Breedbase: a digital ecosystem for modern plant breeding

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dc.creatorMorales, Nicolas
dc.creatorOgbonna, Alex C.
dc.creatorEllerbrock, Bryan J.
dc.creatorBauchet, Guillaume J.
dc.creatorTantikanjana, Titima
dc.creatorTecle, Isaak Y.
dc.creatorPowell, Adrian F.
dc.creatorLyon, David
dc.creatorMenda, Naama
dc.creatorSimoes, Christiano C.
dc.creatorSaha, Surya
dc.creatorHosmani, Prashant
dc.creatorFlores, Mirella
dc.creatorPanitz, Naftali
dc.creatorPreble, Ryan S.
dc.creatorAgbona, Afolabi
dc.creatorRabbi, Ismail
dc.creatorKulakow, Peter A.
dc.creatorPeteti, Prasad
dc.creatorKawuki, Robert
dc.creatorEsuma, Williams
dc.creatorKanaabi, Micheal
dc.creatorChelangat, Doreen M.
dc.creatorUba, Ezenwanyi
dc.creatorOlojede, Adeyemi
dc.creatorOnyeka, Joseph
dc.creatorShah, Trushar
dc.creatorKaranja, Margaret
dc.creatorEgesi, Chiedozie N.
dc.creatorTufan, Hale Ann
dc.creatorPaterne, Agre
dc.creatorAsfaw, Asrat
dc.creatorJannink, Jean-Luc
dc.creatorWolfe, Marnin
dc.creatorBirkett, Clay L.
dc.creatorWaring, David J.
dc.creatorHershberger, Jenna M.
dc.creatorGore, Michael A.
dc.creatorRobbins, Kelly R.
dc.creatorRife, Trevor
dc.creatorCourtney, Chaney
dc.creatorPoland, Jesse A.
dc.creatorArnaud, Elizabeth
dc.creatorLaporte, Marie-Angélique
dc.creatorKulembeka, Heneriko
dc.creatorSalum, Kasele
dc.creatorMrema, Emmanuel
dc.creatorBrown, Allan
dc.creatorBayo, Stanley
dc.creatorUwimana, Brigitte
dc.creatorAkech, Violet
dc.creatorYencho, Craig
dc.creatorBoeck, Bert de
dc.creatorCampos, Hugo
dc.creatorSwennen, Rony L.
dc.creatorEdwards, Jeremy D.
dc.creatorMueller, Lukas A.
dc.date2022-07-06
dc.date2022-04-14T13:36:22Z
dc.date2022-04-14T13:36:22Z
dc.date.accessioned2026-06-27T17:58:21Z
dc.descriptionModern 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.
dc.formatapplication/pdf
dc.identifierhttps://hdl.handle.net/10568/119327
dc.identifier.urihttp://hdl.handle.net/123456789/151088
dc.languageen
dc.publisherOxford University Press
dc.rightsOpen Access
dc.sourceMorales, 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
dc.subjectdata
dc.subjectdatabases
dc.subjectbreeding
dc.subjectphenotypes
dc.subjectgenotyping
dc.subjectmarker-assisted selection
dc.subjectdigital technology
dc.subjectmejora
dc.subjectfenotipos
dc.titleBreedbase: a digital ecosystem for modern plant breeding
dc.typeJournal Article

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Centro Internacional de la Papa (CIP)