Soft launch of CGIAR Breeding Analytics Pipeline enables complex quantitative genetic analyses for CGIAR crop breeders

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In late 2023, Breeding Resources Initiative tasked a fast-track team of biometricians with the development of a Breeding Analytics Pipeline to support CGIAR crop breeding activities, with the endorsement of Genetic Innovation leadership. The tool is now available to internal users.

The Breeding Analytics (BA) Pipeline as a cutting-edge tool designed to guide decision-making processes in global crop breeding. It extracts crop breeding data from diverse databases and conducts complex analyses for crop breeders, such as estimating genetic gains or employing selection indices. 

In mid-February, Nairobi had already witnessed the gathering of biometricians and quantitative geneticists from CGIAR Centers, convened at a hackathon to refine the BA Pipeline following its initial development phase. The aim was to present its structure and enable CGIAR Centers to contribute tailor-made modules, each designed for specific analyses crucial to plant breeding work. 

The soft launch of the BA Pipeline marks a key moment for CGIAR’s crop breeding work, as crop breeding teams across the organization can now access the tool, test it, but also use it, and contribute suggestions for improvement. All CGIAR users can engage in state-of-the-art quantitative genetic analyses using the BA Pipeline by simply requesting access from the Breeding Analytics team and utilizing the production server. 

The tool is set to be officially launched for all users worldwide, including external partners and NARES, in July of this year. 

Presentation of the Breeding Analytics Pipeline at the South Asia Advancement Meeting, Hyderabad, India, 2024. Credit: IRRI.

A scalable tool for crop breeders around the world

Drawing on insights from the crop breeding analytics hackathon and feedback from beta-testers, the BA Pipeline has been meticulously crafted to meet the evolving needs of breeders and researchers. The soft launch serves as a testing ground, allowing for further development and continuous improvement based on CGIAR and real-world usage. 

The production server accessible to the Breeding Analytics team and early adopters from CGIAR crop breeding teams, hosts the BA Pipeline and provides important computing resources, offering crop breeders and researchers access to powerful analytical tools.  

Additionally, a testing and guest server has been made available to facilitate broader engagement and collaboration. This server is accessible to external users, with limited computing capacity for light analyses allowing users to consult the tool even without login credentials. This server will mainly be used for training and demonstrations. 

Looking ahead, CGIAR has set its sights on a full official release of the BA Pipeline slated for July 2024. This release will accommodate more simultaneous users and leverage increased computing resources, enhancing CGIAR’s capacity to drive innovation in crop breeding.  

Integration with CGIAR Service Request Portal, where breeders and partners can seamlessly order Breeding Resources Initiative’s Services, and the availability of online video training materials will further enhance accessibility and usability. 


Broad training initiative for Centers to familiarize with the BA Pipeline

Concurrent with the soft launch, CGIAR has embarked on a comprehensive training initiative to familiarize National Agricultural Research and Extension Systems (NARES) partners with the BA Pipeline. The inaugural training session, held in India and facilitated by the International Rice Research Institute (IRRI), laid the groundwork for future engagements across various Centers. 

During the recent South Asia Advancement Meeting, attended by breeders from Nepal, Bangladesh, and India and where discussions centered on the selection of rice material for field evaluation, a dedicated training session on “Biometrical Genetics Workflow” was conducted, drawing participation from approximately 100 attendees. The training provided the opportunity to show participants the BA Pipeline’s capabilities. 

The feedback from attendees was overwhelmingly positive, as observed by Giovanny Covarrubias, IRRI Breeding Analytics Lead and member of the fast-track team in charge of the development of the BA Pipeline.  

“Many participants expressed eagerness to delve deeper into the platform. They also emphasized the importance of localized support for the future deployment of the tool. The BA Pipeline generates modules to visualize results, and participants expressed their willingness to allocate more time for interpreting them, as this is what they will be using at the breeding program level to make informed data-driven decisions.”. He added: “Overall, the inaugural training session of this extensive series was a success.”  

As the Breeding Analytics team continues to roll out the training initiative for Centers, it remains committed to fostering collaboration and driving innovation in crop breeding worldwide. The BA Pipeline will ultimately enhance operational efficiency but also deliver robust reporting capabilities, as Accelerated Breeding Initiative keeps ensuring alignment with CGIAR global crop breeding programs’ needs.


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Main image: Giovanny Covarrubias IRRI providing support and explanations to South Asia Advancement Meeting participants about the BA Pipeline, Hyderabad, India, 2024. Credit: IRRI. The development of the BA Pipeline is funded by Crops to End Hunger, a broad multi-funder initiative substantially supported by the Federal Ministry for Economic Cooperation and Development (BMZ), and channelled through the Deutsche Gesellschaft für Internationale Zusammenarbeit (GIZ).

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