Current challenges and future of agricultural genomes to phenomes in the USA
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 opportunit...
| Main Authors: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
BMC
2024-01-01
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| Series: | Genome Biology |
| Online Access: | https://doi.org/10.1186/s13059-023-03155-w |
| _version_ | 1797363209601024000 |
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| author | Christopher K. Tuggle Jennifer L. Clarke Brenda M. Murdoch Eric Lyons Nicole M. Scott Bedrich Beneš Jacqueline D. Campbell Henri Chung Courtney L. Daigle Sruti Das Choudhury Jack C. M. Dekkers Joao R. R. Dórea David S. Ertl Max Feldman Breno O. Fragomeni Janet E. Fulton Carmela R. Guadagno Darren E. Hagen Andrew S. Hess Luke M. Kramer Carolyn J. Lawrence-Dill Alexander E. Lipka Thomas Lübberstedt Fiona M. McCarthy Stephanie D. McKay Seth C. Murray Penny K. Riggs Troy N. Rowan Moira J. Sheehan Juan P. Steibel Addie M. Thompson Kara J. Thornton Curtis P. Van Tassell Patrick S. Schnable |
| author_facet | Christopher K. Tuggle Jennifer L. Clarke Brenda M. Murdoch Eric Lyons Nicole M. Scott Bedrich Beneš Jacqueline D. Campbell Henri Chung Courtney L. Daigle Sruti Das Choudhury Jack C. M. Dekkers Joao R. R. Dórea David S. Ertl Max Feldman Breno O. Fragomeni Janet E. Fulton Carmela R. Guadagno Darren E. Hagen Andrew S. Hess Luke M. Kramer Carolyn J. Lawrence-Dill Alexander E. Lipka Thomas Lübberstedt Fiona M. McCarthy Stephanie D. McKay Seth C. Murray Penny K. Riggs Troy N. Rowan Moira J. Sheehan Juan P. Steibel Addie M. Thompson Kara J. Thornton Curtis P. Van Tassell Patrick S. Schnable |
| author_sort | Christopher K. Tuggle |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-08T16:17:58Z |
| format | Article |
| id | doaj.art-16775bc608354ceabfd4ba8fddc9415e |
| institution | Directory Open Access Journal |
| issn | 1474-760X |
| language | English |
| last_indexed | 2024-03-08T16:17:58Z |
| publishDate | 2024-01-01 |
| publisher | BMC |
| record_format | Article |
| series | Genome Biology |
| spelling | doaj.art-16775bc608354ceabfd4ba8fddc9415e2024-01-07T12:28:29ZengBMCGenome Biology1474-760X2024-01-0125111910.1186/s13059-023-03155-wCurrent challenges and future of agricultural genomes to phenomes in the USAChristopher K. Tuggle0Jennifer L. Clarke1Brenda M. Murdoch2Eric Lyons3Nicole M. Scott4Bedrich Beneš5Jacqueline D. Campbell6Henri Chung7Courtney L. Daigle8Sruti Das Choudhury9Jack C. M. Dekkers10Joao R. R. Dórea11David S. Ertl12Max Feldman13Breno O. Fragomeni14Janet E. Fulton15Carmela R. Guadagno16Darren E. Hagen17Andrew S. Hess18Luke M. Kramer19Carolyn J. Lawrence-Dill20Alexander E. Lipka21Thomas Lübberstedt22Fiona M. McCarthy23Stephanie D. McKay24Seth C. Murray25Penny K. Riggs26Troy N. Rowan27Moira J. Sheehan28Juan P. Steibel29Addie M. Thompson30Kara J. Thornton31Curtis P. Van Tassell32Patrick S. Schnable33Iowa State UniversityUniversity of Nebraska-LincolnUniversity of IdahoUniversity of ArizonaIowa State UniversityPurdue UniversityUSDA ARSIowa State UniversityTexas A&M UniversityUniversity of Nebraska-LincolnIowa State UniversityUniversity of Wisconsin-MadisonIowa Corn Growers AssociationUSDA ARSUniversity of ConnecticutHy-Line InternationalUniversity of WyomingOklahoma State UniversityUniversity of Nevada-RenoIowa State UniversityIowa State UniversityUniversity of Illinois Urbana-ChampaignIowa State UniversityUniversity of ArizonaUniversity of VermontTexas A&M UniversityTexas A&M UniversityUniversity of TennesseeCornell UniversityIowa State UniversityMichigan State UniversityUtah State UniversityUSDA ARSIowa State UniversityAbstract 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.https://doi.org/10.1186/s13059-023-03155-w |
| spellingShingle | Christopher K. Tuggle Jennifer L. Clarke Brenda M. Murdoch Eric Lyons Nicole M. Scott Bedrich Beneš Jacqueline D. Campbell Henri Chung Courtney L. Daigle Sruti Das Choudhury Jack C. M. Dekkers Joao R. R. Dórea David S. Ertl Max Feldman Breno O. Fragomeni Janet E. Fulton Carmela R. Guadagno Darren E. Hagen Andrew S. Hess Luke M. Kramer Carolyn J. Lawrence-Dill Alexander E. Lipka Thomas Lübberstedt Fiona M. McCarthy Stephanie D. McKay Seth C. Murray Penny K. Riggs Troy N. Rowan Moira J. Sheehan Juan P. Steibel Addie M. Thompson Kara J. Thornton Curtis P. Van Tassell Patrick S. Schnable Current challenges and future of agricultural genomes to phenomes in the USA Genome Biology |
| title | Current challenges and future of agricultural genomes to phenomes in the USA |
| title_full | Current challenges and future of agricultural genomes to phenomes in the USA |
| title_fullStr | Current challenges and future of agricultural genomes to phenomes in the USA |
| title_full_unstemmed | Current challenges and future of agricultural genomes to phenomes in the USA |
| title_short | Current challenges and future of agricultural genomes to phenomes in the USA |
| title_sort | current challenges and future of agricultural genomes to phenomes in the usa |
| url | https://doi.org/10.1186/s13059-023-03155-w |
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