Breedbase: a Game-Changing Open Software for Plant Breeding Management

June 27, 2023

To meet the grand challenge of breeding the next generation of climate-adapted crops, we’re going to need innovative solutions that enhance and accelerate plant breeding programs. One such game-changer in the field is Breedbase, a comprehensive breeding management and analysis software platform.

Breedbase is designed to assist plant breeders in managing and analyzing their breeding programs efficiently. It can be used to design field trial layouts, collect phenotypic information and genotyping samples in the field, to store large amounts of genotypic information, and to run Genomic Selection analyses.

Unlike traditional software solutions, Breedbase operates in the cloud, eliminating the need for installation, and thus allowing access from anywhere with an internet connection. This approach enables seamless collaboration among breeders, as they can work with the same data, traits, and accessions, facilitating the development of large, unified datasets.

DivSeek had the opportunity to interview Lukas Mueller, a leading scientist involved in the development of Breedbase, who shed light on the inspiration and functionality of this exciting software solution.

Breedbase originated from Solgenomics.net, a genomics website that incorporated both genome annotation and phenotypic information. Mueller explains, “Most breeding information systems at that time were not web-based, but Breedbase changed that.” The aim was to create a cloud-based interface that accommodates different locations and breeding programs, fostering collaboration and unifying datasets. Mueller continues, “All the breeders would have access to the same data, the same traits, accessions, etc., which would spur collaboration.” This web-based approach filled the gap left by other databases, enabling breeders to leverage both phenotypic and genotypic data effectively.

Breedbase offers a range of features and functionalities to assist breeders and researchers in managing and analyzing their data. Mueller emphasizes that Breedbase was designed with Genomic Selection in mind, supporting both phenotypic and genotypic data storage, as well as related analyses. Notable tools such as solGS for models and predictions, GWAS, clustering, and integration of the BrAPI 2.1 specification empower breeders to explore and exploit their data efficiently. Additionally, Breedbase includes Imagebreed, a module for drone-based imaging and analysis, and supports NIRS-based phenotyping.

Breedbase has proven its worth in numerous breeding programs, demonstrating remarkable success stories. Cassavabase, the flagship database, boasts an extensive collection of public breeding data for cassava. Mueller proudly shares, “It probably contains one of the largest amounts of public breeding data for any crop, including 23 million phenotypic datapoints and tens of thousands genotyped accessions.” Other programs, such as Yambase, Sweetpotatobase, and Musabase, have also benefited from Breedbase, resulting in the release of improved varieties. Beyond the CGIAR’s RTB program, Breedbase has gained popularity in academic labs, breeding companies, and instances for various crops worldwide.

Creating a new instance in Breedbase is a straightforward process. Anyone can do it, simply by installing the system and downloading the definition files from GitHub. From there, users can upload their accessions, ontologies, locations, pedigree information, and historic trials data. Mueller highlights that this configuration and initial data load can be time-consuming. “A particular issue is the creation or import of a trait ontology,” he explains. Sometimes, standard ontologies can be imported from projects such as CropOntology.org, but other times researchers must create one from scratch. “Importantly, all breeders using the system should agree on the same traits and analytical procedures!”

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Breedbase has revolutionized plant breeding management and analysis by providing a cloud-based, collaborative platform that integrates phenotypic and genotypic data. With its customizable instances and extensive functionalities, Breedbase empowers breeders and researchers in their quest for improved crop varieties. As Lukas Mueller aptly summarizes, “Breedbase has unlocked the potential for collaboration, unifying vast datasets and fostering progress in breeding programs.” The future of plant breeding looks brighter with this innovative tool.

 

Citation:

Hershberger, J, Morales, N, Simoes, CC, et al. Making waves in Breedbase: An integrated spectral data storage and analysis pipeline for plant breeding programs. Plant Phenome J. 2021; 4:e20012. https://doi.org/10.1002/ppj2.20012  

 

 

 

 

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