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ARS Home » Northeast Area » Ithaca, New York » Robert W. Holley Center for Agriculture & Health » Plant, Soil and Nutrition Research » Research » Research Project #435394

Research Project: Breeding Insight Platform (BIP) Initiative

Location: Plant, Soil and Nutrition Research

Project Number: 8062-21000-043-004-A
Project Type: Cooperative Agreement

Start Date: Sep 1, 2018
End Date: Aug 31, 2023

The Breeding Insight Platform (BIP) will support breeding projects across ARS by building a team of specialists in information technology, genomics, and breeding process design that will partner with individual ARS pre-breeding and breeding groups. The initial two years will focus on recruiting the BIP team and integrating informatics tools. The project will leverage investments in nine open source informatic tools that are already funded by ARS, CGIAR, USAID, and BMGF and being developed by six institutions. Currently, these nine tools cover the domain space (various activities) needed for breeding programs to operate efficiently, but they do not inter-operate well. Additionally, some of the tools have been scaled for very large programs, and they need to be simplified for smaller breeding programs. The software engineers will improve and integrate these tools so they can be applied to specialty breeding programs. Initially, the platform will address four use cases: efficient genotyping, pedigree verification, genomic prediction, and identification of novel favorable variants. A director, a software development team, and application specialist coordinators will lead this effort from Ithaca, NY. In the first two years, the project will focus on five breeding programs during the pilot phase. In years 3-5, the project in collaboration with ARS coordinators will expand along with its advisory team to extend the results to additional remaining pre-breeding and breeding programs. The software engineering team in later years will focus on integration with germplasm collections, scaling, and support for the wide range of biology encountered across dozens of breeding programs. The Breeding Insight Platform has the possibility of more than doubling the efficiency of breeding programs, which would result in more sustainable, nutritious, profitable fruits, vegetables, aquacultural species, and range land plants. The shared open source platform will also allow innovation and talent to be shared much more widely. The open source software system developed by this project will also have broad applicability to numerous non-agricultural species, including species critical for ecology, conservation biology, pathology or any genomic diversity study. This project will conduct training to ensure researchers in other communities can use and contribute to the software platform. Additionally, because of the training and the platform’s open source nature it will provide a catalyst for start-up companies and university-based breeding programs to accelerate their efforts.

To build the Breeding Insight Platform a team of developers and coordinators will develop a software platform the combines the various software so that: 1. Breeding programs can track germplasm resources and field experiment designs. 2. Phenotypic data can be easily collected in the field and integrated with genomic data. 3. Genotyping data can be easily integrated with germplasm and phenotypic data. 4. Pedigree relationship can be evaluated. 5. Whole genome prediction of phenotypic traits. This project will also coordinate the genomic diversity analyses for all species, which includes long read DNA sequencing technology to assemble genomes, resequencing to discover variants, develop low costs assays for genotyping, and then genotype relevant germplasm. The sequencing of the software development will be: 1. Integrate and implement BrAPI and CassavaBase into a container that is easily deployable to cloud services. 2. Re-architect and deploy FieldBook to work with cloud services. 3. Integrate the GOBII module to support genomics. 4. Integrate Sample Tracker to support working with genotyping vendors. 5. Integrate the PHG to support whole genome information. 6. Develop BrAPI communication between BIP and GRINGlobal. Elements 1 & 2 are expected to take a year of software development time. Elements 3-5 another year of time, and element 6 another full year of development. In the first 2 years, the coordinators will work with 5 pilot plant and animal species to develop and test the system on their breeding programs.