Progress 09/01/22 to 08/31/23
Outputs
Target Audience:This project involves researchers, students, businesses, and other organization types (governmental, NGO, etc.) from across the agricultural sector. Individuals from both crop and livestock communities as well as integrative disciplines (e.g., engineers, data scientists, economists, and social scientists) have engaged with AG2PI activities and content. The AG2PI community includes founding stakeholder and partner organizations, both domestic and global (for full list of partner organizations visit https://www.ag2pi.org/institutional-involvement/) that have shared AG2PI communications and events since the start of the project. Since project's start, other organizations' listservs have been added to AG2PI mailings, including Decision Support System for Agrotechnology Transfer (DSSAT), Animal Geneticists' Discussion Group and DivSeek International. To ensure the inclusion of URM, we have supported seed grant proposals that provide an opportunity for increasing involvement in agricultural and G2P research and knowledge-sharing. For example, one seed grant from Round 3 awards supports closing the gap between HBCU (Historically Black Colleges and Universities) education, research, outreach, and the advances in precision agriculture phenotyping technologies compared to R1 schools. This seed grant, and others, have supported undergraduate members of Minorities in Agriculture, Natural Resources, and Related Sciences (MANNRS). Changes/Problems:Executive Board members Eric Lyons and Carolyn Lawrence-Dill have been removed from the project; both have accepted new positions (at National Science Foundation and within Iowa State University, respectively). Although both have contributed mightily to this project, this change will not affect our ability to complete the project's goals during the final year of this award. What opportunities for training and professional development has the project provided?Seed grant principal investigators and teams have provided training workshops and field days in association with AG2PI (activities which are supported in the 2020 AG2PI project; grant no. 2020-70412-32615). These activities provided both opportunities for training and professional development for the presenters as well as professional development to their audiences. Additional training and development opportunities were presented to seed grant PIs during the 2022 and 2023 AG2PI conferences, in which they were asked not only to present on their seed grant project but also to work with others to talk through the biggest challenges facing advancements in agricultural genomes to phenomes research and related work. Discussions during the 2022 conference resulted in a co-authored paper that is designed to direct the community on making progress in the described areas and to inform funding agencies on how the community views future funding priorities. How have the results been disseminated to communities of interest?This project reaches researchers, students, and companies from across the agricultural sector by leveraging stakeholder and partner organizations, both domestic and global, to distribute information on project activities and events. This has led to a great diversity of participants, based on information collected at event registration, from many types of institutions and nations (see demographic details in products) as well as from across disciplines (e.g., Complex Modeling, Crop, Data Science/Bioinformatics, Data Storage/Security/Cyberinfrastructure, Education, Engineering, Ethical/Legal/Social Implications/Policy, Livestock/Aquaculture, Microbes, Model Organisms) that continues to grow. AG2PI includes members who share information on upcoming AG2PI activities with various URM organizations, such as MANNRS and SACNAS, particularly with respect to the seed grant opportunity. Twitter/X (@AG2PI; 590 followers, as of November 7, 2023) and LinkedIn accounts are used for advertising upcoming events and seed grant RFPs. In this way the project cuts across generational differences in communication preferences. AG2PI also supports a Slack workspace designed for asynchronous interaction with community members looking to collaborate on an AG2PI seed grant. Dissemination of seed project activities are primarily the responsibility of the seed project teams, but, when appropriate, AG2PI shares these outcomes on the website under the "Funded Seed Grants" page, retweets or distributes through the AG2PI listserv. These outcomes are organized within the funded project description, along with the narrative from the proposal. Recordings of AG2PI events (field days, workshops, selected conferences) involving seed grant awardees sharing their project outcomes are available on the AG2PI website (ag2pi.org) and the AG2PI YouTube channel (@ag2pi89; 665 subscribers). What do you plan to do during the next reporting period to accomplish the goals?We will support conference travel grants for undergraduate and graduate students studying at institutions in the US; in this way, we can further support and grow the AG2PI community. We will continue to provide virtual events through which the coconut grant awardees will share their outcomes with the community. We will continue to support previous seed grant awardees in promoting their project outcomes and may provide funds for publishing papers related to the projects.
Impacts
What was accomplished under these goals?
Impact Statement: To address the challenges and opportunities of achieving sustainable genetic improvement of agricultural species, and thereby enhancing the sustainability and profitability of US agriculture, the expertise of a broad community of agricultural genome to phenome (AG2P) researchers must be engaged, drawing from both the crop and livestock communities, as well as integrative disciplines (e.g., engineers, data scientists, economists, social scientists). In response, AG2PI created seed grant opportunities aimed at addressing agricultural genomes-to-phenomes challenges, for the benefit of US agriculture and society. In this award, 15 seed projects and 5 community event-like projects have been funded. The seed projects are working towards community solutions that will broadly benefit the crop and livestock communities as well as further grow connections between and within these communities. Objectives: The purpose of this project has been to leverage the activities of the existing NIFA-funded 2020 AG2PI project (grant no. 2020-70412-32615) that has developed a cross-kingdom community prepared to tackle AG2P research. The overall objective of this project is to use a competitive process (seed grants) in coordination and approved by NIFA to specifically (1) develop tools and datasets that can be used to advance genome engineering tools; (2) mitigate environmental impacts from agriculture, and; (3) encourage development of root stocks that increase carbon capture and can support grain crop covers. Broadly, these grants further community solutions to cross-kingdom challenges in agriculture. To meet this overall objective, we have expanded and improved upon the seed grant program effectively deployed during the ongoing 2020 AG2PI project. Seed Grants. AG2PI's Seed Grant program for this award consisted of two types: "rounds" and "community event". "Rounds" were designed to promote cross-kingdom collaboration and support the development and cross-pollination of tools, data, and ideas to enable and facilitate future AG2P research across disciplines, species, and sectors. "Community event" grants funded one-time events, such as a workshop or conference. Over the course of this award, 20 seed grants were funded (6 in Round 2; 9 in Round 3; 5 "Community event") for a total of $894,563 awarded. Round 2 projects had budgets up to $75,000 and average durations of 15 months after many awards requested a 3 month no-cost extension. Round 2 deliverables include training workshops, new software and analytical tools, datasets and databases, as well as publications and conference presentations. Round 3 projects had budgets up to $100,000 and average durations of 13 months, with fewer projects requesting no-cost extensions compared to Round 2. Round 3 deliverables include training workshops, new coursework, publicly available datasets and databases, data pipelines, models and simulations. Continuation of work for these "rounds" projects include federally funded awards to further develop their seed projects (e.g., AG2PI "coconut" grants, NSF grants, or other USDA grants), additional publications and deepening of newly formed network connections among and between teams. One Round 3 awardee was awarded an USDA NIFA AG2PI program grant in 2023 to continue their project. An example of collaborations that have arisen from seed grants comes from Round 3 awardee Jameson Brennan who is working to co-produce a virtual fence user manual with The Nature Conservancy, which received a separate grant to compile and host a series of tutorials. The "Community event" awards were up to $15,000 with average durations of 4 months. Deliverables include manuscripts, new coursework, training workshops, public datasets, presentations and more diverse attendance at a national conference. Continuation of work from these awards include a funded REEU program at Texas A&M University to train Undergraduate minority students in Digital Agriculture. Assessment. Given this project's focus on seed grants, the internal metrics (managed by the project manager) only track seed grants and the external assessment is similarly focused on seed grant teams. External assessment was conducted by Divergent Science - a women-owned business that specializes in the science of team science and social network analyses -with a scope of measuring community building and team connectivity. For the external assessment, seed grant project teams from "Round 3" seed grants were asked about their professional connections with other team members. A network analysis demonstrated that although many team members were already familiar with each other, many new connections were formed through these seed grant awards. Additionally, results indicate that communication across disciplines increased, the publication network has grown, and there is more research being conducted across disciplines through these awards. This advancement of cross-disciplinary connections is evident beyond the seed grant opportunity: when asked "Are there other connections beyond those queried that AG2PI has fostered for you or your research group?" many respondents agreed that new connections had been made. Some examples of new connections made through AG2PI include contacts in human medical research, private producers, federal government agency personnel (NRCS, USFS, BLM), and NGOs; collaborations with individuals overseas working in a similar capacity to phenotype emerging diseases, NASA SERVIR and South-Southeast Asia Research groups; and, fostered conversation with other industry groups and researchers that have synergistic interests, like AgBioData. The external assessment team was also contracted to survey attendees of the 2022 "Thinking Big: Visualizing the Future of AG2PI" two-day workshop held September 9-10, 2022, with USDA NIFA as co-host, in Ames, Iowa, on what connections they made at the in-person conference. As described in the Products section, results showed that the conference expanded attendees' professional connections, particularly across disciplines. A community detection algorithm demonstrated an increase in the number of "communities" among conference attendees and determined that the new communities were no longer identifiable by discipline compared to reported connections held prior to the event. Ride sharing was organized by the AG2PI project manager and anecdotal evidence suggested there was a benefit to pseudorandom grouping (based on flight arrival times); however, the network analysis did not show a visible effect of these new connections. When asked "What changes in your research direction, if any, do you anticipate based on AG2PI's influence?" responses ranged from immediate effects to foreseeable future influences. For example, one participant related, "The AG2PI community has been really shaping my current and future work in biology. It was great for me to see interest and appreciation in my presentation and comments during the activities, meaning that the cross-scale and trans-disciplinary work that I have started with the support of the Initiative has been well spent and I am willing to continue in pushing the envelope of current phenotyping and G2P approaches." Another noted, "I am an economist working on the economics of genomic applications. I always learn a lot that informs my research by attending meetings where the science is the focus. I learned a lot about innovative research that I am currently now studying."
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2023
Citation:
Seed grant deliverable from Broadening diversity in the North American Plant Phenotyping Network (PI: David LeBauer, North American Plant Phenotyping Network): LeBauer, D., Bucksch, A., Clarke, J., Potts, J., & Roy, S. (2023). Increasing racial diversity in the North American Plant Phenotyping Network through conference participation support. The Plant Phenome Journal, 6, e20075. https://doi.org/10.1002/ppj2.20075
- Type:
Journal Articles
Status:
Published
Year Published:
2022
Citation:
Seed grant deliverable from Event-Based Plant Phenotyping using Deep Learning: Algorithms, Tools and Datasets (PI: Sruti Das Choudhury, University of Nebraska-Lincoln): Sruti Das Choudhury, Samarpan Guha, Aankit Das, Amit Kumar Das, Ashok Samal, Tala Awada. FlowerPhenoNet: Automated Flower Detection from Multi-View Image Sequences Using Deep Neural Networks for Temporal Plant Phenotyping Analysis. Remote Sensing. 2022, 14(24), 6252 | doi:10.3390/rs14246252 | December 9, 2022. https://www.mdpi.com/2072-4292/14/24/6252
- Type:
Journal Articles
Status:
Published
Year Published:
2023
Citation:
Seed grant deliverable from Event-Based Plant Phenotyping using Deep Learning: Algorithms, Tools and Datasets (PI: Sruti Das Choudhury, University of Nebraska-Lincoln): Aankit Das, Sruti Das Choudhury, Amit Kumar Das, Ashok Samal, Tala Awada. EmergeNet: A Novel Deep-Learning Based Ensemble Segmentation Model for Emergence Timing Detection of Coleoptile. Frontiers in Plant Science. 2023, 14 | doi:10.3389/fpls.2023.1084778 | February 3, 2023 https://www.frontiersin.org/articles/10.3389/fpls.2023.1084778/
- Type:
Journal Articles
Status:
Published
Year Published:
2023
Citation:
Seed grant deliverable from Event-Based Plant Phenotyping using Deep Learning: Algorithms, Tools and Datasets (PI: Sruti Das Choudhury, University of Nebraska-Lincoln): Drought stress prediction and propagation using time series modeling on multimodal plant image sequences. Front. Plant Sci., 09 February 2023. Sec. Technical Advances in Plant Science. Volume 14 2023. https://doi.org/10.3389/fpls.2023.1003150
- Type:
Journal Articles
Status:
Published
Year Published:
2023
Citation:
Seed grant deliverable from Understanding emergent agricultural phenomena through Big Data
Analytics: creating frameworks for understanding using Physics-guided Machine Learning and agent-based models (PI: Michael Kantar, University of Hawaii at Manao): Runck, B., Streed, A., Wang, D. R., Ewing, P. M., Kantar, M. B., & Raghavan, B. (2023). State spaces for agriculture: A meta-systematic design automation framework. PNAS nexus, 2(4), pgad084.
https://doi.org/10.1093/pnasnexus/pgad084
- Type:
Journal Articles
Status:
Published
Year Published:
2023
Citation:
Seed grant deliverable from Developing Education, Research, and Extension Training on Precision Agriculture Phenotyping Tools at HBCU (PI: Jingqiu Chen, Florida A&M University): Jingqiu Chen, Wei-zhen Liang, Jian Jin, & Violeta M. Tsolova. (2023). Developing Education, Research, and Extension Training on Precision Agriculture Phenotyping Tools at HBCU Communities. Proceedings of the 2023 ASABE Annual International Meeting. Omaha, Nebraska. July 9-12. Conference Proceeding. https://doi.org/10.13031/aim.202301190
- Type:
Journal Articles
Status:
Published
Year Published:
2022
Citation:
Seed grant deliverable from Creating a FAIR data ecosystem for incorporating single cell genomics data into agriculture G2P (PI: Christopher Tuggle, Iowa State University): Fahlgren, N., M. Kapoor, G. Yordanova, J. Waeseb, B. Cole, P. Harrison, D. Ware, A. Burdett, C. G. Elsik, C. K. Tuggle, N. J. Provart. 2022. Toward a Data Infrastructure for the Plant Cell Atlas. Plant Physiology Oct 6; kiac468 on-line ahead of print. doi:10.1093/plphys/kiac468
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2022
Citation:
Seed grant deliverable from Event-Based Plant Phenotyping using Deep Learning: Algorithms, Tools and Datasets (PI: Sruti Das Choudhury, University of Nebraska-Lincoln): FRUITPHENONET: AUTOMATED FRUIT DETECTION AND TRACKING USING TIME-SERIES VISIBLE LIGHT AND HYPERSPECTRAL IMAGERY FOR TEMPORAL FRUIT PHENOTYPING USING A DEEP NEURAL NETWORK poster presented at 7th IPPN Symposium in Wageningen, The Netherlands, September 27-30, 2022.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2022
Citation:
Seed grant deliverable from Event-Based Plant Phenotyping using Deep Learning: Algorithms, Tools and Datasets (PI: Sruti Das Choudhury, University of Nebraska-Lincoln): Sruti Das Choudhury, Ashok Samal, Tala Awada. FlowerPhenoNet: Automated Flower Detection from Multi-view Image Sequences using Deep Neural Networks for 2D and 3D Temporal Plant Phenotyping Analysis . poster presented at 7th IPPN Symposium in Wageningen, The Netherlands, September 27-30, 2022.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2023
Citation:
Seed grant deliverable from Event-Based Plant Phenotyping using Deep Learning: Algorithms, Tools and Datasets (PI: Sruti Das Choudhury, University of Nebraska-Lincoln): Sruti Das Choudhury, Sinjoy Saha, Anastasios Mazis, Ashok Samal, Tala Awada. HyperStressPropagateNet: Time Series Modeling for Drought Stress Propagation in Plants using Hyperspectral Imagery . Poster in North American Plant Phenotyping Network (NAPPN) Annual Conference, St. Louis, Missouri, February 2023.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2022
Citation:
Seed grant deliverable from An Analysis Toolkit for Assessment of Quantitative Locomotor Phenotypes in Livestock (PI: Samantha Brooks, University of Florida): 13th International Havemeyer Equine Genome Workshop [Ithaca, NY], July 24-28, 2022.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2022
Citation:
Seed grant deliverable from An Analysis Toolkit for Assessment of Quantitative Locomotor Phenotypes in Livestock (PI: Samantha Brooks, University of Florida): UF-IFAS Florida Equine Institute [Ocala, FL], September 22, 2022.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2022
Citation:
Seed grant deliverable from An Analysis Toolkit for Assessment of Quantitative Locomotor Phenotypes in Livestock (PI: Samantha Brooks, University of Florida): 8th UF-IFAS Animal Sciences Graduate Research Symposium [St. Augustine, FL] October 7th, 2022.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2022
Citation:
Seed grant deliverable from An Analysis Toolkit for Assessment of Quantitative Locomotor Phenotypes in Livestock (PI: Samantha Brooks, University of Florida): An Analysis Toolkit for Assessment of Quantitative Locomotor Phenotypes in Livestock poster at Florida Genetics Symposium [Gainesville, FL], November 2-4, 2022.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2022
Citation:
Seed grant deliverable from An Analysis Toolkit for Assessment of Quantitative Locomotor Phenotypes in Livestock (PI: Samantha Brooks, University of Florida): Decoding Eventers: Why Should WE Care About the Horse Genome talk at USEA Annual Meeting and Convention [Savannah, GA], December 7-11, 2022.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2023
Citation:
Seed grant deliverable from An Analysis Toolkit for Assessment of Quantitative Locomotor Phenotypes in Livestock (PI: Samantha Brooks, University of Florida): Presentation: Johns, L., M. Smythe, S. Dewberry, E. Staiger, K. Allen, and S. Brooks. 2023. 33 Assessing the effect of fatigue on stadium jumping penalty scores in elite three-day event horses utilizing artificial intelligence. Presented June 6th, Dallas Texas, Equine Science Society Symposium. Abstract published: Journal of Equine Veterinary Science 124:104335 https://doi.org/10.1016/j.jevs.2023.104335
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2023
Citation:
Seed grant deliverable from An Analysis Toolkit for Assessment of Quantitative Locomotor Phenotypes in Livestock (PI: Samantha Brooks, University of Florida): Presentation; Rahael, H., M. Smythe, S. Dewberry, A. Oberdorfer, K. Allen, and S. Brooks. 2023. 44 Detecting conformational differences in Fragile Foal Syndrome carriers utilizing artificial intelligence. Presented June 6th, Dallas Texas, Equine Science Society Symposium. Abstract published: Journal of Equine Veterinary Science 124:104346. https://doi.org/10.1016/j.jevs.2023.104346
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2023
Citation:
Seed grant deliverable from An Analysis Toolkit for Assessment of Quantitative Locomotor Phenotypes in Livestock (PI: Samantha Brooks, University of Florida): Presentation: Smythe, M., S. Dewberry, E. Staiger, K. Allen, and S. Brooks. 2023. 45 Quantifying gait quality changes in fragile foal syndrome carriers using artificial intelligence. Presented June 6th, Dallas Texas, Equine Science Society Symposium. Abstract published: Journal of Equine Veterinary Science 124:104347. https://doi.org/10.1016/j.jevs.2023.104347
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2022
Citation:
Seed grant deliverable from Developing Education, Research, and Extension Training on Precision Agriculture Phenotyping Tools at HBCU (PI: Jingqiu Chen, Florida A&M University): poster. Poster presentation by Jayden C. Burnett, Lauren A. Hawkins, Katie B. Light, Violeta M. Tsolova, Wei-zhen Liang, Jingqiu Chen titled, Experiential Learning on Precision Agriculture Phenotyping Tool in Muscadine Vineyards and Data Analytics at the 2022 FAMU Student Research Forum on. October 26th, 2022. This poster won the 2nd Place.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2023
Citation:
Seed grant deliverable from Developing Education, Research, and Extension Training on Precision Agriculture Phenotyping Tools at HBCU (PI: Jingqiu Chen, Florida A&M University): Jingqiu Chen, Wei-zhen Liang, Violeta Tsolova, Jian Jin authored/presented an invited talk titled, Developing Education, Research, and Extension Training on Precision Agriculture Phenotyping Tools at HBCU Communities for the 2023 Florida Wine & Grape Growers Association (FWGGA) Annual Conference, Deland, FL, on January 13-14, 2023.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2022
Citation:
Seed grant deliverable from Developing Education, Research, and Extension Training on Precision Agriculture Phenotyping Tools at HBCU (PI: Jingqiu Chen, Florida A&M University): Talk by Qiao, X., W.-Z. Liang, J. Chen, and G. Stone titled, Peer-Learning Agricultural Network (PLAN) at the ASA, CSSA, SSSA International Annual Meeting in Baltimore, MD on November 6-9, 2022.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2023
Citation:
Seed grant deliverable from Homomorphic encryption to enable sharing of confidential data (PI: Hao Cheng, University of California, Davis): Cheng, H. Homomorphic encryption to enable sharing of confidential data in agricultural genome to phenome talk at 30th Plant and Animal Genome Conference [San Diego, CA] January 13-18, 2023.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2023
Citation:
Seed grant deliverable from Cross-species genomic analysis of Photosystem II: Building connections from molecular structure to phenotype (PI: Carmela Guadagno, University of Wyoming): Talk at Eastern Regional Photosynthesis Conference 2023: Cross-Scale Water Dynamics to Mechanistically Inform Plant Phenotyping and Productivity Models . Author: Carmela R. Guadagno. April 14-16, 2023. Woods Hole, MA.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2023
Citation:
Seed grant deliverable from Cross-species genomic analysis of Photosystem II: Building connections from molecular structure to phenotype (PI: Carmela Guadagno, University of Wyoming): Poster at Eastern Regional Photosynthesis Conference 2023: Characterizing Variation of PSII Water Channels Between Cyanobacteria and Higher Plants . Authors: Jose C. Ortiz-Soto, Benjamin C. Romanjenko, Carmela R. Guadagno and Marilyn R. Gunner April 14-16, 2023. Woods Hole, MA.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2023
Citation:
Seed grant deliverable from Cross-species genomic analysis of Photosystem II: Building connections from molecular structure to phenotype (PI: Carmela Guadagno, University of Wyoming): Talk at Eastern Regional Photosynthesis Conference 2023: Characterizing Variation of PSII Water Channels Between Cyanobacteria and Higher Plants . Author: Benjamin C. Romanjenko. April 14-16, 2023. Woods Hole, MA.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2022
Citation:
Seed grant deliverable from Developing a new machine learning tool for improved genomic selection (PI: James Polashock, USDA ARS): Presented at American Cranberry Association Meeting in January 20, 2022. Identifying genetic markers for defense mechanisms in cranberry fruit . Joseph K. Kawash, James J. Polashock, Jennifer Johnson-Cicalese, Nicholi Vorsa.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2023
Citation:
Seed grant deliverable from Developing a new machine learning tool for improved genomic selection (PI: James Polashock, USDA ARS): Presented at American Cranberry Association Meeting in January 19, 2023. Updating Approaches to Fruit Rot Resistance Research . Joseph K. Kawash, James J. Polashock.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2023
Citation:
Seed grant deliverable from Developing a cost-effective method for collecting informative, population-level molecular phenotypes (PI: Troy Rowan, University of Tennessee): graduate student Ruwaa Mohamed presented a talk at University of Tennessee Genome Science & Technology Colloquium (Knoxville, TN - March 9th, 2023) titled, Comparing cost-effective gene expression phenotyping methods in cattle .
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2023
Citation:
Seed grant deliverable from Developing a cost-effective method for collecting informative, population-level molecular phenotypes (PI: Troy Rowan, University of Tennessee): graduate student Ruwaa Mohamed presented a poster at Gordon Research Conference & Gordon Research Seminar (Ventura, CA - February 12-16, 2023) titled, Comparing cost-effective gene expression phenotyping methods in cattle .
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2022
Citation:
Seed grant deliverable from Developing a cost-effective method for collecting informative, population-level molecular phenotypes (PI: Troy Rowan, University of Tennessee): graduate student Ruwaa Mohamed presented a poster at University of Tennessee Beef & Forage Center (Knoxville, TN - December 20, 2022) to producers and stakeholders throughout the state of Tennessee. This presentation reached approximately 75 individuals.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2023
Citation:
Seed grant deliverable from Using unmanned aerial vehicles to detect nitrogen stress in alfalfa (Medicago sativa L.) (PI: Anju Biswas and Esteban Rios, University of Florida): Dr. Rios led mulitple sessions during a summer short-course titled Multi-Omic Integration for AI Genomic Prediction Breeding Short Course at University of Florida that included outcomes of this project. The week-long short course included 90 participants from 11 countries (https://conference.ifas.ufl.edu/moiai/index.php) and was held July 10-14 in Gainesville, FL.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2022
Citation:
Seed grant deliverable from Impact of breed type on beef production and sustainability (PI: Kara Thornton, Utah State University): B.L. Brown, L.A. Motsinger, C.C. Reichhardt, G.K. Murdoch, B.M. Murdoch, M.D. Garcia, K.J. Thornton. (2022). Effects of beef cattle breed type and steroid hormones on proliferation rates of bovine satellite cells. Poster presented at the American Society of Animal Science meeting June 26-30, 2022. Research shared with over 3,000 attendees at the ASAS meetings via peer-reviewed abstract and poster presentation.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2022
Citation:
Seed grant deliverable from Impact of breed type on beef production and sustainability (PI: Kara Thornton, Utah State University): L.L. Okamoto, C.C. Reichhardt, A.F. Alberto, L.A. Motsinger, S.A. Bayles, B.W. Roholt, M.D. Garcia, K.J. Thornton. (2022). Effect of beef breed type relative to feedlot performance, feeding behavior, and carcass characteristics. Poster presented at the American Society of Animal Science June 26-30, 2022.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2022
Citation:
Seed grant deliverable from Impact of breed type on beef production and sustainability (PI: Kara Thornton, Utah State University): L.L. Okamoto, C.C. Reichhardt, A.F. Alberto, L.A. Motsinger, S.A. Bayles, B.W. Roholt, M.D. Garcia, K.J. Thornton. (2022). Effect of beef breed type relative to feedlot performance, feeding behavior, and carcass characteristics. Poster presented at the Utah State University Animal, Dairy and Veterinary Science departmental research symposium in August 2022.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2022
Citation:
Seed grant deliverable from Impact of breed type on beef production and sustainability (PI: Kara Thornton, Utah State University): B.L. Brown, L.A. Motsinger, C.C. Reichhardt, G.K. Murdoch, B.M. Murdoch, M.D. Garcia, K.J. Thornton. (2022). Effects of beef cattle breed type and steroid hormones on proliferation and protein synthesis rates of bovine satellite cells. Poster presented at the Utah State University Animal, Dairy and Veterinary Science departmental research symposium in August 2022.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2023
Citation:
Seed grant deliverable from Impact of breed type on beef production and sustainability (PI: Kara Thornton, Utah State University): L. .L. Okamoto, M. Stagemiller, C.C. Reichhardt, A.F. Alberto, L.A. Motsinger, S.A. Bayles, B.W. Roholt, M.D. Garcia, B.M. Murdoch, K.J. Thornton. (2023). Genetic differences related to beef production traits in Bos taurus or Bos indicus influenced cattle. Poster presented at the American Society of Animal Science meeting July 16-20, 2023.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2023
Citation:
Seed grant deliverable from Impact of breed type on beef production and sustainability (PI: Kara Thornton, Utah State University): L.L. Okamoto, M. Stagemiller, C.C. Reichhardt, A.F. Alberto, L.A. Motsinger, S.A. Bayles, B.W. Roholt, M.D. Garcia, B.M. Murdoch, K.J. Thornton. (2023). Genetic differences related to beef production traits in Bos taurus or Bos indicus influenced cattle. Poster presented at the Utah State University Animal, Dairy and Veterinary Science research symposium August 3,2023.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2023
Citation:
Seed grant deliverable from Impact of breed type on beef production and sustainability (PI: Kara Thornton, Utah State University): Oral Presentation by Dr. Kara Thornton at Utah beef field day, February 24, 2023. The findings of this research were shared with over 200 beef producers, extension personnel, and other industry stakeholders at the Utah Beef Field Day in 2023.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2023
Citation:
Seed grant deliverable from Democratizing the access to artificial intelligence solutions for underrepresented and non-expert communities (PI: Joao Dorea, University of Wisconsin-Madison): Published an article in the US Precision Livestock Conference held in Knoxville, TN, May 21-24, 2023, titled, "Democratizing the access to artificial intelligence solutions for underrepresented and non-expert communities". Presentation of this paper won Best Oral Presentation award at the Precision Livestock Conference.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2023
Citation:
Seed grant deliverable from Standardizing data management and terminology for increased adoption of virtual fence systems (PI: Jameson Brennan, South Dakota State University): Organized the Virtual Fence In-Service Workshop , an in-person conference held in Boise Idaho on virtual fence technology and applications across research, land management agencies, extension, industry, and economics. The conference had a total of 18 presentations from 17 presenters. This meeting was attended by 60 individuals representing 12 universities, 2 USDA-ARS stations, 3 federal land management agencies, 1 NGO, and 2 industry partners. These entities represented over 100,000 acres of land and thousands of cattle being managed using this technology, which is scalable across millions of acres and heads of cattle. This event has greatly expanded the reach and collaboration of research entities working with virtual fence systems.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2023
Citation:
Seed grant deliverable from Standardizing data management and terminology for increased adoption of virtual fence systems (PI: Jameson Brennan, South Dakota State University): Symposium titled, Virtual Fence Technology: Challenges and opportunities for implementing virtual fence across public, private, and research sectors. The event was held in Boise, Idaho on February 11-12, 2023 prior to the Society for Range Management international meeting to increase attendance and visibility for the event beyond the initial working group and PIs. sponsored by the seed grant at the international Society for Range Management Meetings in Boise, ID. A total of 9 presentations. Approximately 300+ attendees in the session.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2023
Citation:
Seed grant deliverable from Developing Education, Research, and Extension Training on Precision Agriculture Phenotyping Tools at HBCU (PI: Jingqiu Chen, Florida A&M University): Undergraduate research trainee poster presentation (* denotes undergraduate sponsored by this project) Shomar Bullen*; Wei-zhen Liang; Jingqiu Chen. Image Processing of Plants for Defoliation & Disease Tracking. The 2023 FAMU Undergraduate Research Symposium. April 14th, 2023, Tallahassee, FL.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2023
Citation:
Seed grant deliverable from Developing Education, Research, and Extension Training on Precision Agriculture Phenotyping Tools at HBCU (PI: Jingqiu Chen, Florida A&M University): Undergraduate research trainee poster presentation (* denotes undergraduate sponsored by this project) Lauren A. Hawkins*; Violeta M. Tsolova; Wei-zhen Liang; Jingqiu Chen. Cultivating Learning Material Regrading Precision Agriculture for Grades K- 12th. The 2023 FAMU Undergraduate Research Symposium. April 14th, 2023, Tallahassee, FL.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2023
Citation:
Seed grant deliverable from Developing Education, Research, and Extension Training on Precision Agriculture Phenotyping Tools at HBCU (PI: Jingqiu Chen, Florida A&M University): PI Chen was invited by Pacific Northwest National Laboratory HBCU/MSI Climate Research Network to give a virtual seminar. Jingqiu Chen, Wei-zhen Liang, Violeta Tsolova, Jian Jin. Developing Education, Research, and Extension Training on Precision Agriculture Phenotyping Tools at Muscadine vineyards. Pacific Northwest National Laboratory HBCU/MSI Climate Research Network seminar, June 23, 2023.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2023
Citation:
Seed grant deliverable from Developing Education, Research, and Extension Training on Precision Agriculture Phenotyping Tools at HBCU (PI: Jingqiu Chen, Florida A&M University): Oral presentation by Jingqiu Chen, Wei-zhen Liang, Jian Jin, Violeta Tsolova. Enhancing Precision Agriculture Phenotyping Tools Education, Research, and Extension Training at Muscadine Vineyards. 2023 Florida Section American Society of Agricultural and Biological Engineers (ASABE) Annual Conference, Duck Key, FL, Jun. 4-6, 2023.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2023
Citation:
Seed grant deliverable from Developing Education, Research, and Extension Training on Precision Agriculture Phenotyping Tools at HBCU (PI: Jingqiu Chen, Florida A&M University): Oral presentation by Jingqiu Chen, Wei-zhen Liang, Violeta Tsolova, Jian Jin. Developing Education, Research, and Extension Training on Precision Agriculture Phenotyping Tools at HBCU Communities. 2023 American Society of Agricultural and Biological Engineers (ASABE) Annual International Meeting, Omaha, NE, Jul. 9-12, 2023.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2022
Citation:
Seed grant deliverable from Creating a FAIR data ecosystem for incorporating single cell genomics data into agriculture G2P (PI: Christopher Tuggle, Iowa State University): M. Kapoor presented in 2022 Plant cell atlas symposium focusing on Plant data and use of SCEA and Annotare for data submission, storage, visualization and analysis. M. Kapoor, A. Sokolov, E. S. Ventura, G. Yordanova, N. J. Provart, I. Papatheodorou, N. George, D. Ware, S. Kumari, T. Tickle, B. Cole, T. Burdett, P. Harrison, C. Tuggle. Date: 12-13 December 2022 Location: virtual conference Title: Creating a FAIR data ecosystem for incorporating single cell genomics data into agricultural G2P research
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2023
Citation:
Seed grant deliverable from Creating a FAIR data ecosystem for incorporating single cell genomics data into agriculture G2P (PI: Christopher Tuggle, Iowa State University): M. Kapoor presented a poster at American Society of Animal Science (ASAS) focusing on Ingestion of Animal datasets with use of HCA-DCP ingestion service. Developed a Shiny web application which will be an important resource for improved annotation of porcine immune genes and cell types. M. Kapoor, A. Sokolov, E. S. Ventura, G. Yordanova, N. J. Provart, I. Papatheodorou, N. George, D. Ware, S. Kumari, T. Tickle, B. Cole, T. Burdett, P. Harrison, C. Tuggle. Date: 12-15 March 2023 Location: Madison Title: Computational tools and resources for analysis and exploration of single-cell RNAseq data in agriculture.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2023
Citation:
Seed grant deliverable from Creating a FAIR data ecosystem for incorporating single cell genomics data into agriculture G2P (PI: Christopher Tuggle, Iowa State University): M. Kapoor gave a talk at Interdisciplinary Biological Science Symposium on visualization tool for exploring single cell data, shinyPIGGI and how the data goes in different plant for both plant and animal cell atlas ingestion tools- SCEA and HCA respectively. Focused on how the data was ingested in both plant and animal data ingestion pipelines. M. Kapoor, A. Sokolov, E. S. Ventura, G. Yordanova, N. J. Provart, I. Papatheodorou, N. George, D. Ware, S. Kumari, T. Tickle, J. Koltes, B. Cole, M. Libault, C. Elsik, W. Warren, T. Burdett, P. Harrison, C. Tuggle. Date: 26-27 April 2023 Location: Iowa State University Title: Single-cell genomics data incorporation into agricultural G2P research by building a FAIR data ecosystem
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2023
Citation:
Seed grant deliverable from A genetic data portal to enable discovery of deleterious genetic variants in farmed animals (PI: Theodore S. Kalbfleisch, University of Kentucky): Talk titled, Discovery of Deleterious Genetic Variants in Farmed Animals presented at 39th International Society for Animal Genetics July 2-7, 2023 in Cape Town, South Africa.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2023
Citation:
Seed grant deliverable from Homomorphic encryption to enable sharing of confidential data (PI: Hao Cheng, University of California, Davis): Talk titled, Homomorphic Encryption to Enable Sharing of Confidential Data in Agricultural Genome to Phenome , at AGBT-Ag, Mar 28, 2023 in San Antonio, TX.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2023
Citation:
Seed grant deliverable from Homomorphic encryption to enable sharing of confidential data (PI: Hao Cheng, University of California, Davis): Talk titled, Homomorphic Encryption to Enable Sharing of Confidential Data in Genome to Phenome , at PAG30, Jan 13, 2023, in San Diego, CA.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2023
Citation:
Seed grant deliverable from A genetic data portal to enable discovery of deleterious genetic variants in farmed animals (PI: Theodore S. Kalbfleisch, University of Kentucky): Poster Presentation at PAG XXX, January 13-18, 2023, in San Diego, CA, titled, A Genetic Data Portal to Enable Discovery of Deleterious Genetic Variants in Farmed Animals . This was the first poster presentation for student Xiomara Arias.
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Progress 09/01/21 to 08/31/22
Outputs
Target Audience:This project involves researchers, students, businesses, and other organization types (governmental, NGO, etc.) from across the agricultural sector. Individuals from both crop and livestock communities as well as integrative disciplines (e.g., engineers, data scientists, economists, and social scientists) have engaged with AG2PI activities and content. The AG2PI community includes founding stakeholder and partner organizations, both domestic and global (for full list of partner organizations visit https://www.ag2pi.org/institutional-involvement/) that have shared AG2PI communications and events since the start of the project. To ensure the inclusion of URM, we have supported seed grant proposals that provide an opportunity for increasing involvement in agricultural and G2P research and knowledge-sharing. For example, one seed grant from Round 3 awards supports closing the gap between HBCU (Historically Black Colleges and Universities) education, research, outreach, and the advances in precision agriculture phenotyping technologies compared to R1 schools. This grant will also support undergraduate members of Minorities in Agriculture, Natural Resources, and Related Sciences (MANNRS). Changes/Problems:The seed grant subaward process has been more challenging than expected. For the "Round" research seed grants, we worked with Iowa State University's Office of Sponsored Programs to refine the process and reduce time to award; however, the process continues to be lengthy. This is in part due to the number of steps involved in the awarding process - which we have already cut down - and in part due to the coordination of multiple offices both within and between institutions. AG2PI has been successful in keeping track of the processes on the Iowa State University (ISU) side of the award process but is dependent on "checking in" with the PIs of awarded projects since the process moves into new hands once ISU has fully executed the award to the recipient institution. At that point, the onus is on the seed grant PIs to make sure invoices are being sent and processed in a timely manner, at which point much of the process is difficult to track. These challenges of working with multiple offices within an institution as well as between institutions led us to create a new process within ISU for the "rolling" community event grants, which remove the sponsored programs offices of each institution and instead involve AG2PI, ISU's procurement office, the recipient and the subrecipient's controller's office to ease the administrative burden and decrease time to award. What opportunities for training and professional development has the project provided?Seed grant principal investigators and teams will provide training workshops and field days in association with AG2PI (activities which are supported in the 2020 AG2PI project). These activities will provide both opportunities for training and professional development. How have the results been disseminated to communities of interest?This project reaches researchers, students, and companies from across the agricultural sector by leveraging stakeholder and partner organizations, both domestic and global, to distribute information on project activities and events. This has led to a great diversity of participants, based on information collected at event registration, from many types of institutions and nations (see demographic details in products) as well as from across disciplines (e.g., Complex Modeling, Crop, Data Science/Bioinformatics, Data Storage/Security/Cyberinfrastructure, Education, Engineering, Ethical/Legal/Social Implications/Policy, Livestock/Aquaculture, Microbes, Model Organisms) that continues to grow. AG2PI includes members who share information on upcoming AG2PI activities with various URM organizations, such as MANNRS and SACNAS, particularly with respect to the seed grant opportunity. Twitter (@AG2PI) and LinkedIn accounts are used for advertising upcoming events and seed grant RFPs. In this way the project cuts across generational differences in communication preferences. AG2PI also supports a Slack workspace designed for asynchronous interaction with community members looking to collaborate on an AG2PI seed grant. Dissemination of seed project activities are primarily the responsibility of the seed project teams, but, when appropriate, AG2PI shares these outcomes on the website under the "Funded Seed Grants" page. These outcomes are organized within the funded project description, along with the narrative from the proposal. What do you plan to do during the next reporting period to accomplish the goals?Seed Grants Two seed grant opportunities will continue to be available until April 2023 or until all funds are committed. One of these is a request for applications (RFA) for a community event. This grant opportunity is intended to fund one-time events. Events may fall into one or more of the following agricultural genomes to phenomes (AG2P)-related activities, but are not limited to these suggestions: 1) Participant support for increasing representation of diverse voices at AG2P-related events (e.g., conferences, workshops, etc.); 2) Creation and offering of cross-disciplinary training in AG2P data science/ biology/ engineering; 3) Town hall meetings to jump start working groups or to measure interest in forming a working group; 4) Creation and dissemination of AG2P materials from ethical, legal, social, ecological, and economic perspectives. The other RFA is focused on supporting the formation and management of a new working group (the team working group is analogous to community of special interest or birds of a feather). At minimum, working groups will be expected to host regular virtual and/or in-person meetings that are open to all working group members; write and publish a concept paper addressing the needs identified by the working group; and, give a presentation at an AG2PI conference or workshop. As we have done previously, we will provide reviewer feedback to lead investigators of proposals that were responsive to the call for proposals but not selected for funding and encourage these investigators to revise and reapply in response to future RFAs. At the conclusion of each of the two rounds of "Seed and Feed" proposals funded through this award, the Seed Grant Committee will receive final reports from all awardees. These reports will detail progress made as a result of AG2PI funding, challenges or obstacles encountered, engagement of the project with other AG2PI activities (e.g., field days, workshops, conferences), and future plans. This information will be reviewed by the Committee and shared with the PI team, the Scientific Advisory Committee, and the AG2PI Assessment Team with the intent of modifying future calls for Seed and Feed proposals to maximize the likelihood of project success. Assessment Internal assessment will continue, but external assessment will largely have concluded by early 2023. A survey similar to what was sent to Round 1 and Round 2 research seed grant teams will be sent to Round 3 teams in Fall 2022 to measure community building and team connectivity. Internal assessment will continue to monitor seed grant outcomes.
Impacts
What was accomplished under these goals?
Impact Statement: To address the challenges and opportunities of achieving sustainable genetic improvement of agricultural species, and thereby enhancing the sustainability and profitability of US agriculture, the expertise of a broad community of agricultural genome to phenome (AG2P) researchers must be engaged, drawing from both the crop and livestock communities, as well as integrative disciplines (e.g., engineers, data scientists, economists, social scientists). In response, AG2PI has created seed grant opportunities aimed at addressing agricultural genomes-to-phenomes challenges, for the benefit of US agriculture and society. To date, 15 seed projects and 4 community event-like projects have been funded. The seed projects are working towards community solutions that will broadly benefit the crop or livestock communities, or both. Results of a social network analysis demonstrate how the seed grants are affording more than just advances in science: AG2PI seed grant teams include individuals who have not previously been connected and are centralizing the roles of early career researchers. Objectives: The purpose of the proposed project is to leverage the activities of the existing NIFA-funded AG2PI project (grant no. 2020-70412-32615) that is developing a cross-kingdom community prepared to tackle AG2P research by providing additional opportunities for seed grants. The overall objective of the proposed project is to use a competitive process (seed grants) in coordination and approved by NIFA to specifically (1) develop tools and datasets that can be used to advance genome engineering tools; (2) mitigate environmental impacts from agriculture and; (3) encourage development of root stocks that increase carbon capture and can support grain crop covers. Broadly, these grants will also be used to further community solutions to cross-kingdom challenges in agriculture. To meet this overall objective, we will expand the seed grant program effectively deployed during the ongoing 2020 AG2PI project. Seed Grants. AG2PI's Seed Grant program was designed to promote cross-kingdom collaboration and support the development and cross-pollination of tools, data, and ideas to enable and facilitate future AG2P research across disciplines, species, and sectors. Two rounds of research project funding provided on this award (i.e., Round 2 and Round 3) as well as four community event grants. Eleven proposals were awarded out of 20 applications in the second round of awards; however, only the six projects funded from this award are included in this report. Nine proposals were awarded out of 26 applications in the third round of awards. Early career is defined as holding position at level of assistant professor or more junior (or equivalent for industry). The six second round research seed grant awards made on this award ranged from $20,000-75,000 with durations of 10-18 months starting in December 2021 (see https://www.ag2pi.org/resources/ag2pi-funded-seed-grants/ for details). The nine third round research seed grant awards ranged from $50,000-100,000 with durations of 6-12 months. Project teams (including collaborators) across both rounds represent 31 institutions, including USDA ARS, land grant universities (1860s and 1890), HBCUs, primarily undergraduate institutions, and industry across 23 states (AZ, CA, CO, FL, HI, IA, ID, IN, MA, MD, MN, NE, NV, NJ, NY, OK, SD, TN, UT, WA, WI, WY) plus four countries (England, Scotland, India and Canada). The deliverables include training workshops, new coursework, publicly available datasets and databases and new data pipelines, models and simulations. Progress reports from Round 2 teams have been received. Any institution eligible for subcontract funding under the USDA's AG2PI RFA was eligible to apply for seed grants. Assessment. Given this project's focus on seed grants, the internal metrics (managed by the project manager) only track seed grants and the external assessment is similarly focused on seed grant teams. External assessment is being conducted by Divergent Science - a women-owned business that specializes in the science of team science and social network analyses -with a scope of measuring community building and team connectivity. So far, teams from Round 1 and Round 2 research seed grant teams have been surveyed; Round 3 teams will be assessed later in 2022. Results of the Rounds 1 and 2 surveys and corresponding social network analyses show that new teams are being formed through the AG2PI seed grant mechanism and we know from feedback that some of these teams formed as a result of an AG2PI teaming event offered during mini-conferences (August 2021 and January 2022). Additional teaming through AG2PI is expected because 86% of seed grant team members reported they plan to collaborate with people they met during the AG2PI program. A year into this project, many of the awardees were familiar with each other before receiving an award. However, new connections were made through these awards as indicated by the results of a social network analysis. Early career team members have particularly benefitted considering how their positions in the network moved more towards central roles and away from the periphery of networks. Furthermore, early career team members are providing more learning opportunities to others since joining or forming their teams as they become more engaged with the community. AG2PI's emphasis on early career researchers in the seed grant RFAs may have encouraged more of these researchers to apply and thereby helping to elevate them to leadership positions.
Publications
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