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 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.
Main Authors: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
---|---|
Format: | Journal Article biblioteca |
Language: | English |
Published: |
Oxford University Press
2022-07-06
|
Subjects: | data, databases, breeding, phenotypes, genotyping, marker-assisted selection, digital technology, mejora, fenotipos, |
Online Access: | https://hdl.handle.net/10568/119327 https://doi.org/10.1093/g3journal/jkac078 |
Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
id |
dig-cgspace-10568-119327 |
---|---|
record_format |
koha |
spelling |
dig-cgspace-10568-1193272023-12-08T19:36:04Z 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 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 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 De Boeck, Bert 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 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 2160-1836 https://hdl.handle.net/10568/119327 https://doi.org/10.1093/g3journal/jkac078 en CC-BY-4.0 Open Access application/pdf Oxford University Press G3-Genes Genomes Genetics |
institution |
CGIAR |
collection |
DSpace |
country |
Francia |
countrycode |
FR |
component |
Bibliográfico |
access |
En linea |
databasecode |
dig-cgspace |
tag |
biblioteca |
region |
Europa del Oeste |
libraryname |
Biblioteca del CGIAR |
language |
English |
topic |
data databases breeding phenotypes genotyping marker-assisted selection digital technology mejora fenotipos data databases breeding phenotypes genotyping marker-assisted selection digital technology mejora fenotipos |
spellingShingle |
data databases breeding phenotypes genotyping marker-assisted selection digital technology mejora fenotipos 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 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 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 De Boeck, Bert Campos, Hugo Swennen, Rony L. Edwards, Jeremy D. Mueller, Lukas A. Breedbase: a digital ecosystem for modern plant breeding |
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 |
topic_facet |
data databases breeding phenotypes genotyping marker-assisted selection digital technology mejora fenotipos |
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 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 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 De Boeck, Bert Campos, Hugo Swennen, Rony L. Edwards, Jeremy D. Mueller, Lukas A. |
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 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 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 De Boeck, Bert Campos, Hugo Swennen, Rony L. Edwards, Jeremy D. Mueller, Lukas A. |
author_sort |
Morales, Nicolas |
title |
Breedbase: a digital ecosystem for modern plant breeding |
title_short |
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_sort |
breedbase: a digital ecosystem for modern plant breeding |
publisher |
Oxford University Press |
publishDate |
2022-07-06 |
url |
https://hdl.handle.net/10568/119327 https://doi.org/10.1093/g3journal/jkac078 |
work_keys_str_mv |
AT moralesnicolas breedbaseadigitalecosystemformodernplantbreeding AT ogbonnaalexc breedbaseadigitalecosystemformodernplantbreeding AT ellerbrockbryanj breedbaseadigitalecosystemformodernplantbreeding AT bauchetguillaumej breedbaseadigitalecosystemformodernplantbreeding AT tantikanjanatitima breedbaseadigitalecosystemformodernplantbreeding AT tecleisaaky breedbaseadigitalecosystemformodernplantbreeding AT powelladrianf breedbaseadigitalecosystemformodernplantbreeding AT lyondavid breedbaseadigitalecosystemformodernplantbreeding AT mendanaama breedbaseadigitalecosystemformodernplantbreeding AT simoeschristianoc breedbaseadigitalecosystemformodernplantbreeding AT sahasurya breedbaseadigitalecosystemformodernplantbreeding AT hosmaniprashant breedbaseadigitalecosystemformodernplantbreeding AT floresmirella breedbaseadigitalecosystemformodernplantbreeding AT panitznaftali breedbaseadigitalecosystemformodernplantbreeding AT prebleryans breedbaseadigitalecosystemformodernplantbreeding AT agbonaafolabi breedbaseadigitalecosystemformodernplantbreeding AT rabbiismail breedbaseadigitalecosystemformodernplantbreeding AT kulakowpeter breedbaseadigitalecosystemformodernplantbreeding AT petetiprasad breedbaseadigitalecosystemformodernplantbreeding AT kawukirobert breedbaseadigitalecosystemformodernplantbreeding AT esumawilliams breedbaseadigitalecosystemformodernplantbreeding AT kanaabimicheal breedbaseadigitalecosystemformodernplantbreeding AT chelangatdoreenm breedbaseadigitalecosystemformodernplantbreeding AT ubaezenwanyi breedbaseadigitalecosystemformodernplantbreeding AT olojedeadeyemi breedbaseadigitalecosystemformodernplantbreeding AT onyekajoseph breedbaseadigitalecosystemformodernplantbreeding AT shahtrushar breedbaseadigitalecosystemformodernplantbreeding AT karanjamargaret breedbaseadigitalecosystemformodernplantbreeding AT egesichiedozien breedbaseadigitalecosystemformodernplantbreeding AT tufanhale breedbaseadigitalecosystemformodernplantbreeding AT paterneagre breedbaseadigitalecosystemformodernplantbreeding AT asfawasrat breedbaseadigitalecosystemformodernplantbreeding AT janninkjeanluc breedbaseadigitalecosystemformodernplantbreeding AT wolfemarnin breedbaseadigitalecosystemformodernplantbreeding AT birkettclayl breedbaseadigitalecosystemformodernplantbreeding AT waringdavidj breedbaseadigitalecosystemformodernplantbreeding AT hershbergerjennam breedbaseadigitalecosystemformodernplantbreeding AT goremichaela breedbaseadigitalecosystemformodernplantbreeding AT robbinskellyr breedbaseadigitalecosystemformodernplantbreeding AT rifetrevor breedbaseadigitalecosystemformodernplantbreeding AT courtneychaney breedbaseadigitalecosystemformodernplantbreeding AT polandjessea breedbaseadigitalecosystemformodernplantbreeding AT arnaudelizabeth breedbaseadigitalecosystemformodernplantbreeding AT laportemarieangelique breedbaseadigitalecosystemformodernplantbreeding AT kulembekaheneriko breedbaseadigitalecosystemformodernplantbreeding AT salumkasele breedbaseadigitalecosystemformodernplantbreeding AT mremaemmanuel breedbaseadigitalecosystemformodernplantbreeding AT brownallan breedbaseadigitalecosystemformodernplantbreeding AT bayostanley breedbaseadigitalecosystemformodernplantbreeding AT uwimanabrigitte breedbaseadigitalecosystemformodernplantbreeding AT akechviolet breedbaseadigitalecosystemformodernplantbreeding AT yenchocraig breedbaseadigitalecosystemformodernplantbreeding AT deboeckbert breedbaseadigitalecosystemformodernplantbreeding AT camposhugo breedbaseadigitalecosystemformodernplantbreeding AT swennenronyl breedbaseadigitalecosystemformodernplantbreeding AT edwardsjeremyd breedbaseadigitalecosystemformodernplantbreeding AT muellerlukasa breedbaseadigitalecosystemformodernplantbreeding |
_version_ |
1787229369354158080 |