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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 #444969

Research Project: Breeding Insight 3

Location: Plant, Soil and Nutrition Research

Project Number: 8062-21000-052-003-A
Project Type: Cooperative Agreement

Start Date: Sep 16, 2023
End Date: Sep 15, 2024

Breeding Insight (BI) will continue to support breeding projects across ARS with a team of specialists in information technology, genomics, and breeding process design who partner with individual ARS pre-breeding and breeding groups. The project leverages investments in nine open-source informatics tools that are already funded by ARS, CGIAR, USAID, and BMGF and are being used and developed by six institutions. Currently, these nine tools cover the domain space (various activities) needed for most breeding programs to operate efficiently, but they do not inter-operate well and some needs/activities are not covered (e.g., animal welfare management). 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 continue to improve and integrate these tools and features or create new tools into a new software platform called DeltaBreed. The platform addresses four use cases: efficient genotyping, high-quality phenotyping, bioinformatic support and analytics, and holistic data management of breeding programs. A director, a software development team, and application specialist coordinators lead this effort from Ithaca, NY with some fully remote team members. A sister group, BI-OnRamp, is run out of NC State to support four species. Both BI and OnRamp are in daily contact and function as a single unit. Combined, both groups support a total of nineteen ARS animal and crop breeding programs. The third installment of new species to the program is expected in Fall 2023, which will add ten to twelve more species bringing the total number of species supported to thirty or more. The software engineering team in later years will focus on integration with germplasm collections (i.e., GRIN-Global), scaling, and support for the wide range of biology encountered across dozens of breeding programs. Breeding Insight 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 DeltaBreed platform will also allow innovation and talent to be shared much more widely. DeltaBreed, 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 software, a team of developers and coordinators will develop a platform that combines the various software into DeltaBreed so that: 1. Breeding programs can track germplasm resources, field experiment designs, and document decisions. 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. Bioinformatic and analytic tools can be leveraged in user-friendly software to aid analyses, decisions, and publications that abide by FAIR data principles. 5. Genomic analyses to perform whole genome prediction of phenotypic traits. 6. Animal welfare data can be efficiently tracked, monitored, and reported to regulatory agencies. This project will continue to coordinate the genomic diversity analyses for all included species, which includes both short- and long-read DNA sequencing technology to assemble genomes, resequencing to discover variants, develop low costs assays for genotyping, and then genotype-relevant germplasm. The order of the DeltaBreed software development will be: 1. Integrate and implement BrAPI and BreedBase into a container that is easily deployable to cloud services. 2. Deploy FieldBook to work with Breedbase via BrAPI. 3. Integrate the Gigwa module to support genomics. 4. Develop BrAPI communication between DeltaBreed and GRIN-Global. 5. Integrate Sample Tracker to support working with genotyping vendors. 6. Integrate the PHG to support whole genome information. 7. Identify or develop animal welfare data collection software for improved record keeping. 8. Create and integrate customized, pre-tuned, analytics software modules for genomic analyses. 9. Create and integrate a data quality software module. Elements 1 & 2 have been completed but are in refinement. Elements 3-5 are expected to take a year of software development time. Elements 6-7 another year of time, and elements 8 & 9 another full year of development. In the first 4 years, the coordinators have worked with 19 pilot plant and animal species to develop and test the system on their breeding programs. In years 5-7, coordinators will continue to support the current 19 species needs as well as start new support for an additional 10-12 species.