G3: Genes, Genomes, Genetics (Apr 2022)
Breedbase: a digital ecosystem for modern plant breeding
- Nicolas Morales,
- Alex C Ogbonna,
- Bryan J Ellerbrock,
- Guillaume J Bauchet,
- Titima Tantikanjana,
- Isaak Y Tecle,
- Adrian F Powell,
- David Lyon,
- Naama Menda,
- Christiano C Simoes,
- Surya Saha,
- Prashant Hosmani,
- Mirella Flores,
- Naftali Panitz,
- Ryan S Preble,
- Afolabi Agbona,
- Ismail Rabbi,
- Peter Kulakow,
- Prasad Peteti,
- Robert Kawuki,
- Williams Esuma,
- Micheal Kanaabi,
- Doreen M Chelangat,
- Ezenwanyi Uba,
- Adeyemi Olojede,
- Joseph Onyeka,
- Trushar Shah,
- Margaret Karanja,
- Chiedozie Egesi,
- Hale Tufan,
- Agre Paterne,
- Asrat Asfaw,
- Jean-Luc Jannink,
- Marnin Wolfe,
- Clay L Birkett,
- David J Waring,
- Jenna M Hershberger,
- Michael A Gore,
- Kelly R Robbins,
- Trevor Rife,
- Chaney Courtney,
- Jesse Poland,
- Elizabeth Arnaud,
- Marie-Angélique Laporte,
- Heneriko Kulembeka,
- Kasele Salum,
- Emmanuel Mrema,
- Allan Brown,
- Stanley Bayo,
- Brigitte Uwimana,
- Violet Akech,
- Craig Yencho,
- Bert de Boeck,
- Hugo Campos,
- Rony Swennen,
- Jeremy D Edwards,
- Lukas A Mueller
Affiliations
- Nicolas Morales
- ORCiD
- Boyce Thompson Institute, Ithaca, NY 14853, USA
- Alex C Ogbonna
- ORCiD
- Boyce Thompson Institute, Ithaca, NY 14853, USA
- Bryan J Ellerbrock
- Boyce Thompson Institute, Ithaca, NY 14853, USA
- Guillaume J Bauchet
- ORCiD
- Boyce Thompson Institute, Ithaca, NY 14853, USA
- Titima Tantikanjana
- Boyce Thompson Institute, Ithaca, NY 14853, USA
- Isaak Y Tecle
- ORCiD
- Boyce Thompson Institute, Ithaca, NY 14853, USA
- Adrian F Powell
- ORCiD
- Boyce Thompson Institute, Ithaca, NY 14853, USA
- David Lyon
- ORCiD
- Boyce Thompson Institute, Ithaca, NY 14853, USA
- Naama Menda
- ORCiD
- Boyce Thompson Institute, Ithaca, NY 14853, USA
- Christiano C Simoes
- Boyce Thompson Institute, Ithaca, NY 14853, USA
- Surya Saha
- ORCiD
- Boyce Thompson Institute, Ithaca, NY 14853, USA
- Prashant Hosmani
- ORCiD
- Boyce Thompson Institute, Ithaca, NY 14853, USA
- Mirella Flores
- ORCiD
- Boyce Thompson Institute, Ithaca, NY 14853, USA
- Naftali Panitz
- ORCiD
- Boyce Thompson Institute, Ithaca, NY 14853, USA
- Ryan S Preble
- Boyce Thompson Institute, Ithaca, NY 14853, USA
- Afolabi Agbona
- ORCiD
- IITA Ibadan, 200001 Ibadan, Nigeria
- Ismail Rabbi
- ORCiD
- IITA Ibadan, 200001 Ibadan, Nigeria
- Peter Kulakow
- ORCiD
- IITA Ibadan, 200001 Ibadan, Nigeria
- Prasad Peteti
- ORCiD
- IITA Ibadan, 200001 Ibadan, Nigeria
- Robert Kawuki
- ORCiD
- NaCCRI, Namulonge, Uganda
- Williams Esuma
- ORCiD
- NaCCRI, Namulonge, Uganda
- Micheal Kanaabi
- NaCCRI, Namulonge, Uganda
- Doreen M Chelangat
- ORCiD
- NaCCRI, Namulonge, Uganda
- Ezenwanyi Uba
- National Root Crops Research Institute (NRCRI), 463109 Umudike, Nigeria
- Adeyemi Olojede
- ORCiD
- National Root Crops Research Institute (NRCRI), 463109 Umudike, Nigeria
- Joseph Onyeka
- National Root Crops Research Institute (NRCRI), 463109 Umudike, Nigeria
- Trushar Shah
- ORCiD
- IITA Nairobi, 30709-00100 Nairobi, Kenya
- Margaret Karanja
- ORCiD
- IITA Nairobi, 30709-00100 Nairobi, Kenya
- Chiedozie Egesi
- ORCiD
- Boyce Thompson Institute, Ithaca, NY 14853, USA
- Hale Tufan
- ORCiD
- Cornell University, Ithaca, NY 14853, USA
- Agre Paterne
- ORCiD
- IITA Ibadan, 200001 Ibadan, Nigeria
- Asrat Asfaw
- ORCiD
- IITA Abuja, 901101 Abuja, Nigeria
- Jean-Luc Jannink
- ORCiD
- Cornell University, Ithaca, NY 14853, USA
- Marnin Wolfe
- ORCiD
- Cornell University, Ithaca, NY 14853, USA
- Clay L Birkett
- ORCiD
- Cornell University, Ithaca, NY 14853, USA
- David J Waring
- ORCiD
- Cornell University, Ithaca, NY 14853, USA
- Jenna M Hershberger
- ORCiD
- Cornell University, Ithaca, NY 14853, USA
- Michael A Gore
- ORCiD
- Cornell University, Ithaca, NY 14853, USA
- Kelly R Robbins
- ORCiD
- Cornell University, Ithaca, NY 14853, USA
- Trevor Rife
- ORCiD
- Kansas State University, Manhattan, KS 66506, USA
- Chaney Courtney
- Kansas State University, Manhattan, KS 66506, USA
- Jesse Poland
- ORCiD
- Kansas State University, Manhattan, KS 66506, USA
- Elizabeth Arnaud
- ORCiD
- Bioversity-CIAT Alliance, 34397 Montpellier, France
- Marie-Angélique Laporte
- ORCiD
- Bioversity-CIAT Alliance, 34397 Montpellier, France
- Heneriko Kulembeka
- TARI, 33518 Ukiriguru, Tanzania
- Kasele Salum
- TARI, 33518 Ukiriguru, Tanzania
- Emmanuel Mrema
- TARI, 33518 Ukiriguru, Tanzania
- Allan Brown
- ORCiD
- IITA Ibadan, 200001 Ibadan, Nigeria
- Stanley Bayo
- IITA Ibadan, 200001 Ibadan, Nigeria
- Brigitte Uwimana
- ORCiD
- IITA Ibadan, 200001 Ibadan, Nigeria
- Violet Akech
- IITA Ibadan, 200001 Ibadan, Nigeria
- Craig Yencho
- ORCiD
- North Carolina State University (NCSU), Raleigh, NC 27695, USA
- Bert de Boeck
- ORCiD
- CIP, 15000 Lima, Peru
- Hugo Campos
- ORCiD
- CIP, 15000 Lima, Peru
- Rony Swennen
- ORCiD
- KU Leuven, 3000 Leuven, Belgium
- Jeremy D Edwards
- ORCiD
- USDA-ARS, Stuttgart, AR 72160, USA
- Lukas A Mueller
- ORCiD
- Boyce Thompson Institute, Ithaca, NY 14853, USA
- DOI
- https://doi.org/10.1093/g3journal/jkac078
- Journal volume & issue
-
Vol. 12,
no. 7
Abstract
AbstractModern breeding methods integrate next-generation sequencing 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/, last accessed 4/18/2022https://cassavabase.org/https://www.nextgencassava.org/https://github.com/solgenomics/https://hub.docker.com/u/breedbase
