Source: IOWA STATE UNIVERSITY submitted to
NIFA AG2PI COLLABORATIVE: CREATING A SHARED VISION ACROSS CROP AND LIVESTOCK COMMUNITIES
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
EXTENDED
Funding Source
OTHER GRANTS
Reporting Frequency
Annual
Accession No.
1024061
Grant No.
2020-70412-32615
Project No.
IOW05630
Proposal No.
2020-08485
Multistate No.
(N/A)
Program Code
AG2PI
Project Start Date
Sep 1, 2020
Project End Date
Aug 31, 2024
Grant Year
2020
Project Director
Schnable, P. S.
Recipient Organization
IOWA STATE UNIVERSITY
2229 Lincoln Way
AMES,IA 50011
Performing Department
Agronomy
Non Technical Summary
To address the challenges and opportunities of achieving sustainable genetic improvement of agricultural species, 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 crop and livestock communities, as well as integrative disciplines (e.g., engineers, data scientists, economists, and social scientists). The overall objective of this AG2PI is to assemble and prepare a transdisciplinary community to conduct AG2P research. The project will: Develop a vision for AG2P research by identifying research gaps and opportunities; foster first steps towards the development of community solutions to these challenges and gaps; and rapidly disseminate findings to the broader community. Towards these ends, AG2PI will sponsor and coordinate field days, conferences, training workshops, and seed grants. AG2PI features a robust project management plan, involving leaders with the requisite experience managing large complex projects, implementation plans based on best practices and the science of team science, coupled with a robust assessment plan to refine best practices. A comprehensive and inclusive group of scientific partner organizations (including those serving the global community), a renowned scientific advisory board, and an external stakeholder group will assist the AG2PI in meeting its objectives and ensuring that its activities coordinate and complement existing programs in plant and livestock G2P. Development of a cross-kingdom community prepared to tackle AG2P research offers opportunities to develop novel and creative solutions to enhance our understanding of both kingdoms, for the benefit of US agriculture and society.
Animal Health Component
0%
Research Effort Categories
Basic
(N/A)
Applied
(N/A)
Developmental
(N/A)
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
2012410106050%
3043910106050%
Knowledge Area
201 - Plant Genome, Genetics, and Genetic Mechanisms; 304 - Animal Genome;

Subject Of Investigation
3910 - Cross-commodity research--multiple animal species; 2410 - Cross-commodity research--multiple crops;

Field Of Science
1060 - Biology (whole systems);
Goals / Objectives
To meet the challenges of an increasing global population and multiple environmental stressors on agricultural production, it is essential that we better understand how genotype (G) and environment (E) influence phenotype for the complex traits of crops and livestock that are important to agriculture. This relationship is complicated by the fact that genotypes respond differently to environmental variation. An NSF-funded workshop demonstrated that "phenotypic space" has almost infinite dimensions. As such, to accurately predict phenotype, it is necessary to understand not only the roles of G and E on phenotype, but also their interaction (GxE). Advances in crop and livestock sciences, genetics, genomics, computational and data sciences, and engineering offer the potential to address these challenges. Towards this end, Congress established the Agricultural Genome to Phenome Initiative (AG2PI).The focus of this proposal is on building a cross-kingdom research community to address the challenges of AG2P. The crop and livestock (including avian and aquatic species) research communities have separately begun to address these challenges. But given the commonalities in the needs of these communities, there is significant potential to work together. That said, there are also significant differences between the crop and livestock research communities and in their needs and goals. These differences are driven by biology, commercial landscape and how the research communities are organized. There are also many similarities and shared needs between the crop and livestock G2P communities. Both require mechanisms for data sharing and access; the integration of multiple sources and types of data; access to advanced cyberinfrastructure and expertise in data sciences; the development of novel sensors, robotics, imaging platforms; and the sharing of best practices. Importantly, they also both share the need to train and facilitate the flow of information to junior researchers and stakeholders for the benefit of US agriculture and society.While the specific scientific goals of the crop and livestock G2P communities exhibit some overlap in methods, their needs dovetail with regards to accessing computational and data management resources, as well as advanced data analytics. Both communities make use of shared public resources such as NCBI for depositing genetic data, and CyVerse for access to cyberinfrastructure for sharing private research data and running large-scale computational analyses. While some computational resources exist that serve both plant and animal research communities, these communities often have specialized data resources for their organisms, which leads to some siloing of knowledge and information.In addition, these communities face similar challenges with regards to accessing emerging technologies. Often, an advance is developed to solve a problem in one area of life science research, and a lag time is experienced before it is "discovered" and adapted by other communities. There is a unique and timely opportunity to address these challenges by bringing together members of the crop and livestock communities to share best practices, identify common analytical pain-points, and co-develop solutions. In addition, this coordinated effort to increase communication among these communities will enable assemblages of G2P research teams, including researchers from engineering, and computational and data sciences who often seek new high-impact challenges.There are many specific opportunities for interactions between crops and livestock research. The proposed project will work to further strengthen the ties between these communities and identify a shared vision for G2P research where common problems can be solved together.The overall goal of this project is to assemble a transdisciplinary community and to prepare this community for an anticipated large-scale R&D effort in AG2P that will address the sustainable genetic improvement of crops and livestock. To meet this overall goal, we will undertake three highly interrelated objectives.Develop a vision for AG2PI by identifying research needs and opportunities, as well as gaps in physical infrastructure and data management.Foster first steps towards the development of community solutions to challenges identified in #1.Communicate and disseminate findings of all activities through white papers, websites, and other scientific publications.
Project Methods
To address the challenge of achieving sustainable genetic improvement across crops and livestock, it will be necessary to engage the expertise of a broad community of researchers, drawing from crop and livestock communities as well as more distant communities (e.g., engineering and data sciences). Towards this end, the AG2PI team has engaged diverse organizations as partners; the PI team includes leaders of several of these Partner Organizations. The AG2PI participating organizations span institutions and nations, enabling their diverse members to become aware of and gain access to ideas, methods, and tools, while still in the proof-of-concept and early testing stages. We will leverage these existing networks to extend the reach of AG2PI's activities. This will: (1) speed knowledge transfer; (2) create and reinforce an environment of inclusion by recognizing prior perspectives and achievements; (3) identify challenges for these communities to address together.To further the development of a transdisciplinary community, the AG2PI will sponsor and coordinate four types of activities: virtual field days, conferences, training workshops, and seed grants. In combination, these will contribute to our overall goal of building a community across the crop and livestock communities and preparing this community to tackle the challenges of G2P.The re:Work project developed by Google identified the five most important aspects of interaction which are Psychological safety, Dependability, Structure and clarity, Meaning and Impact. To ensure that members of AG2PI are enabled to work together, not only will these five standards for positive engagement be messaged, but as part of our assessment plan team members will be queried during and after projects to determine whether group dynamics were positive in these dimensions and to learn where failures occurred and how they might be prevented in the future.Field DaysTo expose the G2P community to the diversity of research activities and resources across crops and livestock, we will host virtual "Field Days". The focus will be on sharing research methods, approaches, and capacities, and on identifying research gaps and challenges, which will inform our white papers. We plan to offer a training session for Field Day presenters on how to communicate across disciplines, which PI Schnable has used successfully with the PSI Scholars at ISU. A key difference between Field Days and the Conferences described below is that the former consists of informal presentations about specific projects and/or infrastructure facilities, somewhat analogous to virtual "open houses".ConferencesThe year 1 goal of the conferences will be to identify gaps in knowledge, infrastructure, protocols, and coordination, as well as opportunities within the crop and livestock G2P communities. Although a few of these conference events will be focused on specific species (e.g., maize or cattle), most will cross species boundaries (e.g., cyberinfrastructure, bioinformatics, imaging, data storage, sharing and re-use, statistics). Prior to conferences, on-line surveys will be used to identify gaps in knowledge and issues of common concern in building community for advancing AG2P. Thus, the conferences will be "front-loaded" with organized discussion points and agendas to encourage thoughtful discussion and produce community consensus and progress toward solutions. Each conference will be coupled with relevant training workshops (below) and will be followed up by participants collaborating on-line to draft white papers. In years 2 and 3, conferences will focus on presenting results/deliverables from the seed grants (below), developing additional white papers on community perspectives, and supporting discussions within and across stakeholder communities to further strengthen nascent connections across diverse communities. We will also host events to describe available G2P funding opportunities for community members.Training WorkshopsTo build technical strengths and future collaborative G2P communities, we will offer a suite of workshops to enable researchers from all backgrounds and computational skill levels to develop best practices, common vocabularies, and technical expertise around genomic and phenomic cyberinfrastructure, data tools and pipelines, statistics, and experimental techniques.All workshops will be delivered virtually to increase accessibility and participation. In addition, all workshop materials will be made available online through ReadTheDocs [55], and delivered workshops will be recorded and made available via YouTube and other channels for subsequent asynchronous learning. We will teach 12 workshops per year (1 per month), with the general structure of one long-format and two short-format workshops per quarter.Seed GrantsThe AG2PI's Seed Grant program is designed to promote collaboration and support the development and cross-pollination of tools, data, and ideas to enable and facilitate future G2P research across disciplines, species and sectors. Seed grant awards will be on topics relevant to G2P (interpreted broadly) and will range from $5,000-10,000 and have durations of 6-12 months. Given the size of these awards, the deliverables will typically be scoping or prototypes, rather than completed research projects. Any institution eligible for subcontract funding under the USDA's AG2PI RFA will be eligible to apply for seed grants.

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 created and 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. Over the past three years, other organizations' listservs have been added to AG2PI mailings, including Decision Support System for Agrotechnology Transfer (DSSAT), Animal Geneticists' Discussion Group and DivSeek International. This diverse community continues to grow as measured by website visits and activity attendance. For example, since its launch in October 2020 the AG2PI website has had 53,363 unique visitors from across 172 countries and every inhabited continent of the world (as of August 8, 2023). The AG2PI listserv currently includes 4,994 members. Activities are advertised via AG2PI and partner listservs as well as through Plantae's Global Plant Science Calendar, Twitter/X, and LinkedIn. To ensure the inclusion of URM audiences, we have shared AG2PI activities with various URM organizations, such as MANNRS and SACNAS, as well as with 1890 Agriculture Research Station Directors. 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?Field days and workshops provide both training activities and professional development activities for AG2PI community members. Each field day or workshop is led by individuals who are recognized by AG2PI leadership as experts on the topic of the given event. Some field day and workshop presenters are seed grant awardees who are sharing the outcomes of their awarded projects. Leading one of these events provides all presenters, but particularly early-career presenters, the opportunity to gain skills, confidence and community recognition. The purpose of each of these events is to disseminate information, increase knowledge and skills and provide an opportunity to meet other community members. Both event types are offered as Zoom meetings rather than webinars to encourage broad community participation, engagement and interaction. The first 23 field days have an associated Slack workspace wherein community members can continue conversations begun during the field day, particularly with the presenter, not just for intellectual enrichment but for professional networking expansion. Conferences have also been an avenue of professional development for community members, both general members and seed grant awardees. For both in-person conferences, graduate students were invited to attend as scribes for the benefit of seeing firsthand how the community can come together to direct the future of the field. Furthermore, the project manager is receiving professional development through membership in the International Network for Science of Team Science. This professional group provides biweekly meetings that discuss the science of team science through the Intereach group. 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. In Year 3, engagement with the website is over 53,000 visitors; with nearly 5,000 listserv members. Although registrations for virtual Field Days remain similar to Year 2 (around 200 per event), each event sees on average 50 attendees who are joining a Field Day for the first time. Workshop registrations have increased over the past year with an average of 259 (compared to 177 in Year 2) with average attendance holding steady at about 60 per event. When considering asynchronous viewing of these events via YouTube (633 subscribers), workshops, in particular, appear to be meeting a critical need: two workshops from Year 1 now have over 9000 combined views (workshops #3 & 4). Event details and links to registration pages are shared through AG2PI mailing lists. Since most registration pages are hosted on the AG2PI website, we are able to collect information on first-time users and give them the opportunity to opt-out of getting added to our mailing lists; otherwise, they are automatically added. The website also has a webform where interested parties can register to join a mailing list or to request that their organization be added as an institutional partner. Recordings of each field day, workshop and selected conference sessions are available on the AG2PI website; we track views through YouTube. Twitter/X (@AG2PI; 566 followers) and LinkedIn accounts (166 followers) are used for advertising upcoming events and to reach broader audiences who may prefer social media over email for their communications. In this way the project cuts across generational differences in communication preferences. We also advertise events through community event calendar's like Plantae.org. AG2PI has two Slack workspaces that are designed for asynchronous interaction with 1) field day presenters and attendees and 2) other community members looking to collaborate on a prospective AG2PI seed grant. However, these Slack spaces have not received many interactions outside of event days and, thus, have been discontinued. Press releases, newsletters (e.g., AG2PI) and mailings to other adjacent community groups (such as DSSAT, Animal Geneticists Discussion Group) have also been used to reach target audiences. 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. Dissemination of seed project activities are primarily the responsibility of the seed project teams, but when appropriate, and in keeping with data management plans, AG2PI shares these outcomes on the website under the "Funded Seed Grants" page. For example, a Tellus feature on UAV applications in potato was published in 2021 (https://tellus.ars.usda.gov/stories/articles/cutting-to-the-chase/) on a Round 1 seed grant and is now linked on the AG2PI website. Outcomes, including final reports, are organized within the funded project description box along with the narrative from the proposal. Outside organizations have tapped into this resource page as a reservoir of information regarding the future of AG2PI research and funding. For example, the Breakthrough Institute's Growing Green report on the environmental benefits of public agricultural research and development as well as the Genetic Literacy Project have consulted the AG2PI webpage and seed grant outcomes for their articles (https://geneticliteracyproject.org/2022/09/21/viewpoint-underrated-and-underfunded-its-time-for-congress-to-increase-support-for-biotechnology-tools-in-next-farm-bill/). To ensure AG2PI recordings are accessible to those with hearing challenges, we have been utilizing the "live closed captioning" option within Zoom meetings as well as editing the closed captioning within YouTube for our recordings. To accommodate those with visual impairments, we create digitally accessible versions of our flyers, which we post on our event webpages. We also include image descriptions of our flyers within our social media posts. AG2PI Partner Organizations have been critical to sharing AG2PI news and events. We have enjoyed a reciprocal, mutually beneficial relationship with these organizations such that AG2PI shares news and events from Partner Organizations, as well. We have shared our knowledge gained from this project with newly funded projects such as AIIRA (USDA NIFA-NSF funded AI Institute) and NAPDC (USDA NFIA funded) to accelerate their growth and potential for impact. What do you plan to do during the next reporting period to accomplish the goals?We are planning to support the deposit of seed grant derived data, pipelines and other digital information into a digital repository (i.e., CyVerse) over the next year, as part of a no-cost extension. We are also considering the organization of a conference for 2024 or other activities that will further support the growing AG2PI community as well as provide the coconut grant awardees an opportunity to share their outcomes with this 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 & 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 formed, and continues to grow, a community of researchers, students, industry and commodity groups prepared to develop novel and creative solutions to agricultural genomes-to-phenomes challenges, for the benefit of US agriculture and society. The project is working to: Develop a vision for AG2P research, develop community solutions to challenges and gaps, and rapidly disseminate findings. To these ends, AG2PI organizes four types of activities: virtual field days, conferences, training workshops, and seed grants. Since the project's first event in October 2020, over 53,000 participants from across every inhabited continent of the world has engaged with our website to join an activity or learn more about this project. As a hub for those working across sectors to improve agriculture, AG2PI has been leveraged by new groups - such as AI Institute for Resilient Agriculture (funded by NSF & USDA NIFA) and National Agriculture Producers Data Cooperative (funded by USDA NIFA) - to connect with our community and thereby magnify their activities and strengthen their objectives. Objectives: 1. Develop a vision for AG2PI by identifying research needs and opportunities, as well as gaps in physical infrastructure and data management. Outside the 4 main activities, we deployed conferences in September 2022 and June 2023 to gather community input on how future funding should be directed to advance agricultural G2P work, as well as to share what work has been accomplished through AG2PI seed funding. 2. Foster first steps towards the development of community solutions to challenges identified in #1. This has been accomplished, to date, through 13 seed grant awards across 3 seed grant opportunities. 3. Communicate and disseminate findings of all activities through the AG2PI websites and other publications. AG2PI activities (field days, training workshops and select conference sessions) are advertised via social media and listservs; activity recordings are available on the AG2PI website. Deliverables from the seed grant projects are also available via the website and through social media, when appropriate. Four Main Activities Supporting Objectives Field Days. Monthly virtual talks are designed to appeal to a diverse audience, find intersections with other research interests and introduce the G2P community to a diversity of research activities and available resources applicable across sectors. Each field day is recorded and posted to the AG2PI website (https://www.ag2pi.org/workshops-and-activities/) soon after the event ends along with presenters' slides, when these are made available. Eight virtual field days were offered in Year 3 (see Products section for list) with cumulative attendance of 379 (maximum = 171; minimum = 10). For each field day, over 50% of attendees were first time attendees suggesting that we hit upon an adequate diversity of topics that were important to different subgroups within the community and also that we were continuously expanding our community. Registrants hail from 49 states (not including AK). Training Workshops. These enable researchers from diverse backgrounds and computational skill levels to develop best practices, common vocabularies, and technical expertise around cyberinfrastructure, data tools and pipelines, statistics, and experimental techniques. Year 3 has included 9 workshops (see Products section for list) with an average attendance above 60 (maximum = 111; minimum = 33). Registrants hail from 48 states (not including AK, NH). Workshops are recorded and available on the AG2PI website (https://www.ag2pi.org/workshops-and-activities/) along with supplemental materials (e.g., GitHub). Seed Grants. AG2PI's Seed Grant program for this award consisted of two types of awards: rounds and working groups. "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. "Working group" grants supported the work of newly formed working groups. Any institution eligible for subcontract funding under the USDA's AG2PI RFA was eligible to apply for seed grants. Final reports and deliverables can be found on the AG2PI website at https://www.ag2pi.org/resources/ag2pi-funded-seed-grants/. One Working Group grant was awarded this year out of three applications. Projects were allowed budgets up to $20,000 and duration of up to 12 months; however, the funded project was completed in 6 months. Deliverables for this project included formation of an interdisciplinary working group that could bridge the knowledge gaps in goat genome to phenome research as well as a database that includes the phenotypic data that has already been generated at the International Goat Research Center at Prairie View A&M University, an HBCU. Conferences. Goals of conferences have been to identify gaps in knowledge, infrastructure, protocols, and coordination, as well as opportunities within the crop and livestock communities. In Year 3, we held two in-person conferences (see Other Products for details). Recordings of talks and panels are available on the AG2PI website (https://www.ag2pi.org/workshops-and-activities/). The first conference, "Thinking Big: Visualizing the Future of AG2PI" was in the style of a two-day workshop and held September 9-10, 2022, with USDA NIFA as co-host, in Ames, Iowa. The goal of this conferences was to bring stakeholders from across the AG2P community to discuss where the field should be headed and communicate what is needed to get there. Results of the third community survey, deployed in June 2022 (reported in 2022 progress report), and topics submitted from the Scientific Advisory Board were used to direct small group discussions on what would be easiest to achieve with immediate funding and what is most critical to fund. The ideas generated have been written into a manuscript that is currently under review for publication. The 2nd conference "Mapping the Future of Agricultural Genome to Phenome Research" was held June 15-16 in Kansas City, MO, and co-hosted by USDA NIFA. The goals of this conference were to disseminate knowledge, gather community input on the future of R&D in the AG2P space and connect researchers across sectors and disciplines. Attendance was both by invitation and by free, public registration via the AG2PI website. Organization of this conference centered on talks and panel discussions followed by small group breakouts. Topics for small groups were taken from the preceding panels for further discussion regarding: 1) how the topic connects to their current work, 2) what are the opportunities in the short-term to address the topic, and 3) what might be the long-term opportunities. Assessment: Post-event assessments have been provided following every AG2PI event via Qualtrics or Zoom. Responses have been overwhelmingly positive across field days, workshops and conferences. Participants have indicated AG2PI activities have been useful and fulfill a need. These assessments included space for participants to provide their ideas for future activity topics and presenters. A "collaboration exploration" survey available on the AG2PI website homepage asks about respondents' experiences with collaboration and how they might collaborate in the future. This was created as part of our contract with The Filament. See Products section for summary of results.

Publications

  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Seed grant deliverable from Empowering high-throughput phenotyping using UAVs (PI: Max Feldman, USDA ARS): Workshop at NAPPN Conference in 2022. Hosted a community engagement workshop to kick-off quantitative survey on UAS use and deployment bottlenecks: https://www.plant-phenotyping.org/index.php?index=580&event=NaPPN_Annual_Conference. Between 50 -100 attendees.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2021 Citation: Seed grant deliverable from Empowering high-throughput phenotyping using UAVs (PI: Max Feldman, USDA ARS): Presentation of project objectives at Oregon State University Hermiston Potato Field Day in 2021. Link to agenda: https://ag01.noco.net/sites/agscid7/files/harec/potatofieldday2021.pdf. Between 50 -100 stakeholder attendees.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Seed grant deliverable from Empowering high-throughput phenotyping using UAVs (PI: Max Feldman, USDA ARS): Presentation at 106th Annual Potato Association of America Meeting. Link to presentation: https://zenodo.org/record/6859791#.Y-LIVy-B1z8. Between 50  150 research/scientific attendees. July 19, 2022
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Seed grant deliverable from Empowering high-throughput phenotyping using UAVs (PI: Max Feldman, USDA ARS): Presentation at Washington Oregon Potato Conference. Link to presentation: https://zenodo.org/record/7618620#.Y-LIqy-B1z8. Between 200  1000 stakeholder attendees. January 26, 2023.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Seed grant deliverable from Empowering high-throughput phenotyping using UAVs (PI: Max Feldman, USDA ARS): Presentation at ASA-CSSA-SSSA 2022. Presented on open source UAS data processing approaches for small plots research https://scisoc.confex.com/scisoc/2022am/meetingapp.cgi/Paper/141647. Between 10-30 research/scientific attendees. November 6-9, 2022.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: 22. Seed grant deliverable from Empowering high-throughput phenotyping using UAVs (PI: Max Feldman, USDA ARS): Presentation at ASA-CSSA-SSSA 2022. Presented on best practices for drone data collection and analysis https://scisoc.confex.com/scisoc/2022am/meetingapp.cgi/Paper/141170. Between 10-30 research/scientific attendees. November 6-9, 2022.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Seed grant deliverable from Empowering high-throughput phenotyping using UAVs (PI: Max Feldman, USDA ARS): Poster presenting on the community survey results on barriers of using UAS in agriculture: https://scisoc.confex.com/scisoc/2022am/meetingapp.cgi/Paper/146333. Won 1st place poster award at ASA-CSSA-SSSA 2022 in the Diversity Research division. Poster session attendance included thousands of attendees. November 6-9, 2022.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Seed grant deliverable from Community engagement to improve standards and integration for genotype, phenotype, and environmental data for model and non-model plants (PI: Irene Cobo Sim�n, University of Connecticut): Workshop titled, CartograPlant Workshop: Hands-On Training With an Analysis Framework Integrating Genotype, Phenotype, and Environmental Data, at the PAG 30 International conference (San Diego, California, https://plan.core-apps.com/pag_2023/event/3cee484866e6d00c5e492240c4d5e8c5) to audience of 31. New features have been added to CartograPlant and disseminated to the workshop participants, including data quality filtering and visualization tools (e.g. histograms, Venn diagrams for phenotypes and genotypes, population structure analysis, multicollinearity calculation and visualization). January 13, 2023.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Seed grant deliverable from Community engagement to improve standards and integration for genotype, phenotype, and environmental data for model and non-model plants (PI: Irene Cobo Sim�n, University of Connecticut): Workshop at PAG 30 International conference entitled The AgBioData Consortium: Challenges and Recommendations for FAIR Genetic, Genomic and Breeding Data. Session entitled: Challenges and Opportunities in Connecting Genotype to Phenotype Data (https://plan.core-apps.com/pag_2023/event/3cee484866e6d00c5e492240c4d27482). The workshop had a total of 50 participants. January 13, 2023.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Seed grant deliverable from Community engagement to improve standards and integration for genotype, phenotype, and environmental data for model and non-model plants (PI: Irene Cobo Sim�n, University of Connecticut): Plant and Animal Genome Conference PAG 30, January 13-18, 2023. San Diego (California, USA). Talk by Emily Grau, Irene Cobo-Sim�n, Risharde Ramnath, Jill Wegrzyn. Cartograplant: Leveraging Ontologies for Landscape and Association Genetics.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Seed grant deliverable from Community engagement to improve standards and integration for genotype, phenotype, and environmental data for model and non-model plants (PI: Irene Cobo Sim�n, University of Connecticut): Plant and Animal Genome International Conference (PAG) XXIX. Jan. 9-11, 2022. Virtual Talk by Irene Cobo-Sim�n, Risharde Ramnath, Sean Buehler, Peter Richter, Charlie Demurjian, Barnaly Pande, Emily Strickland, Alicia Abrams, Alex Lowe, Emily Grau, Abdullah Almsaeed, Nic Herndon, Margaret Staton, Jill Wegrzyn titled, Cartograplant: Cyberinfrastructure to Improve Forest Health and Productivity in the Context of a Changing Climate held during Forest Tree Session.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Seed grant deliverable from Community engagement to improve standards and integration for genotype, phenotype, and environmental data for model and non-model plants (PI: Irene Cobo Sim�n, University of Connecticut): Botany 2022, Anchorage (Alaska, USA), July 24-27, 2022. Talk: Irene Cobo-Sim�n, Risharde Ramnath, Sean Buehler, Peter Richter, Charles Demurjian, Barnaly Pande, Emily Strickland, Victoria Burton, Nicole Butch, Alicia Abrams, Alex Lowe, Emily Grau, Abdullah Almsaeed, Nic Herndon, Margaret Staton, Jill Wegrzyn titled, CartograPlant: Cyberinfrastructure to improve plant health and productivity in the context of a changing climate.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Seed grant deliverable from Community engagement to improve standards and integration for genotype, phenotype, and environmental data for model and non-model plants (PI: Irene Cobo Sim�n, University of Connecticut): 1st North American Forest Genetics Society Meeting (Asilomar, California) (June 14-16, 2022): Talk by Emily Grau titled, TreeGenes and CartograPlant: Resources for Forest Tree Genetics.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Seed grant deliverable from Community engagement to improve standards and integration for genotype, phenotype, and environmental data for model and non-model plants (PI: Irene Cobo Sim�n, University of Connecticut): Plant Genomes Online (April 27-28, 2022): Talk by Irene Cobo-Sim�n, Risharde Ramnath, Sean Buehler, Peter Richter, Charles Demurjian, Barnaly Pande, Emily Strickland, Victoria Burton, Nicole Butch, Alicia Abrams, Alex Lowe, Emily Grau, Abdullah Almsaeed, Nic Herndon, Margaret Staton, Jill Wegrzyn titled, Cartograplant: Cyberinfrastructure to Improve Plant Health and Productivity in the Context of a Changing Climate.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Seed grant deliverable from Community engagement to improve standards and integration for genotype, phenotype, and environmental data for model and non-model plants (PI: Irene Cobo Sim�n, University of Connecticut): Plant and Animal Genome International Conference (PAG) XXIX. Jan. 9-11, 2022. Virtual Talk by Irene Cobo-Sim�n, Nic Herndon, Margaret Staton, Emily Grau, Sean Buehler, Peter Richter, Risharde Ramnath, Charlie Demurjian, Abdullah Almsaeed, Jill Wegrzyn titled, Integrating, visualizing and analyzing tree environment, phenotype and genotype using CartograPlant, WildType and Tripal Galaxy during Digital Tools and Resources, Session 3.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Seed grant deliverable from Community engagement to improve standards and integration for genotype, phenotype, and environmental data for model and non-model plants (PI: Irene Cobo Sim�n, University of Connecticut): Plant and Animal Genome International Conference (PAG) XXIX. Jan. 9-11, 2022. Virtual Poster by Irene Cobo-Sim�n, Nic Herndon, Margaret Staton, Emily Grau, Sean Buehler, Peter Richter, Risharde Ramnath, Charlie Demurjian, Abdullah Almsaeed, Jill Wegrzyn titled, Integrating, visualizing and analyzing tree environment, phenotype and genotype using CartograPlant, WildType and Tripal Galaxy.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Seed grant deliverable from Harnessing Ag Genomics Data to link genotype to phenotype (PI: James Koltes, Iowa State University): A talk entitled, Data reuse working group: First steps and goals was presented at the AgbioData meeting in Chicago, IL, USA on May 1, 2023 by Alenka Hafner. Authors: Alenka Hafner, Chris Elsik, Boas Pucker, Cecilia Deng, Peter Harrison, Ted Kalbfleisch, Elsa Herminia Quezada Rodriguez, Vicotoria DeLeo, Bruna Petry, Anne Thessen, and James Koltes A link to the presentation (at ~47:00) is available here: https://www.youtube.com/watch?v=FzkoGIRX2Ng&list=PL7PHQZk3QU4s_B1yAfve6MiGiizsTfPe_&index=1. This talk was presented at the AgBioData Meeting to all attendees. The talk is also available online and has been viewed 18 times. The talk was followed by a work group discussion that asked participants if additional topics should be covered in the white paper or if additional survey questions should be asked regarding data reuse.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Seed grant deliverable from Harnessing Ag Genomics Data to link genotype to phenotype (PI: James Koltes, Iowa State University): A talk at PAG30/ US National Animal Genome Research Program (NRSP8) workshop Encode registry of candidate cis-regulatory elements (cCREs) for annotating the human genome by Zhiping Weng: https://plan.core-apps.com/pag_2023/event/3cee484866e6d00c5e492240c4d56f00. January 15, 2023
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Seed grant deliverable from Harnessing Ag Genomics Data to link genotype to phenotype (PI: James Koltes, Iowa State University): Two talks at PAG30 session, Big Data: Manage your data before your data kills you, (authors in parentheses) with link included to the meeting sessions where talks were presented: https://plan.core-apps.com/pag_2023/event/3cee484866e6d00c5e492240c4d5637f. FAANGMine: Tools for Exploring Functional Annotation of Animal Genomes (by Chris Elsik) and Risks and Rewards of Data reuse: Methylome Re-Analysis Yields Novel information (by Alenka Hafner). January 15, 2023
  • Type: Conference Papers and Presentations Status: Published Year Published: 2021 Citation: Seed grant deliverable from Seeding public-private partnerships for AG2P training (PI: Addie Thompson, Michigan State University): Brewbaker Lecture, University of Hawaii, Nov 2021  university attendees
  • Type: Conference Papers and Presentations Status: Published Year Published: 2021 Citation: Seed grant deliverable from Seeding public-private partnerships for AG2P training (PI: Addie Thompson, Michigan State University): International Sweet Corn Development Association (ISCDA), Dec 2021  public and private breeders
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Seed grant deliverable from Seeding public-private partnerships for AG2P training (PI: Addie Thompson, Michigan State University): Corn Marketing Program of Michigan (CMPM) campus visit, March 2022  farmers
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Seed grant deliverable from Seeding public-private partnerships for AG2P training (PI: Addie Thompson, Michigan State University): FFA state convention, March 2022  high school students and club advisors
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Seed grant deliverable from Seeding public-private partnerships for AG2P training (PI: Addie Thompson, Michigan State University): MSU Genomics Symposium (GGS), May 2022  university attendees
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Seed grant deliverable from Seeding public-private partnerships for AG2P training (PI: Addie Thompson, Michigan State University): Genomics REU career talk, July 2022  undergraduate researchers from across the US
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Seed grant deliverable from Seeding public-private partnerships for AG2P training (PI: Addie Thompson, Michigan State University): International Society for Computational Biology (ISMB) Digital Agriculture at Scale panel, July 2022  computational conference attendees
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Seed grant deliverable from Seeding public-private partnerships for AG2P training (PI: Addie Thompson, Michigan State University): National Association of Plant Breeders (NAPB) conference, August 2022  breeding conference attendees
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Seed grant deliverable from Seeding public-private partnerships for AG2P training (PI: Addie Thompson, Michigan State University): MSU Engineering (ECE) faculty meeting, Nov 2022  ECE faculty, invitation to participate/collaborate
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Seed grant deliverable from Seeding public-private partnerships for AG2P training (PI: Addie Thompson, Michigan State University): Midwest Food Products Association Processing Crops Conference, Nov 2022  food processing industry
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Seed grant deliverable from Seeding public-private partnerships for AG2P training (PI: Addie Thompson, Michigan State University): Poster presented at AG2PI workshops in September 2022 and June 2023 and talk at mini conference #3 in January 2022
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Seed grant deliverable from GPS collars as precision agriculture tools for managing extensive rangeland production systems (PI: Andrew Hess, University of Nevada - Reno): Title: Using GPS Collars to Measure Rangeland Utilization and Resilience of Livestock. Authors: John Bergeron, Scott Huber, Tracy Shane, Jason Karl, Melanie Hess, Robert Washington-Allen, Mike Cox, Andrew Hess. Oral and poster presentation. Conference: Gordon Research Seminar in Quantitative Genetics and Genomics. Date: February 12-17, 2023. Location: Ventura, CA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Seed grant deliverable from GPS collars as precision agriculture tools for managing extensive rangeland production systems (PI: Andrew Hess, University of Nevada - Reno): Title: Wheres Waldo? Describing resilience linked land use behaviors of sheep via GPS collars. Authors: John Bergeron, Scott Huber, Tracy Shane, Jason Karl, Melanie Hess, Robert Washington-Allen, Mike Cox, Andrew Hess. Oral presentation. Conference: AGBT-Ag. Date: March 27-29, 2023. Location: San Antonio, TX.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Seed grant deliverable from GPS collars as precision agriculture tools for managing extensive rangeland production systems (PI: Andrew Hess, University of Nevada - Reno): Title: Repeatability of Rangeland Behavioral and Social Traits Derived from GPS Collars. Authors: John Bergeron, Scott Huber, Tracy Shane, Jason Karl, Melanie Hess, Robert Washington-Allen, Mike Cox, Andrew Hess. Oral presentation. Conference: ASAS Annual Meeting. Date: July 16-20, 2023. Location: Albuquerque, NM
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Seed grant deliverable from Empowering high-throughput phenotyping using UAVs (PI: Max Feldman, USDA ARS): Presentation at S1069 Multi-state project meeting held May 26-27, 2022. Provided update on drone usage as part of update from Washington state. Between 10  30 research/scientific attendees.
  • Type: Journal Articles Status: Published Year Published: 2022 Citation: Clarke, Jennifer, Jack Dekkers, David Ertl, Carolyn J. Lawrence-Dill, Eric Lyons, Brenda M. Murdoch, Nicole M. Scott, et al. 2022. Community Perspectives: Genome to Phenome in Agricultural Sciences. OSF Preprints. December 12. doi:10.31219/osf.io/p89vk.
  • Type: Journal Articles Status: Published Year Published: 2023 Citation: Tuggle, Christopher K., Jennifer Clarke, Brenda M. Murdoch, Eric Lyons, Nicole M. Scott, Bedrich Benes, Jacqueline Campbell, et al. 2023. Current Challenges and Future of Agricultural Genomes to Phenomes in the U.S. OSF Preprints. March 22. doi:10.31219/osf.io/m346e.
  • Type: Journal Articles Status: Published Year Published: 2022 Citation: Matias, F. I., Green, A., Lachowiec, J. A., LeBauer, D., & Feldman, M. (2022). Bison-Fly: An open-source UAV pipeline for plant breeding data collection. The Plant Phenome Journal, 5, e20048. https://doi.org/10.1002/ppj2.20048
  • Type: Other Status: Published Year Published: 2023 Citation: Seed grant deliverable from Community engagement to improve standards and integration for genotype, phenotype, and environmental data for model and non-model plants (PI: Irene Cobo, University of Connecticut): Dr. Cobo as Chair of the Genotype-Phenotype WG (https://www.agbiodata.org/past-working-groups) - White paper entitled Agricultural sciences in the big data era: omics data standardization, utilization and integration in crops. Published online June 14, 2023, via Preprints.org at https://www.preprints.org/manuscript/202306.1013/v1
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: September 2, 2022: Farm Journal Foundation roundtable at Iowa State University, in association with Senator Joni Ernst, included a presentation by AG2PI PI, Patrick Schnable, on the future of agriculture and the AG2PI project.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: November 2, 2022: co-PI Jack Dekkers presented on the AG2PI project with an invited talk titled, The Agricultural Genomes 2 Phenomes Initiative (AG2PI): Charting the Future of Livestock and Crop Genetics Research to the joint meeting Poultry Breeders and National Swine Improvement Federation.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: November 11, 2022: co-PI Jack Dekkers presented on the AG2PI project with a talk titled, The Agricultural Genomes 2 Phenomes Initiative (AG2PI): Charting the Future of Livestock and Crop Genetics Research as part of the Iowa State University Department of Animal Science seminar.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: January 15, 2023: co-PI Christopher Tuggle presented on the AG2PI project with a talk titled, Visualizing the Road to Genome to Phenome in Agriculture at the Plant and Animal Genome conference as part of the NRSP-8 workshop.
  • Type: Journal Articles Status: Published Year Published: 2022 Citation: Seed grant deliverable from GPS collars as precision agriculture tools for managing extensive rangeland production systems (PI: Andrew Hess, University of Nevada - Reno): Producer-oriented magazine article. Using Precision Agriculture Tools to Produce More Sustainable Animals Author: Andrew Hess. Journal: Sheep Industry News. 2022 Genetics Issue
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: January 15, 2023: co-PI Brenda Murdoch presented on the AG2PI project at the Plant and Animal Genome Cattle/Sheep/Goat Workshop II.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: March 1, 2023: co-PI Christopher Tuggle presented on the AG2PI project with a talk titled, Building the Tools to Solve the Genome to Phenome Puzzle in Agriculture at the Midwest section of American Society of Animal Science conference.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Conferences A poster that outlined the AG2PI project was displayed at the AGBT-ag conference (March 27-29, 2023) by Dr. Jack Dekkers. We do not have metrics on how many attendees viewed the poster.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Conferences A poster that outlined the AG2PI project was displayed at the Conference: Gordon Research Seminar in Quantitative Genetics and Genomics by Dr. Jack Dekkers. Date: February 12-17, 2023. Location: Ventura, CA Gordon.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2021 Citation: Seed grant deliverable from Cattle Genome to Herd Phenotyping for Precision Agriculture (PI: Stephanie McKay, University of Vermont): Conference poster and oral: McKay, SD, DE Hagen, RD Schnabel and BM Murdoch. 2021. The Future of Animal Genetics: Pan-Genomics, Pan-Epigenomics and High-Throughput Phenotyping. Visions III Star Gazing the Galaxy of Animal Genetics and Genomics. Ames, Iowa.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2021 Citation: Seed grant deliverable from Machine learning competitions for G2P and end-of-season phenotype prediction (PI: Abby Stylianou, Saint Louis University): A paper What Does TERRA-REFs High Resolution, Multi Sensor Plant Sensing Public Domain Data Offer the Computer Vision Community? presented at the ICCV 2021 Workshop on Computer Vision Problems in Plant Phenotyping and Agriculture proposing a number of different tasks and competitions that would be of interest to the computer vision and machine learning communities using the TERRA-REF data (the dataset leveraged in the competitions run under this grant). Recipient for the Best Paper Award (tied) at the ICCV 2021 Workshop on Computer Vision Problems in Plant Phenotyping and Agriculture.


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. This diverse community continues to grow as measured by website visits and activity attendance. For example, since its launch in October 2020 the AG2PI website has had around 30,000 unique viewers from across every inhabited continent of the world. Over 650 attendees have participated in at least one Field Day this past year with an average of 51 attendees logging in each month for their first AG2PI field day. To ensure the inclusion of URM audiences, we have shared AG2PI activities with various URM organizations, such as MANNRS and SACNAS, particularly with respect to the seed grant opportunity. For example, AG2PI organized a virtual panel at the 2021 SACNAS conference which included four agricultural G2P researchers from diverse backgrounds who shared their career path with 62 attendees, who might consider similar paths. Changes/Problems:As reported in the first progress report, Co-PI Carolyn Lawrence-Dill began a new position as Associate Dean for Research and Discovery at Iowa State University. Due to her increased duties outside of the AG2PI project, she has decreased her duties within this project. As a result, she will no longer be a member of the seed grant steering committee or the conferences subcommittee. She will continue to lead the assessment activities for AG2PI since an external team has been hired to conduct much of the assessment for the project. She was not receiving compensation for any of these activities; therefore, there is no financial impact to this project. AG2PI was expecting to have a large presence at PAG XXIX to help expand awareness of the project. Activities would have included a scavenger hunt to promote networking, a poster detailing the AG2PI project, and several talks by co-PIs that would have featured AG2PI. However, the conference was canceled due to a rise in COVID-19 cases. A few of the AG2PI funded seed projects had planned events at PAG, but one project was particularly affected since its planned workshop was to be hosted at this conference. The workshop was hosted by AG2PI via Zoom, instead, and had a respectable attendance; however, attendance at the conference may have differed in significant ways. Regardless, the workshop was recorded and is currently available for viewing on the AG2PI website. This recording was also made available during the NAPPN conference as an on-demand option. 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?Field days and workshops provide training and professional development activities for AG2PI community members. Each field day or workshop is led by individuals who are recognized by AG2PI leadership as experts on the topic of the given event. Leading one of these events provides all presenters, but particularly early-career presenters, to gain skills, confidence and community recognition. The purpose of each of these events is to disseminate information, increase knowledge and skills and provide an opportunity to meet other community members. Both event types are offered as Zoom meetings rather than webinars to encourage broad community participation, engagement and interaction. The field days have an associated Slack workspace wherein community members can continue conversations begun during the field day, particularly with the presenter, not just for intellectual enrichment but for professional networking expansion. Additionally, AG2PI provided two team science trainings: one reserved for seed grant teams and one open to the broader community. Team science trainings served as both training and professional development as many of the attendees were already working in teams on cross-disciplinary projects. Furthermore, the project manager is receiving professional development through membership in the International Network for Science of Team Science. This professional group provides biweekly meetings that discuss the science of team science as well as an annual conference aimed at advancing team science through sharing of empirical evidence and practice. 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. For example, by the end of the first year, engagement with the AG2PI website was over 10,000 unique viewers from across every inhabited continent of the world; that figure is now over 30,000 as year 2 closes. Although registrations for virtual Field Days remain similar (over 2000 each year), each event sees on average 50 attendees who are joining a Field Day for the first time. Workshop registrations are growing exponentially - nearly 2000 in year 2 compared to about 800 in year 1 - and so appear to be meeting a critical need. This is particularly evident when considering YouTube views (see Products section); notably, two workshops from year 1 have over 2000 views. Event details and links to registration pages are shared through AG2PI mailing lists. Since most registration pages are hosted on the AG2PI website, we are able to collect information on first-time users and give them the opportunity to opt-out of getting added to our mailing lists; otherwise, they are automatically added. The website also has a webform where interested parties can register to join a mailing list or to request that their organization be added as an institutional partner. Recordings of each field day, workshop and conference are available on the AG2PI website and we track views through YouTube. Twitter (@AG2PI) and LinkedIn accounts are used for advertising upcoming events and to reach broader audiences who may prefer social media over email for their communications. In this way the project cuts across generational differences in communication preferences. AG2PI also has two Slack workspaces that are designed for asynchronous interaction with 1) field day presenters and attendees and 2) other community members looking to collaborate on an AG2PI seed grant. However, these spaces do not receive many interactions outside of event days. Press releases, newsletters (e.g., AG2PI, American Sheep Industry Association, ASPB Signal) and postings in community calendars (e.g., Plantae) have also been used to reach target audiences. 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. Furthermore, 1890 Research Directors were directly emailed with invitations to participate in the 2021 AG2PI community survey and to join future AG2PI events. 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. To ensure AG2PI recordings are accessible to those with hearing challenges, we have been utilizing the "live closed captioning" option within Zoom meetings as well as editing the closed captioning within YouTube for our recordings. To accommodate those with visual impairments, we create digitally accessible versions of our flyers, which we post on our event webpages. We also include image descriptions of our flyers within our tweets. What do you plan to do during the next reporting period to accomplish the goals?Field days We will continue to rotate topics for each monthly event, particularly focusing on topics that cut across crop and livestock research needs. Field day speakers have represented all career levels, from undergraduate students to senior career scientists; we will continue to thoughtfully select diverse speakers. Presentations often include poll questions to engage the audience, and audience members are able to pose questions via Zoom's chat function. Recordings will continue to be made available on the AG2PI website soon after the close of the event. Slack channels will continue to be created to serve as a repository of the Q&A from the event as well as serve as an opportunity to ask questions later. Training Workshops Our monthly workshops have and will continue to cover a range of topics from developing core computational competencies and Open Science through specialized topics using advanced machine learning for plant and animal genomics and phenomics. Workshops follow two general formats: Short format (1-2 hours) and Long format (1-2 hours, multiple days). Short format workshops begin with a lecture followed by a hands-on/interactive session and a discussion of strengths, limitations, best practices, and areas for future development. The goal of the long format workshops is to help onboard and level the skills of people new to computationally intensive science. We will continue to invite professionals from all career stages to lead workshops. We are collecting post-Workshop assessments from the participants so that we can determine future training needs of the community. Recordings, slides and other relevant materials will be made available on the AG2PI website soon after the close of the event. Seed Grants Two seed grant opportunities will continue to be available until April 2023 or 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. Conferences Two conferences will be held in year 3. The first will be held September 9-10, 2022, with USDA NIFA as co-host, in Ames, Iowa with a limited number of invitees. The goal of this conferences is to bring representatives from across the AG2P community (i.e., seed grant PIs, stakeholder organization representatives, USDA NIFA representatives, AG2PI scientific advisory board members and other thought leaders) to discuss where the field should be headed and communicate what is needed to get there. The outcomes of this conference will be written into a concept paper and shared with USDA NIFA and possibly published in a peer-reviewed journal for the community to reference. This conference is being informed by the results of the third community survey that was deployed in June 2022. A conference is currently being planned for June 15-16, 2023, in Kansas City, Missouri which will showcase the outcomes of the AG2PI project. This will include presenting on the findings from community surveys, reporting on deliverables from the seed grants, engaging in discourse between AG2P disciplines and institutional types and possibly developing additional concept papers containing community perspectives. A major goal of this conference is to support discussions within and across stakeholder communities to further strengthen burgeoning connections across these diverse communities. This conference will also be informed by the outcomes of the 2022 conference as well as any additional feedback received from the community. Assessment AG2PI's contracted external assessor, Filament, will facilitate the 2022 conference in Ames, Iowa. They will also help collect and organize results of the conference activities. Some of these results will be organized into a concept paper detailing the future of AG2P as a field and recommendations on how to get there. This paper will be shared with USDA NIFA and possibly published for the community.

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 formed, and continues to grow, a community of researchers, students, industry and commodity groups prepared to develop novel and creative solutions to agricultural genomes-to-phenomes challenges, for the benefit of US agriculture and society. The project is working to: Develop a vision for AG2P research, develop community solutions to challenges and gaps, and rapidly disseminate findings. To these ends, AG2PI organizes four types of activities: virtual field days, conferences, training workshops, and seed grants. Since the project's first event in October 2020, nearly 30,000 participants from across every inhabited continent of the world have engaged with our website to join an activity or learn more about this project. Objectives: AG2PI has three main objectives, which are each met by four organized activities. See next section for details on summary statistics, data collected and key outcomes associated with each activity. 1. Develop a vision for AG2PI by identifying research needs and opportunities, as well as gaps in physical infrastructure and data management. Outside of the four main activities, we deployed Community Surveysin November 2021 and June 2022 to gather community input on what barriers currently exist in advancing agricultural G2P work, what resources are needed and which areas should be prioritized for future funding and development. 2. Foster first steps towards the development of community solutions to challenges identified in #1. 3. Communicate and disseminate findings of all activities through the AG2PI websites and other publications. In addition to making recordings of activities available on the website, as well as results of the community surveys, we have links to two papers published in 2022: a project overview in Genome Biology and a "Ten Things" style paper in PLoS Computational Biology. Four Main Activities Supporting Objectives Field Days. AG2PI virtual field days are held monthly and are designed to find intersections within the G2P community regarding crop and livestock work. Each field day is recorded and posted to the AG2PI website soon after the event. Engagement is encouraged through Zoom polls and chat as well as a Slack workspace. Over 2000 attendees have participated in at least one of the 19 Field Days since the beginning of this project and an average of 92 people attend each field day (maximum = 233; minimum = 44). Registrants hail from 48 states (not including AK or NH). Training Workshops. Monthly virtual workshops follow two general formats: Short format (1-2 hours) and Long format (1-2 hours, multiple days). Year 2 has included mostly short-format workshops (8 out of 11 sessions); average attendance this year has been around 60. Workshop attendance is around 1100 since the beginning of this project and an average of 58 people have attended each session this year (maximum = 103; minimum = 22). Registrants hail from 44 states (not including AK, ME, MS, NH, RI, VT; see Products for additional details). Each workshop is recorded and available on the AG2PI website along with supplemental materials (e.g., GitHub). Post-Workshop assessments inform future training plans; feedback has been overwhelmingly positive and indicate a community need. 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. The five second round 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). Project teams represented 16 institutions, including USDA ARS, land grant universities, primarily undergraduate institutions, and industry across 12 states (CA, CT, IA, ID, IN, MA, MDNV, PA, TN, TX, WI) plus Europe. The deliverables span publicly available datasets and training materials, workshops, open-source software and new models. Progress reports from Round 1 and Round 2 teams have been received and final reports from Round 1 teams are now coming due. Any institution eligible for subcontract funding under the USDA's AG2PI RFA was eligible to apply for seed grants. Eleven seed grants were awarded out of 20 applications in the second round of awards. However, only the five projects funded from this award are included in this report. All five projects involve early career PI/co-PIs who holdpositions at level of assistant professor or more junior (or equivalent for industry). Deliverables and outcomes can be found on the AG2PI website at https://www.ag2pi.org/resources/ag2pi-funded-seed-grants/. Conferences. The goals of the conferences have been to identify gaps in knowledge, infrastructure, protocols, and coordination, as well as opportunities within the crop and livestock communities. In year 2, we held two in-conference workshops (SACNAS NDiSTEM and NAPPN), one AG2PI-organized mini-conference focused on the seed grant mechanism and one poster at an international conference (AGBT-ag; see Other Products for details). Our seed grant, virtual mini-conference (January 19, 2022) focused on explaining and advertising our seed grant program. Out of the 210 registrants from 30 states (not including AK, CT, DE, HI, KS, LA, ME, MT, NV, NH, NM, OH, PA, RI, SC, TN, VT, WV, WI, WY) and 46 countries, 82 attendees listened to presentations then met in breakout rooms for a teaming session designed to introduce potential collaborators from multiple disciplines. Conversations were tracked in Google Docs during the sessions and moved onto Slack following the conferences. Recordings are available on the AG2PI website (https://www.ag2pi.org/workshops-and-activities/) for asynchronous viewing. Surveys. Although not explicitly one of AG2PI's four main activities, community surveys have been a powerful tool for achieving objectives #1 and #2, and we have shared our findings in accordance with objective #3. In year 2, we conducted two community surveys. Our second community survey was distributed in the fall of 2021, contained 25 questions, and focused on access and barriers to resources in G2P research, training and other efforts. A portion of the survey findings are available on the AG2PI website along with a spreadsheet containing contact information of those community members willing to share their resources. This survey produced results consistent with results of our first survey (deployed in November 2020) on questions regarding areas for future funding: these areas included education and training, data management and integration, increasing collaborations, and developing new technologies. Our third community survey contained 15 questions, was released in June of 2022, and focused on narrowing the scope of future funding to areas that are most critical to advancing G2P research and those that are easiest to achieve.

Publications

  • Type: Journal Articles Status: Published Year Published: 2022 Citation: Lawrence-Dill CJ, Allscheid RL, Boaitey A, Bauman T, Buckler ES IV, et al. (2022) Ten simple rules to ruin a collaborative environment. PLOS Computational Biology 18(4): e1009957. https://doi.org/10.1371/journal.pcbi.1009957
  • Type: Journal Articles Status: Published Year Published: 2022 Citation: Tuggle, C.K., Clarke, J., Dekkers, J.C.M. et al. The Agricultural Genome to Phenome Initiative (AG2PI): creating a shared vision across crop and livestock research communities. Genome Biol 23, 3 (2022). https://doi.org/10.1186/s13059-021-02570-1
  • Type: Conference Papers and Presentations Status: Published Year Published: 2021 Citation: On October 25, 2021, AG2PI Co-PI, Jennifer Clarke, led a career path panel titled, Agricultural Genome To Phenome Initiative: Introduction and Community Building Session at the 2021 SACNAS National Diversity in STEM (NDiSTEM) Conference. This was a virtual event in which Dr. Clarke used a portion of the time to describe the AG2PI project before introducing three panel speakers.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2021 Citation: On October 26, 2021, AG2PI Co-PI Jennifer Clarke presented the invited talk Agricultural Genome To Phenome Initiative: Shared Data Science Across Crop And Livestock Communities at the INFORMS conference in. In her talk, Dr. Clarke introduced the AG2PI project.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2021 Citation: On November 4, 2021, AG2PI Co-PI Christopher Tuggle presented A Vision for Resources in Agricultural Genomics by 2030 at the Visions III conference. This was an in-person event in which Dr. Tuggle discussed the AG2PI project.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: On February 25, 2022, AG2PI Lead PI, Pat Schnable, presented an invited talk titled, Advancing Agricultural Genome to Phenome Research at the Association for the Advancement of Artificial Intelligence (AAAI-22) conference.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: On April 6, 2022, AG2PI Co-PI, Jack Dekkers presented a poster at AGBT-ag that described the AG2PI project and encouraged seed grant applications.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: On July 10, 2022, Co-PIs Jennifer Clarke and Christopher Tuggle participated in a special session on digital agriculture at the 30th Conference on Intelligent Systems for Molecular Biology.


Progress 09/01/20 to 08/31/21

Outputs
Target Audience:This project involves researchers, students and businesses from across the agricultural sector; including, those from both crop and livestock communities as well as integrative disciplines (e.g., engineers, data scientists, economists, and social scientists). 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. A great diversity of participants, that continues to grow, engage with this project monthly. For example, since its launch in October 2020 the AG2PI website has had over 10,000 unique viewers from across every inhabited continent of the world. Over 800 attendees have participated in at least one Field Day and an average of 30 new people login for the first time with each new, monthly field day. The audience for AG2PI continues to grow as new organizations join as institutional partners. For example, four additional organizations have joined the project as partners, three of which have global membership. Both DivSeek International Network Inc. (90 members) and International Wheat Genome Sequencing Consortium (IWGSC; 3200 members) joined as global engagement partners. The International Maize and Wheat Improvement Center (CIMMYT) joined as a stakeholder organization. The final new partner, GenoPhenoEnvo (20 members), required a new category of involvement which we termed "External Project Partners". Each of these groups shares project news and events with their members and contributes to growing the AG2PI community. To ensure the inclusion of URM audiences, AG2PI seed grant steering committee members have shared AG2PI activities with various URM organizations, such as MANNRS and SACNAS, particularly with respect to the seed grant opportunity. There are also plans to host an informational workshop at the 2021 SACNAS conference. Changes/Problems:Co-PI Carolyn Lawrence-Dill began a new position as Associate Dean for Research and Discovery at Iowa State University. Due to her increased duties outside of the AG2PI project, she has decreased her duties within this project. As a result, she will no longer be a member of the seed grant steering committee nor the conferences subcommittee. She will continue to lead the assessment activities for AG2PI since an external team has been hired to conduct much of the assessment for the project. She was not receiving compensation for any of these activities; therefore, there is no financial impact to this project. The proposed in-person conference in Year One is postponed this to Year 2 due to the pandemic. What opportunities for training and professional development has the project provided?Field days and workshops both provide both training activities and professional development activities for AG2PI community members. Each field day or workshop is led by individuals who are recognized by AG2PI leadership as experts on the topic of the given event. Leading one of these events provides all presenters, but particularly early-career presenters, to gain skills, confidence and community recognition. The purpose of each of these events is to disseminate information, increase knowledge and skills and provide an opportunity to meet other community members. Both event types are offered as Zoom meetings rather than webinars to encourage broad community participation, engagement and interaction. The field days have an associated Slack workspace wherein community members can continue conversations begun during the field day, particularly with the presenter, not just for intellectual enrichment but for professional networking expansion. 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. For example, engagement with the AG2PI website currently includes over 10,000 unique viewers from across every inhabited continent of the world. Over 800 attendees have participated in at least one Field Day and an average of 30 new people login for the first time with each new, monthly field day. Most event registrations are hosted on the AG2PI website where they have the opportunity to opt-out of getting added to our mailing lists. The website also has a webform where interested parties can register to join a mailing list or to request that their organization be added as an institutional partner. Recordings of each field day, workshop and conference are available on the AG2PI website. Twitter (@AG2PI) and LinkedIn accounts are used for advertising upcoming events and to reach broader audiences who may prefer social media over email for their communications. In this way the project cuts across generational differences in communication preferences, particularly since bringing new students into the agricultural sciences and related fields is a need commonly brought up by the AG2PI community, both in the 2020 community survey and in conference workshops. AG2PI also has two Slack workspaces that are designed for asynchronous interaction with 1) field day presenters and attendees and 2) other community members looking to collaborate on an AG2PI seed grant. Press releases, blogs and community calendars (https://iastate.box.com/s/6ke3vonfwam2u8eggsaz38kq0y3ls7n2) have also been used to reach target audiences. Additionally, project PI and co-PIs have given informational talks to eleven stakeholder and scientific groups over this first year of the project. AG2PI includes members who the AG2PI activities with various URM organizations, such as MANNRS and SACNAS, particularly with respect to the seed grant opportunity. To reach STEM scientists in training, AG2PI will be hosting an informational workshop at the SACNAS NDiSTEM conference in October 2021 in which attendees will hear from four diverse researchers (two early career) on their path to careers in STEM. What do you plan to do during the next reporting period to accomplish the goals?Field days We will continue to rotate topics for each monthly event among plant-focused, animal-focused and data- or facility-focused. Field day speakers have represented all career levels, from undergraduate student to senior career scientist; we will continue to thoughtfully select diverse speakers. Presentations often include poll questions to engage the audience, audience members are able to pose questions via Zoom's chat function. Recordings will be made available on the AG2PI website soon after the close of the event. Training Workshops Our monthly workshops have and will continue to cover a range of topics from developing core computational competencies and Open Science through specialized topics using advanced machine learning for plant and animal genomics and phenomics. Workshops follow two general formats: Short format (1-2 hours) and Long format (1-2 hours, multiple days). Short format workshops begin with a lecture followed by a hands-on/interactive session and a discussion of strengths, limitations, best practices, and areas for future development. The goal of the long format workshops is to help onboard and level the skills of people new to computationally intensive science. We will continue to invite professionals from all career stages to lead workshops. We are collecting post-Workshop assessments from the participants so that we can determine future training needs of the community. Recordings, slides and other relevant materials will be made available on the AG2PI website soon after the close of the event. Seed Grants The AG2PI team will organize and release two additional calls for proposals requesting support for "seed and feed" grant projects at several levels of maturity. One call will be released in summer 2021 (application deadline of September 19, 2021) and the other will be released in early 2022; between $400,000 and $500,000 of awards will be distributed in each cycle. These calls will incorporate feedback from applicants and the seed grant steering committee received during the current project with a goal of improving and streamlining the proposal submission and review process. Seed grant awards will be offered at three different levels of funding: emerging (seed), enabling (sprouting), and established (spreading) awards. We will continue to prioritize scientific merit, the goals of the AG2PI, and proposals led by early career scientists and members of underrepresented communities. 1.Emerging grants (6-12 months in duration, up to $20k): These awards will be similar in scope to the awards from the initial round of AG2PI seed grants during the current project. For example, an emerge grant might support the launch of an online repository of software for visible image phenotyping with applications in crop and poultry sciences. 2.Enabling grants (12 months in duration, up to $50k): These awards will be aimed at enlarging the scope or supporting further development of a project that has successfully completed an emerge grant award or are at a similar stage of development. For example, a project that has successfully launched an online repository of software for visible image phenotyping may propose to expand the repository to include software for other imaging modalities and develop educational programs demonstrating the use of the repository. 3.Established grants (12-18 months in duration, up to $75k): These awards will be aimed at providing support towards long-term sustainability and ability to enable cross-kingdom AG2P research and engagement of a project that has successfully completed an enable-like project from the current project or is at a similar stage of development. For example, a project that has successfully expanded a repository for include multi-modal imaging software may propose to secure initial partners and develop a sustainability plan or complete the preliminary work necessary to secure substantial federal or industry funding. We will request that applicants include a request for travel funding so that they can present the results of their awards at relevant scientific venues. 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 round of Seed and Feed proposals the Seed Grant Steering 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. Conferences In years 2 and 3, conferences will focus on presenting results/deliverables from the seed grants (below), developing additional concept papers on community perspectives, and supporting discussions within and across stakeholder communities to further strengthen nascent connections across diverse communities. These conferences will be informed by the community survey that was deployed in December 2020 and expanded in conjunction with the "listening session" conferences during 2021, and with advice from the SAB and steering committee. Community Survey Building from the community survey that was distributed in December 2020 (and continued in the conference workshops) a second survey is being planned for distribution in Fall 2021. Unlike the first survey, which was largely aimed at assessing the current state of the research and tools being used, this second survey will focus on the research that could be possible if all barriers were removed. The survey will also ask about what barriers exist, such as institutional infrastructure, human infrastructure and access to resources. Assessment The hired assessment firm, The Filament, will design, host, and facilitate one more 2-hour virtual workshop for ~30 attendees to better understand the cross-discipline collaboration goals of AG2PI and to explore assessment metrics. The assessment deliverables include: •Exploration and documentation of both obvious and novel assessment metrics that measure both near- and longer-term cross-discipline collaboration. •Review of types of data currently collected and proposed new data anticipated to provide value to the initiative. •Definition of a collection of collaboration metrics that can be tracked via simple survey and/or other easily accessible data and tools. Synthesis and Reporting: After the two-part workshop, Filament will summarize the results and create a report with the recommendations of the metrics to track, the methods to collect them, and the appropriate channels for sharing to the broader community.

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 formed, and continues to grow, a community prepared to develop novel and creative solutions to agricultural genomes-to-phenomes challenges, for the benefit of US agriculture and society. The project is working to: Develop a vision for AG2P research by identifying research gaps and opportunities; foster first steps towards the development of community solutions to these challenges and gaps; and rapidly disseminate findings to the broader community. To these ends, AG2PI organizes four types of activities: virtual field days, conferences, training workshops, and seed grants. Since the project's first event in October 2020, over 10,000 participants from across every inhabited continent of the world has engaged in our activities and website. Objectives: 1. Develop a vision for AG2PI by identifying research needs and opportunities, as well as gaps in physical infrastructure and data management. In December 2020, we deployed a Community Survey seeking community perspectives on the needs for accelerating AG2P research and ideas about which specific activities would meet those needs. When asked about AG2PI's planned activities, the majority of US-based (69% of 535) respondents reported personal interest in all activities and identified phenotyping/phenomics, managing data, and machine learning as top topics. 2. Foster first steps towards the development of community solutions to challenges identified in #1. See section, "Four Main Activities Supporting Objectives", for supporting activities. 3. Communicate and disseminate findings of all activities through the AG2PI websites and other publications. One such paper, coming soon, stems from our Assessment activities, with support from The Filament (https://www.thefilament.com/), a company that specializes in facilitating collaboration, led a two-part summit in May/June 2021, to help define the cross-discipline collaboration goals of AG2PI and to explore assessment metrics. The results are being summarized in a "10 simple rules" style paper written collaboratively by AG2PI leadership, Filament and summit participants. Four Main Activities Supporting Objectives Field Days. AG2PI virtual field days expose the G2P community to a diversity of research activities and available resources, for crop and livestock work. Held monthly, these talks are designed to appeal to a diverse audience and find intersections with other research interests. Topics rotate monthly among plant-, animal- and data- or facility-focused to ensure a variety of topics are explored. Poll questions and Zoom chat are encouraged to engage the audience. We share registration information with presenters so they can better engage the live audience. To date, 10 field days have been offered (see products section for list). Each field day is recorded and posted to the AG2PI website soon after the event ends (typically the same day) along with presenters' slides, when these are made available. Over 800 attendees have participated in at least one Field Day and an average of 100 people attend each field day (maximum = 233; minimum = 45). Registrants hail from 47 states (not including AK, NV, NH). Training Workshops. To build technical strengths and future collaborative G2P communities, AG2PI has offered a suite of workshops to enable researchers from diverse backgrounds and computational skill levels to develop best practices, common vocabularies, and technical expertise around AG2P cyberinfrastructure, data tools and pipelines, statistics, and experimental techniques. Our monthly workshops are delivered virtually to increase accessibility. Workshops follow two general formats: Short format (1-2 hours) and Long format (1-2 hours, multiple days). Short format workshops are limited to 50 virtual seats while long format workshops have not had limited registrations and average 40 participants. Registrants from the two workshops for which data are available hail from at least 35 states (not including AK, CT, GA, ME, MA, MS, MT NV, NH, NM, RI, UT, VA, VT, WV). Exact dates and attendance records for the Workshops conducted to date are listed in the Products section. Each workshop is recorded and added to the AG2PI website (https://www.ag2pi.org/workshops-and-activities/) along with any supplemental materials (e.g., GitHub, ReadTheDocs). We are collecting post-Workshop assessments from the participants so that we can determine future training needs of the community; to date, participants have reported overwhelmingly positive experiences and indicate that the workshops useful and fulfilling a need. Seed Grants. AG2PI's Seed Grant program was designed to promote 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. Seed grant awards focused on five topics relevant to AG2P. Identifying best practices, tools, and techniques for AG2P data sharing and storage. Encouraging cross-fertilization of existing or novel AG2P tools, data, or ideas. Coordination of available educational resources and/or determine best approaches for expanding cross-disciplinary training in AG2P data science/biology/engineering. Motivate agriculture-focused analyses of AG2P from ethical, legal, social, ecological, and economic perspectives. The use of sensors in agricultural genome to phenome research. Awards were given in each of the five topics areas, ranged from $15,000-20,000 and have durations of 6-12 months with a start date of May 15, 2021. Five of the sixteen submitted proposals were awarded without revision and two proposals were awarded after revision for a total of $130,000 in awards (see https://www.ag2pi.org/resources/ag2pi-funded-seed-grants/ for details). The PIs of seed grant awards represented 15 unique institutions - including USDA ARS, land grant universities, and HBCUs - across 14 states (AZ, CT, IA, ID, IN, MI, MO, MT, NC, ND, NE, OK, VT, WA). The deliverables range across awarded projects and include publicly available datasets, training materials, workshops, machine learning simulations, publications, conference presentations and an online catalog presenting the available resources for data science in animal and plant agricultural genomics. Any institution eligible for subcontract funding under the USDA's AG2PI RFA was eligible to apply for seed grants. Conferences. The goals of the conferences have been to identify gaps in knowledge, infrastructure, protocols, and coordination, as well as opportunities within the crop and livestock communities. In year 1, we held two in-conference workshops/listening sessions, two AG2PI-organized mini-conferences and one poster at an international conference (see Other Products for details). Our seed grant, virtual mini-conferences (February 24 and August 12, 2021) focused on explaining and advertising our seed grant program. Out of the 262 registrants from 42 states (not including AK, HI, KY, LA, NV, NH, ND, WV) and 29 countries, 176 attendees listened to presentations then met in breakout rooms for a teaming session designed to introduce potential collaborators from multiple disciplines. Conversations were tracked in Google Docs during the sessions and moved onto Slack following the conferences. At least one new team that self-organized during the first conference was awarded a seed grant. Recordings are available on the AG2PI website (https://www.ag2pi.org/workshops-and-activities/) for asynchronous viewing.

Publications

  • Type: Conference Papers and Presentations Status: Other Year Published: 2020 Citation: On October 6, 2020, AG2PI Lead PI, Pat Schnable, provided a presentation titled, Advancing Agricultural Genome to Phenome Research at the Digital Ag Summit. This was a virtual event in which Dr. Schnable used a portion of his talk to introduce the AG2PI project.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2020 Citation: On November 18, 2020, AG2PI Co-PI Jennifer Clarke presented Perspectives on Digital Agriculture in the United States at the 2020 Global Bioeconomy Summit. This was a virtual event in which Dr. Clarke used a portion of her talk to introduce the AG2PI project.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2021 Citation: On June 7, 2021, AG2PI Co-PI Brenda Murdoch presented Constructing the Ovine pangenome at the International Sheep Genomics Consortium. This was a virtual event in which Dr. Murdoch used a portion of her talk to introduce the AG2PI project.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2021 Citation: On July 20, 2021, AG2PI Lead PI, Pat Schnable, provided a webinar titled, Introduction to the Agricultural Genome to Phenome Initiative to the Government-University-Industry Research Roundtable (GUIRR). This was a virtual event in which Dr. Schnable introduced the AG2PI project to 79 attendees from various government agencies, universities and industries. A recording is publicly available on the GUIRR website (https://www.nationalacademies.org/event/07-20-2021/introduction-to-the-agricultural-genome-to-phenome-initiative).
  • Type: Conference Papers and Presentations Status: Published Year Published: 2021 Citation: On August 3, 2021, Co-PI Jennifer Clarke discussed the AG2PI project with RFD TV/Rural Radio. This was a virtual interview in which Dr. Clarke used a portion of her talk to discuss the AG2PI project. Her interview can be found on University of Nebraska-Lincolns Mediahub (https://mediahub.unl.edu/media/17587) as well as publicly on Youtube (https://youtu.be/9mf4pTrkfpY).
  • Type: Websites Status: Published Year Published: 2020 Citation: Visitors to the projects website (ag2pi.org) can learn about the projects goal of Creating a Shared Vision Across Crop and Livestock Communities, read the project summary, obtain information on how to apply for seed grants, join mailing lists, and how to register for AG2PI events. It also describes our governance structure, lists our partner institutions, and provides access to AG2PI-related resources, such as our data management plan, code of conduct, and DEI statement. The website hosts recordings of AG2PI events enabling allowing asynchronous viewing.
  • Type: Other Status: Published Year Published: 2021 Citation: A newsletter was sent via email on 6/24/21 to all members and institutional partners. Headlines included: Grant Funded for Next AG2PI Phase, First Seed Grants Awarded, and Upcoming Events. Available on the AG2PI website at https://www.ag2pi.org/resources/newsletters/.