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
Research Effort Categories
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.
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 , 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.