Location: Plant, Soil and Nutrition Research
Project Number: 8062-21000-052-020-A
Project Type: Cooperative Agreement
Start Date: Aug 15, 2025
End Date: Aug 14, 2026
Objective:
The goal of the Cooperator is to place advanced artificial intelligence (AI), genomic, and bioinformatic tools in the hands of Agricultural Research Service (ARS) crop and animal breeders. These tools will enhance efficiency and improve breeding decisions to meet public demand for more nutritious, flavorful, and sustainable U.S.-grown foods. The effort will enable U.S. farmers to respond more rapidly to new pests, pathogens, market changes, and environmental pressures. It is expected to accelerate the development and delivery of new varieties by two-fold or more.
The Cooperator will continue supporting ARS breeding projects with a team of specialists in information technology, AI, genomics, and breeding process design. This work is done in direct collaboration with individual ARS pre-breeding and breeding programs across the United States.
The project builds on ARS-funded investments in nine open-source informatics tools. These tools support a broad range of breeding program activities and improve data-driven decision-making throughout the breeding cycle. However, many tools do not currently interoperate, and some critical needs such as animal welfare tracking remain unmet. The Cooperator will continue improving interoperability, simplifying tools for smaller programs, and creating new tools where gaps remain. All software will be delivered through the DeltaBreed platform.
DeltaBreed supports four major use cases:
• Genotyping workflow optimization
• High-quality phenotyping
• Bioinformatics and analytics integration
• Centralized, holistic breeding data management
With partners within ARS, the project will support 31 ARS crop and animal breeding programs, and develop infrastructure to expand to as many as 90 species in the future.
Future efforts will include deeper integration with U.S. germplasm repositories such as the Germplasm Resources Information Network – Global (GRIN-Global), improved scalability of tools, and expanded biological support across diverse breeding domains.
The project will continue to substantially increase efficiency across ARS breeding programs, reduce data loss, improve data publication and reuse, and ensure long-term stewardship of publicly funded research. DeltaBreed will also support training and knowledge transfer to university breeding programs and other U.S.-based research communities. As an open-source platform, DeltaBreed may serve as a foundation for innovation in forestry, land management, and mid-sized commercial breeding efforts.
Approach:
The BI team of developers and coordinators will continue expanding DeltaBreed to connect it with other tools for rapid customization. This includes tools and features that:
Track germplasm, field designs, traits, genotyping experiments, and breeding decisions
Improve quality and efficiency of phenotypic data collection the ARS unit
Incentivize genotyping and accelerate utilization for faster, data-driven decisions
Integrate bioinformatic and analytical tools into user-friendly, interoperable software
Help ARS breeders meet public data mandates and align with FAIR data principles
Enable breeders to run whole-genome predictions on their own
Improve animal welfare data tracking, monitoring, and reporting
Use AI and machine learning to increase power, efficiency, and decision speed at no extra cost
The project will continue coordinating genomic diversity analysis across species, including genome assembly using short- and long-read sequencing, variant discovery, low-cost genotyping assay development, and genotyping of relevant germplasm. Additional support will focus on complex and polyploid genomes requiring extra data types for informed selection.
Custom pipelines created in prior phases have been highly successful and remain in demand. BI-developed tools, co-created with ARS scientists, may have broader application. BI will work with the Digital Ag Solutions Hub (DASH) to share tools more widely within ARS.
Planned DeltaBreed software development steps include:
Containerize BrAPI and DeltaBreed to deployable on cloud services
Integrate the Gigwa module for genomics
Develop BrAPI links between DeltaBreed and GRIN-Global
Integrate Sample Tracker for genotyping vendor coordination
Add the Practical Haplotype Graph (PHG) for full genome support
Identify or develop animal welfare data collection tools
Add pre-tuned AI/ML modules for genomic analyses, and image-based and high-throughput phenotyping
Add breeding decision support tools]
Add a data quality assurance module
Elements 1, 2, 7-9 and are complete but undergoing refinement. Elements 3–4 are expected to require one year of development. Element 6 will require an additional year, and element 5 will take another full year.
In the first five years, BI coordinators supported 31 crop and animal species. In years 6–8, support will continue for all USDA-ARS breeding efforts on a project-by-project basis.