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. 2024 Jan 3;25(1):8.
doi: 10.1186/s13059-023-03155-w.

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

Christopher K Tuggle #  1 , Jennifer L Clarke #  2 , Brenda M Murdoch #  3 , Eric Lyons #  4 , Nicole M Scott #  5 , Bedrich Beneš  6 , Jacqueline D Campbell  7 , Henri Chung  5 , Courtney L Daigle  8 , Sruti Das Choudhury  2 , Jack C M Dekkers  5 , Joao R R Dórea  9 , David S Ertl  10 , Max Feldman  11 , Breno O Fragomeni  12 , Janet E Fulton  13 , Carmela R Guadagno  14 , Darren E Hagen  15 , Andrew S Hess  16 , Luke M Kramer  5 , Carolyn J Lawrence-Dill  5 , Alexander E Lipka  17 , Thomas Lübberstedt  5 , Fiona M McCarthy  4 , Stephanie D McKay  18 , Seth C Murray  8 , Penny K Riggs  8 , Troy N Rowan  19 , Moira J Sheehan  20 , Juan P Steibel  5 , Addie M Thompson  21 , Kara J Thornton  22 , Curtis P Van Tassell  23 , Patrick S Schnable  24
Affiliations

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

Christopher K Tuggle et al. Genome Biol. .

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.

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Conflict of interest statement

Tuggle, Clarke, Dekkers, Ertl, Lawrence-Dill, Lyons, Murdoch, and Schnable are on the executive board of the Agricultural Genome To Phenome Initiative. Tuggle is co-lead of the Functional Annotation of Animal Genomes consortium and is a recipient of research funding from Recombinetics, Inc. Ertl is an executive committee member of the Genomes to Fields Initiative. Lyons is the principal investigator of CyVerse funded by the NSF and a Founder of uPetsia, Inc. Scott is the project manager for the USDA-NIFA funded Agricultural Genome to Phenome Initiative. Schnable is a co-lead of the Genomes to Fields Initiative; co-founder of Data2Bio, LLC; Dryland Genetics, Inc; EnGeniousAg, LLC; and LookAhead Breeding, LLC; a member of the scientific advisory board and a shareholder of Hi-Fidelity Genetics, Inc.; a member of the scientific advisory boards of Kemin Industries and Centro de Tecnologia Canavieira; and a recipient of research funding from Iowa Corn and Bayer Crop Science. Benes, Daigle, Das Choudhury, Dorea, Feldman, Fragomeni, Guadagno, Hess, McKay, Rowan, Thompson and Thornton are all recipients of AG2PI seed grants. Lipka and Sheehan serve on the AG2PI Steering Committee. Hagen and Murray serve on the AG2PI Seed Grant Steering Committee.

Figures

Fig. 1
Fig. 1
Survey rankings of topics for furthering AG2P science by both ease in achieving and criticality of funding
Fig. 2
Fig. 2
Challenges (A) and solutions (B) identified across the multiple topic discussions
See this image and copyright information in PMC

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