Sunday, April 12
Meeting Registration
9:00 a.m. – 7:00 p.m.
Pre-Conference Workshops
9:00 a.m. – 1:00 p.m.
Innovative approaches and technologies for crop improvement
Description: This workshop explores innovative approaches and technologies designed to enhance crop improvement. Talks will cover diverse research that develops or utilizes emerging methods with the goal of accelerating genetic gain, or understanding and manipulating quantitative genetic variation. With this scope, the workshop aims to foster interdisciplinary collaboration between researchers in the fields of quantitative genetics, functional genomics, and molecular biology. The first session of the workshop will examine advanced quantitative tools, including novel statistical approaches to dissect complex genotype-by-environment (GxE) interactions, methods for enhancing multi-trait genomic prediction, and haplotype-based parent selection strategies. The second session bridges these predictive methods with functional applications, exploring how biological knowledge can improve breeding outcomes. Key topics include the application of AI and crop modeling, the integration of novel epi-genomic data (UMR-seq) and the use of targeted genome engineering to optimize complex agronomic traits, such as root architecture. This workshop unifies diverse perspectives to build synergistic strategies for future crop improvement.
Organizers: Jessica Rutkoski, University of Illinois and Lee Hickey, University of Queensland (AU)
1:00 p.m. – 4:00 p.m.
Professional development workshop
Description: In this interactive workshop you will experience your own default communication style and those of others. You will gain the ability to read others preferred styles and how you and them can modify your styles to communicate more effectively, meeting ideally somewhere in the middle. This workshop will increase your awareness about a simple differentiating four main styles called DISC. This is a very common training used in most companies to increase awareness about effective and constructive between team members.
Organizers: Klaus Koehler, former Corteva Agrisciences
Rebecca Lowdon, Bayer Crop Sciences
Alencar Xavier, Corteva Agrisciences
1:00 p.m. – 5:00 p.m.
Pangenomes and the genetics of agricultural improvement
Description: Reference genomes for crops and livestock allowed us to progress from QTL to specific markers utilized across breeding programs and thus paved the way for genomics-based breeding and genomic prediction. The very recent ability to de novo assemble and annotate multiple genomes within any species, brings us to the pangenome era. Such data can reveal the full scale of variation such as indels and copy-number variation in particular gene models up to presence absence and inversions of larger genomic regions.
The goals of this workshop are to review the current state of the art Ag-related pangenome research, to identify the remaining gaps, and foster community discussion and collaboration to develop innovations and solutions.
Organizers: John McKay, Colorado State University and Nils Stein, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)
5:00 p.m. – 7:00 p.m.
One graph to herd them all, one graph to align them, one graph to include all breeds and in the pangenome bind them
Description: Long-read sequencing and pangenome assembly methods have revolutionized our ability to detect and evaluate genomic variation in agricultural species. By integrating multiple assemblies across many populations and breeds rather than relying on a single linear reference, pangenomes provide a more complete representation of species-level composition and reduce reference bias. As reference models, pangenome graphs can improve mapping rates, variant calling accuracy (particularly for structural variants), and haplotype resolved analyses. This workshop for agricultural researchers will demonstrate the construction and application of pangenomes using the horse as an example. Participants will learn how to leverage containerized workflows to build pangenomes, explore multiple cutting-edge visualization tools, align short reads using the “personalized pangenome” approach, and genotype short and structural variants. Using the equine pangenome as a case study, we will showcase the detection and characterization of previously documented equine structural variants. By the end of the workshop, participants will have gained theoretical insight and practical experience in pangenome construction, visualization, and the identification of biologically relevant variation from pangenome-based point of view.
Organizers: Jonah Cullen, University of Minnesota and Ted Kalbfleisch, University of Kentucky
5:00 p.m. – 7:00 p.m.
Innovative applications of pangenomes in agriculture
Description: Despite the explosion of pangenome-related research over the last 12 months, aside from some very notable exceptions, most such papers do little beyond variant counting and applications of standard single-reference methods. This workshop will seek to fill this void by providing a forum for leaders in pangenome applications in agriculture to present recent findings and new approaches.
Organizers: John Lovell, HudsonAlpha and Rachel Rusholme-Picher, Earlham Institute
Monday, April 13
7:30 a.m. – 7:00 p.m.
Meeting Registration / Hospitality Desk
7:30 a.m. – 9:00 a.m.
Breakfast
7:30 a.m. – 9:00 a.m.
Women’s Networking Event
9:00 a.m. – 9:10 a.m.
Opening Remarks: Sarah Hearne, Chief Science and Innovation Officer, CIMMYT, and Daniela Lourenco, Associate Professor, Animal Breeding, Genetics, and Genomics, Department of Animal and Dairy Science, University of Georgia; Co-Chairs of the AGBT Agriculture Scientific Organizing Committee
Plenary Session I:
Session Chair: Sarah Hearne, Chief Science and Innovation Officer, CIMMYT and Co-Chair of the AGBT Agriculture Scientific Organizing Committee
9:10 a.m. – 9:40 a.m.
Rob Martienssen, Cold Spring Harbor Laboratory
“Sink or swim: how duckweeds escaped the ice age”
9:40 a.m. – 10:10 a.m.
Peter Dearden, University of Otago, New Zealand
“The wonder of bees”
10:10 a.m. – 10:25 a.m.
Joshua Stein, International Wheat Genome Sequencing Consortium (Abstract Selected Talk)
“The IWGSC Wheat Diversity Project: Foundational genome resources to advance a global food security crop”
10:25 a.m. – 11:00 a.m.
Coffee Break & Exhibits – Sponsored by SPT Labtech
Plenary Session II:
Session Chair: Jack Dekkers, Distinguished Professor, Animal Breeding and Genetics, Department of Animal Science, Iowa State University, and Organizing Committee Member
11:00 a.m. – 11:30 a.m.
Andrea Doeschl-Wilson, The Roslin Institute, University of Edinburgh
“Unleashing genetic diversity to combat infectious diseases”
11:30 a.m. – 12:00 p.m.
Alyx Shigenaga, University of California, Davis
12:00 p.m. – 1:40 p.m.
AGBT Lunch & Exhibitor Showcase
12:40 p.m. – 1:40 p.m.
Desserts & Exhibitor Showcase
Plenary Session III:
Session Chair: Nathan Lakey, The Genome Partnership Board and Organizing Committee Member
1:40 p.m. – 2:10 p.m.
Krishna Niyogi, University of California, Berkeley
“Understanding and altering photoprotection to improve crop productivity”
2:10 p.m. – 2:25 p.m.
Alencar Xavier, Corteva Agrisciences, Purdue University (Abstract Selected Talk)
“Tricks and extensions for multivariate modeling of genomic and breeding values”
2:25 p.m. – 2:45 p.m.
Gold Sponsor Talk
Illumina, Andre Eggen, Director Global Agrigenomics
“Genomic innovations for animals and plants: what’s next for research and breeding”
2:45 p.m. – 3:30 p.m.
Coffee Break & Exhibits
Plenary Session IV:
Session Chair: Nathan Lakey, The Genome Partnership Board and Organizing Committee Member
3:30 p.m. – 4:00 p.m.
Gloria Coruzzi, New York University
“Ratcheting up nitrogen and water use efficiency in crops – an AI inspired approach”
4:00 p.m. – 4:30 p.m.
Yniv Palti, USDA Agricultural Research Service (REE-ARS)
“Government, academia and industry collaborations to advance selective breeding and genetic research in rainbow trout aquaculture and recreational fisheries.”
4:30 p.m. – 5:00 p.m.
Poster Flash Talks
5:00 p.m. – 5:15 p.m.
Katie Jenike, University of Cambridge (Abstract Selected Talk)
“Haplotype architecture shapes phenotypic diversity across plant and animal pangenomes.”
5:15 p.m. – 5:30 p.m.
Jack Dekkers, Iowa State University (Abstract-Selected Talk)
“Stress hormones in hair as genetic indicators of (disease) resilience in pigs.”
5:30 p.m. – 5:45 p.m.
Lucas Borges Dos Santos, University of Illinois at Urbana-Champaign (Abstract-Selected Talk)
“Pangenome analysis of nine soybean cyst nematode genomes reveals hidden variation contributing to diversity and adaptation.”
5:45 p.m. – 6:00 p.m.
Charlotte Brault, University of Minnesota (Abstract-Selected Talk)
“Advancing Fusarium head blight resistance in wheat: genetic gains and genomic selection strategies.”
6:00 p.m. – 9:00 p.m.
Posters, Pours & Plates: AGBT Agriculture Welcome Reception
Sponsored by Twist Bioscience
Tuesday, April 14
6:30 a.m. – 7:30 a.m.
Rise and Shine with AGBT (Optional Activity)
7:30 a.m. – 7:00 p.m.
Hospitality / Information Desk
7:30 a.m. – 9:00 a.m.
Breakfast
Plenary Session V:
Session Chairs: Daniela Lourenco, Associate Professor, Animal Breeding, Genetics, and Genomics, Department of Animal and Dairy Science, University of Georgia; and Organizing Committee Member
Bruce Walsh, Professor of Ecology and Evolutionary Biology, University of Arizona; and Organizing Committee Member
9:00 a.m. – 9:30 a.m.
Julie Gray, University of Sheffield
“Stomata and climate resilience”
9:30 a.m. – 10:00 a.m.
Jeffrey Endelman, University of Wisconsin, Madison
“Quantitative genetics and genomics in potato”
10:00 a.m. – 10:15 a.m.
Enrique Sanchez Molano, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh (Abstract-Selected Talk)
“From local records to global impact: Integrating farmer-led data and genomics in livestock systems for LMICs.”
10:15 a.m. – 11:00 a.m.
Coffee Break & Exhibits
11:00 a.m. – 11:30 a.m.
AGBT Next Gen Leadership Awards
11:30 a.m. – 11:45 a.m.
Marina Bernardes, University of Georgia (Abstract-Selected Talk)
“Fine-tuning Monte Carlo single-step genomic REML for variance components estimation in large datasets.”
11:45 a.m. – 12:00 p.m.
Joseph Guhlin, University of Otago (Abstract-Selected Talk)
“𝒟-BLUP: Making genomic BLUP differentiable for end-to-end genomic prediction.”
12:00 p.m. – 2:00 p.m.
AGBT Lunch & Workshop(s)
12:00 p.m. – 2:00 p.m.
Lunch & Learn: Women in Genomics
Description: This 90-minute workshop will provide a dynamic forum of panelists including distinguished female scientists and male allies who have built impactful careers in academia, government, and industry. Panelists will discuss a range of topics such as lessons learned from early career experiences that impact their leadership style; overcoming systemic barriers; effective allyship in the workplace; thriving during uncertain economic and political times; shaping the next era of genomic innovation to ensure sustainable food production and global nutritional security; and strategies that enabled them to thrive in their careers.
Facilitator: Lori Leach, Eversole Associates
Panelists:
C. Robin Buell, The University of Georgia
Noelle Cockett, Utah State University
Charlotte Rambla, Ph.D., Land and Carbon, Inc.
Amy Charkowski, Colorado State University
Easter David, CIMMYT
Plenary Session VI:
Session Chair: Alison Van Eenennaam, Distinguished Professor of Cooperative Extension, Animal Biotechnology and Genomics, University of California, Davis; and Organizing Committee Member
2:00 p.m. – 2:30 p.m.
Kathy Munkvold, Foundation for Food & Agriculture Research
“Agriculture Under Pressure: Advancing Solutions from Genome to Field Through Cross-Sector Collaboration”
2:30 p.m. – 2:40 p.m.
Bronze 1 Sponsor Talk
Twist Bioscience, Paul Doran, Director of Business Development
“Next level genotyping with Twist”
2:40 p.m. – 2:50 p.m.
Bronze 2 Sponsor Talk
SPT Labtech, Laura Henry, Field Applications Scientist
“Scale your science. Not your cost per sample.”
2:50 p.m. – 3:00 p.m.
Bronze 3 Sponsor Talk
Cellanome, Gary Schroth, Ph.D., Chief Scientific Officer
“An integrated platform for longitudinal single-cell analysis in plant systems”
3:00 p.m. – 3:40 p.m.
Coffee Break & Exhibits
3:40 p.m. – 4:10 p.m.
Leif Andersson, Uppsala University, Sweden
“How the Atlantic herring became a keystone species in the brackish Baltic Sea”
4:10 p.m. – 4:25 p.m.
Elinor Karlsson, UMass Chan Medical School (Abstract-Selected Talk)
“Translating sequencing innovation into practice: A scalable genotyping platform for working dogs.”
4:25 p.m. – 4:40 p.m.
Talita Estefani Zunino Santana, University of Wisconsin-Madison (Abstract-Selected Talk)
“Enviromics-based modeling of genotype-by-environment-by-management interactions for growth, reproductive, and carcass traits in pasture-raised beef cattle.”
4:40 p.m. – 4:55 p.m.
Jicai Jiang, NC State University (Abstract-Selected Talk)
“Mapping the functional landscape of complex trait heritability in dairy cattle.”
4:55 p.m. – 5:10 p.m.
David Omar Gonzales Dieguez, CIMMYT/CGIAR (Abstract-Selected Talk)
“Turning farmers’ fields into selection environments: accelerating CGIAR crop genetic gain through on-farm sparse testing.”
5:10 p.m. – 5:25 p.m.
Nelson Lubanga, Aberystwyth University (Abstract Selected Talk)
“Sparse testing strategies to increase genetic gains in Miscanthus breeding program.”
5:25 p.m. – 5:30 p.m.
Final Remarks for the day
5:30 p.m. – 6:30 p.m.
Wine Reception, Posters, & Exhibits
6:30 p.m. – 8:00 p.m.
AGBT Dinner
8:00 p.m.
Sponsor Social
Wednesday, April 15
7:30 a.m. – 7:00 p.m.
Hospitality / Information Desk
7:30 a.m. – 9:00 a.m.
Breakfast
Plenary Session VII:
Session Chairs: Guilherme Rosa, Professor of Quantitative Genetics and Data Science in the Department of Animal and Dairy Sciences, University of Wisconsin-Madison; and Organizing Committee Member
9:00 a.m. – 9:30 a.m.
JoÃo Reboucas Dorea, University of Wisconsin-Madison
“Digital Tools and Artificial Intelligence for Scalable Phenotyping of Novel Traits”
9:30 a.m. – 10:00 a.m.
Kelly Wrighton, Colorado State University
“From sequence to system: unlocking microbiome-enabled agriculture”
10:00 a.m. – 10:15 a.m.
Timothy Jeffers, New York University, Center for Genomics and Systems Biology (Abstract-Selected Talk)
“Bipartite machine learning identifies TF interactions underlying agricultural traits.”
10:15 a.m. – 11:00 a.m.
Coffee Break & Exhibits
11:00 a.m. – 11:30 a.m.
Alexander Bucksch, The University of Arizona
“Root Phenomics: Shaping agriculture from belowground”
11:30 a.m. – 11:45 a.m.
Guillermo Martinez-Boggio, University of California Davis (Abstract-Selected Talk)
“Lifetime Net Merit index and the correlated response on enteric methane emissions.”
11:45 a.m. – 12:00 p.m.
Mohit Verma, Marshall University (Abstract-Selected Talk)
“From data to discovery: multi-omics learning platforms for Brassicaceae biofuel crops.”
12:00 p.m. – 2:00 p.m.
AGBT Lunch & Workshop
12:20 p.m. – 1:50 p.m.
Lunch & Learn: Animal telomere-to-telomere genomes: new assemblies, new biology, new voices
Description: This workshop will highlight outstanding trainees in advancing telomere-to-telomere (T2T) genome assemblies across diverse animal species, bringing together expertise from genomics, data science, and agricultural biology across multiple institutions. Speakers will showcase new assemblies and analytical strategies while critically examining technical and translational challenges that currently limit adoption of complete genomes in agricultural genomics. The session will identify emerging opportunities at the intersection of long-read sequencing, computational methods, and biological discovery, and will foster discussion of innovative, community-driven approaches to accelerate translation of T2T resources into applications for food, feed, fuel, and fiber production.
Organizers: Brenda Murdoch, University of Idaho and Stephanie McKay, University of Missouri
Plenary Session VIII:
Session Chair: Renee Lafitte, Director for Crops R&D, Gates Foundation; and Organizing Committee Member
2:00 p.m. – 2:30 p.m.
Noelle Cockett, Utah State University
“The Benefits of Connecting with the Farm Animal Genomics Collective”
2:30 p.m. – 3:00 p.m.
Ian Henderson, University of Cambridge, United Kingdom
“Genetic and epigenetic identity of plant centromeres”
3:00 p.m. – 3:30 p.m.
Coffee Break
3:30 p.m. – 3:45 p.m.
Leo Baumgart, Lawrence Berkeley National Laboratory, DOE Joint Genome Institute (Abstract Selected Talk)
“Mapping the plant gene regulatory landscape: A multi-species atlas of transcription factor binding and single-nucleus transcriptomes.”
3:45 p.m. – 4:00 p.m.
Abraham Morales-Cruz, Lawrence Berkeley National Laboratory, DOE Joint Genome Institute (Abstract Selected Talk)
“Conserved regulatory element location shapes cell type-specific gene activity in plants.”
4:00 p.m. – 4:15 p.m.
Anindya Bandyopadhyay, CIMMYT (Abstract Selected Talk)
“A high-throughput gene-editing platform for pearl millet flour shelf-life improvement via rancidity mitigation.”
4:15 p.m. – 4:30 p.m.
Patty Kiesler, National Institute of Standards and Technology (Abstract Selected Talk)
“U.S. Food and Drug Administration (FDA) and U.S. National Institute of Standards and Technology (NIST) collaboration: Evaluation of assays and control materials for characterizing animal biotechnology products generated by genome editing.”
4:30 p.m. – 5:15 p.m.
Seeds of Innovation: Navigating IP in Agricultural Genomics
Panel discussion exploring how intellectual property strategies are shaping innovation in genomics for crops, livestock, and microbes, balancing public research, private investment, and global access.
Facilitator: Sarah Hearne, Chief Science and Innovation Officer, CIMMYT
Panelists:
Neha Kothari, Agricultural Research Service, U.S. Department of Agriculture
Karina Najarro, Legal Counsel, Intellectual Assets, CIMMYT
Meghan Poon, Morrison Foerster
5:15 p.m. – 5:30 p.m.
Closing Remarks
Sarah Hearne, Chief Science and Innovation Officer, CIMMYT, and Daniela Lourenco, Associate Professor, Animal Breeding, Genetics, and Genomics, Department of Animal and Dairy Science, University of Georgia; Co-Chairs of the AGBT Agriculture Scientific Organizing Committee
6:00 p.m. – 9:00 p.m.