Integrated breeding platform - Plant breeding software

Partnerships at the heart of IBP deployment approach

August 5, 2015

The Integrated Breeding Platform (IBP) is positioning itself as one of the most comprehensive resources for best practices in plant breeding, with a notable focus on addressing the needs of breeders in developing countries. It is a comprehensive web-based platform enabling plant breeders to access and apply modern breeding in a practical and sustainable way, by providing them with the tools and support they require to strengthen their capacities and instigate innovation.

At the core of this offer lays the IBP Breeding Management System (BMS), a complete software suite combining crop information management, data analysis and decision-support tools, to assist plant breeders in conducting most of their routine breeding activities, including the integration of different levels of marker use.  A range of breeding services are also accessible to complement the software suite, such as genotyping, breeding materials and related information for a broad array of crops (including germplasm, trait dictionaries and predictive markers), training opportunities, dedicated technological support, and community spaces.

The IBP is not alone in this effort, nor can it achieve the change it aspires to in a vacuum. Consequently, working closely with partners is at the heart of its deployment approach.

“As we learnt from the GCP experience (the former entity under which the IBP was conceived), building true partnerships, where all actors share a sense of responsibility and ownership, will prove to be a powerful success factor if we are serious about optimising plant breeding in developing countries”, shares Jean-Marcel Ribaut, IBP Director. “A combined effort between collaborators, in initiatives such as the Genomes to Fields project (G2F), the Genomic & Open-source Breeding Informatics Initiative (GOBII), academic networks and other developer and crop communities, will magnify the impact we can achieve.” 

Our follow-up story delves deeper in the workings of these partnerships, explore the conditions that make for fruitful collaborations, and give a sense of the impact they aspire to accomplish. Read on to learn more of the Lawrence Lab at Iowa State University, the iPlant Collaborative, and the IBP collaborating in the Genomes to Fields project (G2F), where maize breeders are using the BMS to manage germplasm information and phenotyping evaluation, but also contributing to BMS development through feedback and coding.

The G2F collaboration

“The true impact of the G2F initiative lays on our ability to effectively exploit and combine large scale genomic, phenomic and envirotyping data that characterizes the diversity of germplam resources and relevant environments to determine what portion of the functional variation that we can measure would effectively help us make better predictions of end-of-the-season performance. Such effort is only possible if researchers, no matter where they are, can access these dynamic and interconnected datasets that we are generating in a timely, useful and reliable way. That is why we are thrilled that the IBP has truly embraced the collaborative spirit of this effort and has worked with us so diligently to identify ways to make these critical resources meet the needs of this multi-investigator research effort. We also hope that the work that is currently being developed for maize will be nothing but the start of a wave of similar efforts sprouting across many species and around the world,” says Natalia de Leon, co-lead on the G2F Executive Committee, Associate Professor, Department of Agronomy, University of Wisconsin.

Steve Goff, iPlant's former Principal Investigator during the beginnings of IBP, agrees: "This initiative is an ideal route toward the development of the high throughput phenotyping tools needed to bridge the gap between genomic information and accelerated crop enhancement via molecular breeding. The analysis pipelines provided by the IBP also are essential components to handle the large datasets and complex association challenges, and we at iPlant feel perfectly situated to support such public-private collaborations."

Collaborating with Cornell University

The Buckler Lab for Maize Genetics and Diversity at Cornell University is also participating in G2F and therefore part of the first wave to adapt the BMS as their lab’s system: “At the heart of every genetics and breeding group is the ability to keep track of germplasm and phenotypes.  We had been using our own custom system for the last 15 years, but the BMS provided an exciting opportunity to work with a global community to help build a system that would be useful for 1000s of groups globally,” explains Ed Buckler, USDA-ARS Research Geneticist & Group Leader, Cornell University.

Cornell University intersects with the IBP through the G2F effort, but also through the Genomic & Open-source Breeding Informatics Initiative (GOBII), where the BMS is intended to work in complementarity to GOBII’s pipeline for allelic mining.

iPlant Collaborative, a partner since inception

From hosting the IBP Portal to providing IBP registered users with access to public datasets, personal data storage space and complementary tools and services, through playing a key role in wider partnerships such as the Genomes to Fields project, the iPlant Collaborative has been a close partner since the very beginnings of the IBP.


>The IBP works closely with the Lawrence Lab (Iowa State University) and the iPlant Collaborative under the Genomes to Fields project to improve breeding data management


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