New grants awarded in Agricultural Genome-to-Phenome research

Agricultural Genome to Phenome Initiative

Ames, IA — The Agricultural Genome to Phenome Initiative has awarded nine grants to 27 institutions in the third and final round of project seed grant competition.

The Agricultural Genome to Phenome Initiative, a three-year project ending in 2023, is funded by the U.S. Department of Agriculture’s National Institute of Food and Agriculture. The goal of AG2PI is to connect crop and livestock scientists to each other and to those working in data science, statistics, engineering and social sciences to identify shared problems and collaborate on solutions.

The awarded projects help advance multidisciplinary crop and livestock research by addressing genome-to-phenome challenges, developing solutions for research infrastructure needs, or sharing solutions across kingdoms.

The seed grant projects awarded in Round 3 will run from 6 to 12 months and span three funding levels:

  • Emerging grants, funded up to $50,000, broaden interactions and synergies across communities and organization types
  • Enabling grants, funded up to $75,000, enlarge the scope of or further develop an existing project
  • Establishing grants, funded up to $100,000, provide support towards sustainable AG2P research and engagement.

Two of the new grants, which support critical needs in research data management and standardization, involve Iowa State University faculty.

An enabling-level grant, “Creating a FAIR Data Ecosystem for Incorporating Single Cell Genomics Data into Agricultural G2P Research” is a project led by Christopher Tuggle, professor in the Department of Animal Science, Iowa State University. The international team includes: Christine Elsik, University of Missouri; Peter Harrison, EMBL-European Bioinformatics Institute, Cambridge, UK; Nicholas Provart, University of Toronto; and collaborators Tony Burdett, EMBL-European Bioinformatics Institute; Tim Tickle, the Broad Institute of MIT and Harvard; Marc Libault, University of Nebraska-Lincoln; Wes Warren, University of Missouri; Ben Cole, Lawrence Berkeley National Laboratory; and James Koltes, Iowa State.

Through deep international collaboration, the project aims to create an agricultural equivalent to the Human Cell Atlas Data Coordination Platform (HCA DCP), which will improve the availability of RNA single-cell data sequencing output to crop and livestock researchers. The project will provide training to early career scientists under Tuggle’s and Elsik’s advisement, who will be working directly with scientists at HCA DCP and testing the agricultural metadata standards for usability.

An emerging-level grant, led by Hao Cheng at the University of California-Davis, also includes ISU faculty as well as international collaborators. Tuggle and Distinguished Professor Jack C.M. Dekkers, also in the ISU Department of Animal Science, are co-investigators; collaborators Richard Mott and Lingzhao Fang, both based in the UK, round out the team members. The project, “Homomorphic Encryption to Enable Sharing of Confidential Data,” will test and evaluate an approach that allows multiple researchers to access and analyze encrypted datasets while protecting intellectual property and ensuring FAIR (Findable, Accessible, Interoperable, and Reusable) data use principles.

Other project teams receiving AG2PI Round 3 seed grants include:

Emerging Grants:

  • Understanding Emergent Agricultural Phenomena Through Big Data Analytics: Creating Frameworks for Understanding Using Physics-guided Machine Learning and Agent-based Models: Michael Kantar, University of Hawaii; Diane Wang, Purdue University; Bryan Runck, University of Minnesota; Barath Raghavan, University of Southern California; Adam Streed, Center for Digital Agriculture; Patrick Ewing, North Central Agricultural Research Lab
  • An AI Toolkit for Video Phenotyping in Livestock: Samantha Brooks, Madelyn Smythe, Kyle Allen, Adam Biedrzycki, João Bittar, University of Florida

Enabling Grants:

  • Leveraging Single-cell Genomics in QTL Mapping: Susanta Kumar Behura, Jarad Egan Decker, University of Missouri
  • Standardizing Data Management and Terminology for Increased Adoption of Virtual Fence Systems: Jameson Brennan, Logan Vandermark, Krista Ehlert, Hector Menendez, South Dakota State University; Ryan Reuter, Oklahoma State University; Mitchell Stephenson, University of Nebraska-Lincoln; Dana Hoag, Colorado State University, Paul Meiman, University of Nevada-Reno; Joslyn Beard, University of Arizona; Rory Charles O’Conner, USDA-ARS
  • A Genetic Data Portal to Enable Discovery of Deleterious Genetic Variants in Farmed Animals: Theodore Kalbfleisch, University of Kentucky

Establishing Grants:

  • Using Unmanned Aerial Vehicles to Detect Nitrogen Stress in Alfalfa: Anju Biswas, Esteban F. Rios, Aditya Singh, University of Florida
  • Developing Education, Research and Extension Training on Precision Agriculture Phenotyping Tools at HBCU: Jingqiu Chen, Violeta M. Tsolova, Florida A&M University; Wei-zhen Liang, University of Nebraska-Lincoln; Jian Jin, Purdue University.

For more information on all the awarded AG2PI seed grants as well as other grant opportunities, visit the webpage:

The AG2PI is funded by the U.S. Department of Agriculture’s National Institute of Food and Agriculture. The goal of AG2PI is to build communities that address the challenges of genome-to-phenome research across crops and livestock. The AG2PI partners include Iowa State University, University of Nebraska, University of Arizona, University of Idaho and the Iowa Corn Promotion Board.