The Cassavabase System, a Web-Based Breeding Platform Adaptable for Many Crops

Cassava (Manihot esculenta) is the main source of calories for 500 million people worldwide and indispensable for food security in Africa. CassavaBase (https://cassavabase.org) is the central datastore for the NextGen Cassava Project, aiming to leverage cassava genomic breeding and accelerate variety development in Africa (http://www.nextgencassava.org/). Cassavabase aims to provide a complete bioinformatic toolset to the cassava research and breeding communites. From the field to the lab to the breeders office, it can track information, streamline management of genotypic and phenotypic data, and implements genomic selection analyses.

Through its web interface Cassavabase can be accessed from anywhere on the globe, enhancing data sharing and communication within cassava research community in Africa and overseas. User feedback drives new development and improvements through active communication with users and breeders. Current tools cover phenotyping data (trait ontology dictionary, fieldbook app), sequencing data (GBS pipeline, Jbrowse), breeding management (breeding program, trial, trait, pedigree search) and molecular breeding (trait descriptive statistics, genetic maps, genomic selection).

Since its inception, almost 10 million phenotypic datapoints and 18,000 genotyped accessions have been stored from 500+ users across half dozen breeding programs. All current development and data are open source and available to the community (https://github.com/solgenomics/). To enable easy data exchange with other tools and databases, Cassavabase implements the Plant Breeding API (BrAPI, http://brapi.org/).