Breedbase: a digital ecosystem for modern plant breeding

Author:

Morales Nicolas12ORCID,Ogbonna Alex C12ORCID,Ellerbrock Bryan J1,Bauchet Guillaume J1ORCID,Tantikanjana Titima1,Tecle Isaak Y1ORCID,Powell Adrian F1ORCID,Lyon David1ORCID,Menda Naama1ORCID,Simoes Christiano C1,Saha Surya1ORCID,Hosmani Prashant1ORCID,Flores Mirella1ORCID,Panitz Naftali1ORCID,Preble Ryan S1,Agbona Afolabi3ORCID,Rabbi Ismail3ORCID,Kulakow Peter3ORCID,Peteti Prasad3ORCID,Kawuki Robert4ORCID,Esuma Williams4ORCID,Kanaabi Micheal4,Chelangat Doreen M4ORCID,Uba Ezenwanyi5,Olojede Adeyemi5ORCID,Onyeka Joseph5,Shah Trushar6ORCID,Karanja Margaret6ORCID,Egesi Chiedozie135ORCID,Tufan Hale2ORCID,Paterne Agre3ORCID,Asfaw Asrat7ORCID,Jannink Jean-Luc28ORCID,Wolfe Marnin2ORCID,Birkett Clay L28ORCID,Waring David J28ORCID,Hershberger Jenna M2ORCID,Gore Michael A2ORCID,Robbins Kelly R2ORCID,Rife Trevor9ORCID,Courtney Chaney9,Poland Jesse9ORCID,Arnaud Elizabeth10ORCID,Laporte Marie-Angélique10ORCID,Kulembeka Heneriko11,Salum Kasele11,Mrema Emmanuel11,Brown Allan3ORCID,Bayo Stanley3,Uwimana Brigitte3ORCID,Akech Violet3,Yencho Craig12ORCID,de Boeck Bert13ORCID,Campos Hugo13ORCID,Swennen Rony14ORCID,Edwards Jeremy D15ORCID,Mueller Lukas A1ORCID

Affiliation:

1. Boyce Thompson Institute , Ithaca, NY 14853, USA

2. Cornell University , Ithaca, NY 14853, USA

3. IITA Ibadan , 200001 Ibadan, Nigeria

4. NaCCRI , Namulonge, Uganda

5. National Root Crops Research Institute (NRCRI) , 463109 Umudike, Nigeria

6. IITA Nairobi , 30709-00100 Nairobi, Kenya

7. IITA Abuja , 901101 Abuja, Nigeria

8. USDA-ARS , Ithaca, NY 14853, USA

9. Kansas State University , Manhattan, KS 66506, USA

10. Bioversity-CIAT Alliance , 34397 Montpellier, France

11. TARI , 33518 Ukiriguru, Tanzania

12. North Carolina State University (NCSU) , Raleigh, NC 27695, USA

13. CIP , 15000 Lima, Peru

14. KU Leuven , 3000 Leuven, Belgium

15. USDA-ARS , Stuttgart, AR 72160, USA

Abstract

Abstract Modern 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 4/18/2022). Originally initiated as Cassavabase (https://cassavabase.org/, last accessed 4/18/2022) with the NextGen Cassava project (https://www.nextgencassava.org/, last accessed 4/18/2022), 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/, last accessed 4/18/2022) and packaged in a Docker image for deployment (https://hub.docker.com/u/breedbase, last accessed 4/18/2022). The Breedbase system enables breeding programs to better manage and leverage their data for decision making within a fully integrated digital ecosystem.

Funder

Cornell University

Bill & Melinda Gates Foundation

UK’s Foreign, Commonwealth & Development Office

Publisher

Oxford University Press (OUP)

Subject

Genetics (clinical),Genetics,Molecular Biology

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