Current challenges and future of agricultural genomes to phenomes in the USA

Authors: TUGGLE, CHRISTOPHER - Iowa State University; CLARKE, JENNIFER - University Of Nebraska; MURDOCH, BRENDA - University Of Idaho; LYONS, ERIC - University Of Arizona; SCOTT, NICOLE - Iowa State University; MCKAY, STEPHANIE - University Of Vermont; LIPKA, ALEX - University Of Illinois; FULTON, JANET - Hy-Line International; HESS, ANDREW - University Of Nevada; LUBBERSTEDT, THOMAS - Iowa State University; FRAGOMENI, BRENO - University Of Connecticut; ROWAN, TROY - University Of Tennessee; MCCARTHY, FIONA - University Of Arizona; GUADAGNO, CARMELA ROSARIA - University Of Wyoming; GODDARD, ELLEN - University Of Alberta; DAS CHOUDHURY, SRUTI - University Of Nebraska; SHEEHAN, MOIRA - Breeding Insight; KRAMER, LUKE - Iowa State University; Feldman, Max; DAIGLE, COURTNEY - Texas A&M University; STEIBEL, JUAN - Iowa State University; BENES, BEDRICH - Purdue University; MURRAY, SETH - Texas A&M University; RIGGS, PENNY - Texas A&M University; THOMPSON, ADDIE - Michigan State University; HAGEN, DARREN - Oklahoma State University; THORNTON-KURTH, KARA - Utah State University; Van Tassell, Curtis - Curt; Campbell, Jacqueline; DOREA, JOAO - University Of Wisconsin; CHUNG, HENRI - Iowa State University; DEKKERS, JACK - Iowa State University; ERTL, DAVID - Collaborator; LAWRENCE-DILL, CAROLYN - Iowa State University; SCHNABLE, PATRICK - Iowa State University

Submitted to: Genome Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/21/2023
Publication Date: 1/3/2024
Citation: Tuggle, C.K., Clarke, J.L., Murdoch, B.M., Lyons, E., Scott, N.M., Mckay, S., Lipka, A., Fulton, J., Hess, A., Lubberstedt, T., Fragomeni, B., Rowan, T., Mccarthy, F., Guadagno, C., Goddard, E., Das Choudhury, S., Sheehan, M., Kramer, L., Feldman, M.J., Daigle, C., Steibel, J.P., Benes, B., Murray, S., Riggs, P., Thompson, A., Hagen, D., Thornton-Kurth, K., Van Tassell, C.P., Campbell, J.D., Dorea, J., Chung, H., Dekkers, J.C., Ertl, D., Lawrence-Dill, C.A., Schnable, P.S. 2024. Current challenges and future of agricultural genomes to phenomes in the USA. Genome Biology. 25:8. https://doi.org/10.1186/s13059-023-03155-w.
DOI: https://doi.org/10.1186/s13059-023-03155-w

Interpretive Summary: Dramatic improvements in measuring genetic abilities across agriculturally relevant populations (genomics) must be matched by improvements in identifying and measuring relevant performance in such populations across many environments (phenomics). Identifying the most critical opportunities and challenges in the area of genome to phenome (G2P) research is the focus of this paper. The ideas and recommendations laid out herein were developed during the “Thinking Big: Visualizing the Future of AG2PI” two-day workshop held September 9-10, 2022, in Ames, Iowa, organized by the Agricultural Genome to Phenome Initiative (AG2PI) and co-hosted with USDA NIFA.

Technical 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 the area of genome to phenome (G2P) research is the focus of this paper. The ideas and recommendations laid out herein were developed during the “Thinking Big: Visualizing the Future of AG2PI” two-day workshop held September 9-10, 2022, in Ames, Iowa, organized by the Agricultural Genome to Phenome Initiative (AG2PI) and co-hosted with USDA NIFA. During the meeting, attendees were asked to use their experience and curiosity to review the current status and envision the future of agricultural genome-to-phenome (AG2P) and where the field needs to go. To tackle some of these big challenges in agricultural G2P, we designed this workshop to include diverse voices with the intention of including the different perspectives important to solving these challenges. The topic summaries composing this paper are distilled from two 1.5-hour small group discussions that included 6-8 participants, each representing a mix of crop researchers, livestock researchers, data scientists, social scientists, and engineers. Subsequent to the conference, additional writing, idea exchanges, and e-mails were shared among participants and the output of those conversations is summarized in this report. Challenges and solutions identified across multiple topics are listed in tables 1 and 2 (respectively). We end our discussion with a vision for the future of agricultural progress and detail five recommendations to be implemented in support of advancing AG2P research.