Building a Transdisciplinary Agricultural Single-Cell Genomics Community: Highlights from the AG2PI-AgBioData Workshop

Workshop description:

Title: "Building a Transdisciplinary Agricultural Single-Cell Genomics Community"

Conference: AGBT Agricultural Meeting
Date: March 29-20, 2025
Location: Orlando (FL)

About

The AG2PI Single Cell Workshop Organizing Committee and AgBioData Single Cell Biocuration Working Group co-hosted an in-person workshop to advance agricultural single-cell genomics. The event brought together a dynamic group of researchers, bioinformaticians, and data curators at the forefront of plant and animal single-cell biology.

This workshop was organized by leading experts including Chris Tuggle (University of Iowa), Sunita Kumari (Cold Spring Harbor Laboratory, CSHL), Doreen Ware (CSHL), Jennifer Clarke (University of Nebraska-Lincoln), Ben Cole (Lawrence Berkeley National Laboratory), Marc Libault (University of Missouri), Fiona McCarthy (University of Arizona), Irene Papatheodorou (Earlham Institute), and Wes Warren (University of Missouri).  The workshop featured a blend of keynote presentations, breakout sessions, and collaborative discussions aimed at developing a transdisciplinary and community-driven approach to single-cell data management in agriculture. The workshop's primary goal was to foster a community of agricultural researchers and data infrastructure specialists to address the unique challenges posed by single-cell data management, particularly in ensuring that data are Findable, Accessible, Interoperable, and Reusable (FAIR).

Workshop agenda:

• Featured Presentations:
  • Jennifer Clarke (University of Nebraska-Lincoln), “Lessons Learned from Interdisciplinary Projects: Core Values, Orientation, and Organization” 
  • Sharon Greenblum (Joint Genome Institute), “Data Management and Infrastructure within the Plant Cell Atlas Community”
  • Irene Papatheodorou (Earlham Institute), “Data and Metadata Management for Re-using and Integrating Cell Atlases”
  • Wes Warren (University of Missouri), “A Single Nuclei and Cell Perspective on the Chicken Immune System”
• Breakout Sessions & Community Engagement
  • ​​​​​​​We held seven breakout sessions, focusing on developing best practices for describing, storing, and sharing agricultural single-cell data in compliance with FAIR principles. These sessions explored practical strategies for implementation within diverse research communities and infrastructures.

Future perspectives:

These discussions laid the groundwork for strategic planning and actionable next steps, including developing genotype-to-phenotype (G2P) frameworks at the single-cell level. The workshop also underscored the critical role of the AgBioData Single Cell Biocuration Working Group in facilitating ongoing efforts to resolve challenges in data integration, sharing, and curation. This workshop represents a pivotal moment in agricultural genomics, mobilizing expertise across domains and species to build a robust, collaborative ecosystem for single-cell research.

More information about the workshop and upcoming events can be found at the AGBT AG Workshops page.