Breedbase is a comprehensive, open-source, breeding data management system [@doi:10.1093/g3journal/jkac078;@doi:10.1371/journal.pone.0240059] that implements a digital ecosystem for all breeding data, including trial data, phenotypic data, and genotypic data. Data acquisition is supported through data collection apps such as Fieldbook [@doi:10.2135/cropsci2013.08.0579], Coordinate, and InterCross, as well as through drone imagery, Near Infra-Red Spectroscopy (NIRS), and other technologies. Search functions, such as the Search Wizard interface, provide powerful query capabilities. Various breeding-centric analysis tools are available, including mixed models, heritability, stability, principal component analysis (PCA), and various clustering algorithms. The original impetus for creating Breedbase was the advent of new breeding paradigms based on genomic information such as genomic prediction algorithms [@doi:10.1093/genetics/157.4.1819] and the accompanying data management challenges. Thus, complete genomic prediction workflow is integrated in the system.
The BrAPI interface is crucial for Breedbase. Breedbase uses BrAPI to connect with the data collection apps, other projects such as CLIMMOB [@doi:10.1016/j.compag.2023.108539], and native BrAPPs built into the Breedbase webpage. Users also appreciate the ability to connect to Breedbase instances using packages such as QBMS [@doi:10.5281/zenodo.10791627] for data import into R for custom analyses. The Breedbase team has been part of the BrAPI community since its inception and has continuously adopted and contributed to the BrAPI standard.