Current challenges and future of agricultural genomes to phenomes in the USA
Christopher K. Tuggle, Jennifer Clarke, Brenda M. Murdoch, Eric Lyons, Nicole Scott, Bedřich Beneš, Jacqueline Campbell, Henri Chung, Courtney L Daigle, Sruti Das Choudhury, Jack C. M. Dekkers, J.R.R. Dórea, David Ertl, Max Feldman, Breno Fragomeni, Janet E. Fulton, Carmela R. Guadagno, Darren E. Hagen, Andrew S. Hess, Luke Kramer, Carolyn J. Lawrence‐Dill, Alexander E. Lipka, Thomas Lübberstedt, Fiona McCarthy, Stephanie McKay, Seth C. Murray, Penny K. Riggs, Troy N. Rowan, Moira J. Sheehan, Juan P. Steibel, Addie Thompson, Kara J Thornton, Curtis P. Van Tassell, Patrick S. Schnable
Abstract
Dramatic improvements in measuring genetic variation across agriculturally relevant populations (genomics) must be matched by improvements in identifying and measuring relevant trait variation in such populations across many environments (phenomics). Identifying the most critical opportunities and challenges in genome to phenome (G2P) research is the focus of this paper. Previously (Genome Biol, 23(1):1-11, 2022), we laid out how Agricultural Genome to Phenome Initiative (AG2PI) will coordinate activities with USA federal government agencies expand public-private partnerships, and engage with external stakeholders to achieve a shared vision of future the AG2PI. Acting on this latter step, AG2PI organized the "Thinking Big: Visualizing the Future of AG2PI" two-day workshop held September 9-10, 2022, in Ames, Iowa, co-hosted with the United State Department of Agriculture's National Institute of Food and Agriculture (USDA NIFA). During the meeting, attendees were asked to use their experience and curiosity to review the current status of agricultural genome to phenome (AG2P) work and envision the future of the AG2P field. The topic summaries composing this paper are distilled from two 1.5-h small group discussions. Challenges and solutions identified across multiple topics at the workshop were explored. We end our discussion with a vision for the future of agricultural progress, identifying two areas of innovation needed: (1) innovate in genetic improvement methods development and evaluation and (2) innovate in agricultural research processes to solve societal problems. To address these needs, we then provide six specific goals that we recommend be implemented immediately in support of advancing AG2P research.