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Breedbase: a digital ecosystem for modern plant breeding

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Title Breedbase: a digital ecosystem for modern plant breeding
 
Creator 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.
 
Subject data
databases
breeding
phenotypes
genotyping
marker-assisted selection
digital technology
mejora
fenotipos
 
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.
 
Date 2022-07-06
2022-04-14T13:36:22Z
2022-04-14T13:36:22Z
 
Type Journal Article
 
Identifier 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
 
Language en
 
Rights CC-BY-4.0
Open Access
 
Format application/pdf
 
Publisher Oxford University Press (OUP)
 
Source G3-Genes Genomes Genetics