title_fullStr | Breedbase: a digital ecosystem for modern plant breeding |
| title_full_unstemmed | Breedbase: a digital ecosystem for modern plant breeding |
| title_short | Breedbase: a digital ecosystem for modern plant breeding |
| title_sort | breedbase a digital ecosystem for modern plant breeding |
| topic | data databases breeding phenotypes genotyping marker-assisted selection digital technology mejora fenotipos |
| url | https://hdl.handle.net/10568/119327 |
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