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Breedbase: a digital ecosystem for modern plant breeding

dc.contributor.authorMorales, N.
dc.contributor.authorOgbonna, A.C.
dc.contributor.authorEllerbrock, B.J.
dc.contributor.authorBauchet, G.J.
dc.contributor.authorTantikanjana, T.
dc.contributor.authorTecle, I.Y.
dc.contributor.authorPowell, A.
dc.contributor.authorLyon, D.
dc.contributor.authorMenda, N.
dc.contributor.authorSimoes, C.C.
dc.contributor.authorSaha, S.
dc.contributor.authorHosmani, P.
dc.contributor.authorFlores, M.
dc.contributor.authorPanitz, N.
dc.contributor.authorPreble, R.S.
dc.contributor.authorAgbona, A.
dc.contributor.authorRabbi, I.Y.
dc.contributor.authorKulakow, P.
dc.contributor.authorPeteti, P.
dc.contributor.authorKawuki, R.
dc.contributor.authorEsuma, W.
dc.contributor.authorKanaabi, M.
dc.contributor.authorChelangat, D.M.
dc.contributor.authorUba, E.
dc.contributor.authorOlojede, A.O.
dc.contributor.authorOnyeka, J.
dc.contributor.authorShah, T.
dc.contributor.authorKaranja, M.
dc.contributor.authorEgesi, C.
dc.contributor.authorTufan, H.A.
dc.contributor.authorAgre, A.P.
dc.contributor.authorAsfaw, A.
dc.contributor.authorJannink, J.
dc.contributor.authorWolfe, M.
dc.contributor.authorBirkett, C.L.
dc.contributor.authorWaring, D.J.
dc.contributor.authorHershberger, J.M.
dc.contributor.authorGore, M.A.
dc.contributor.authorRobbins, K.
dc.contributor.authorRife, T.
dc.contributor.authorCourtney, C.
dc.contributor.authorPoland, J.
dc.contributor.authorArnaud, E.
dc.contributor.authorLaporte, M.A.
dc.contributor.authorKulembeka, H.
dc.contributor.authorSalum, K.
dc.contributor.authorMrema, E.
dc.contributor.authorBrown, A.
dc.contributor.authorBayo, S.
dc.contributor.authorUwimana, B.
dc.contributor.authorAkech, V.
dc.contributor.authorYencho, C.
dc.contributor.authorde Boeck, B.
dc.contributor.authorCampos, H.
dc.contributor.authorSwennen, R.
dc.contributor.authorEdwards, J.D.
dc.contributor.authorMueller, L.
dc.date.accessioned2022-06-09T08:52:36Z
dc.date.available2022-06-09T08:52:36Z
dc.date.issued2022
dc.identifier.citationMorales, N., Ogbonna, A.C., Ellerbrock, B.J., Bauchet, G.J., Tantikanjana, T., Tecle, I.Y., ... & Mueller, L.A. (2022). Breedbase: a digital ecosystem for modern plant breeding. G3-Genes Genomes Genetics, 1-12.
dc.identifier.issn2160-1836
dc.identifier.urihttps://hdl.handle.net/20.500.12478/7499
dc.description.abstractModern 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.description.sponsorshipBill & Melinda Gates Foundation
dc.description.sponsorshipUK’s Foreign, Commonwealth & Development Office
dc.format.extent1-12
dc.language.isoen
dc.subjectDatabases
dc.subjectBreeding
dc.subjectPhenotypes
dc.subjectGenotyping
dc.subjectMarker-Assisted Selection
dc.subjectDigital Technology
dc.titleBreedbase: a digital ecosystem for modern plant breeding
dc.typeJournal Article
cg.contributor.crpRoots, Tubers and Bananas
cg.contributor.affiliationBoyce Thompson Institute
cg.contributor.affiliationCornell University
cg.contributor.affiliationInternational Institute of Tropical Agriculture
cg.contributor.affiliationNaCCRI, Uganda
cg.contributor.affiliationNational Root Crops Research Institute, Nigeria
cg.contributor.affiliationUnited States Department of Agriculture
cg.contributor.affiliationKansas State University
cg.contributor.affiliationThe Alliance of Bioversity International and the International Center for Tropical Agriculture
cg.contributor.affiliationTanzania Agricultural Research Institute
cg.contributor.affiliationNorth Carolina State University
cg.contributor.affiliationInternational Potato Center
cg.contributor.affiliationKatholieke Universiteit Leuven
cg.coverage.regionACP
cg.coverage.regionNorth America
cg.coverage.countryUnited States of America
cg.coverage.hubHeadquarters and Western Africa Hub
cg.researchthemeBiotech and Plant Breeding
cg.identifier.bibtexciteidMORALES:2022
cg.isijournalISI Journal
cg.authorship.typesCGIAR and developing country institute
cg.iitasubjectAgronomy
cg.iitasubjectFood Security
cg.iitasubjectGenetic Improvement
cg.iitasubjectPlant Breeding
cg.iitasubjectPlant Genetic Resources
cg.iitasubjectPlant Production
cg.journalG3-Genes Genomes Genetics
cg.notesOpen Access Journal; Published online: 06 Apr 2022
cg.accessibilitystatusOpen Access
cg.reviewstatusPeer Review
cg.usagerightslicenseCreative Commons Attribution 4.0 (CC BY 0.0)
cg.targetaudienceScientists
cg.identifier.doihttps://doi.org/10.1093/g3journal/jkac078
cg.iitaauthor.identifierIsmail Rabbi: 0000-0001-9966-2941
cg.iitaauthor.identifierPeter Kulakow: 0000-0002-7574-2645
cg.iitaauthor.identifierTrushar Shah: 0000-0002-0091-7981
cg.iitaauthor.identifierChiedozie Egesi: 0000-0002-9063-2727
cg.iitaauthor.identifierPaterne AGRE: 0000-0003-1231-2530
cg.iitaauthor.identifierAsrat Asfaw: 0000-0002-4859-0631
cg.iitaauthor.identifierAllen Brown: 0000-0002-4468-5932
cg.iitaauthor.identifierBrigitte Uwimana: 0000-0001-7460-9001
cg.iitaauthor.identifierRony Swennen: 0000-0002-5258-9043
cg.futureupdate.requiredNo
cg.identifier.issue7
cg.identifier.volume12


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