Building the Tools to Solve the Genome to Phenome Puzzle in Agriculture

Abstract The USDA-NIFA is developing a vision for agricultural genomics to phenomics research (AG2P) through two programs. In 2017, the Functional Annotation of Animal Genomes (FAANG) request for proposals was released, which has provided over $9 Million in funding to groups over the past five years to create public resources for the study of regulatory and other functional elements in agriculturally important species. This effort has been extended by other countries who have contributed another $20 Million+ (equivalent). These initial resource-building efforts are providing extensive new epigenetic data that are used to better understand the function of animal genomes and to enhance animal genetic improvement. However, such research demonstrates new infrastructure is needed across the agricultural enterprise to predict phenotypes from genome information. In 2020, NIFA inaugurated the Agricultural Genome to Phenome Initiative program (AG2PI), and an important objective of this presentation is to encourage strong participation of animal genomic researchers and industry in the AG2PI project. The purpose of AG2PI is to assemble and prepare a community to conduct AG2P research across the plant and animal kingdoms. The focus of the AG2PI is: a) identifying research gaps and opportunities, b) fostering community solutions to these challenges, and c) rapidly disseminating findings. Training workshops, field days, conferences, community surveys, and seed grants have all contributed to these goals. Opinions and ideas from the crop, livestock and aquaculture genetics communities are key to advancing G2P science and related work. The AG2PI uses online community surveys and in-person conferences to gather these and to facilitate transdisciplinary communications. In September 2022, AG2PI held a conference entitled “Thinking Big: Visualizing the Future of AG2PI”, in which attendees focused small group discussions to identify which agricultural G2P-related topics are most critical for future R&D funding and which may be the most difficult to achieve. These discussions have been summarized in a concept paper for the community and shared with USDA-NIFA. A follow-up conference is planned for June 2023 in Kansas City, which we hope many members from animal genetics research and industry will attend. The future of agricultural genomics will be shaped by both the participants in AG2PI and the solutions developed by the AG2PI community. USDA NIFA awards 2022-70412-38454, 2021-70412-35233, and 2020-70412-32615.