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Todd Michael, PhD
Research Professor
The Salk Institute for Biological Studies
SPEAKER
CULTIVATION

Cannabis Pangenome Exposes Minor Cannabinoid Pathway Potential

Cannabis has been intertwined with the human experience for thousands of years. However, the last century of prohibition severely constrained legal breeding efforts and slowed the development of germplasm resources, leaving the full potential of hemp-based oil, fiber, and pharmaceutical products untapped. Existing cultivars remain highly heterozygous and uncompetitive in the fiber and grain markets, restricting hemp cultivation to fewer than 200,000 hectares globally. The relaxation of drug laws in recent decades has sparked widespread interest in reintroducing cannabis into agricultural systems, but progress has been hindered by a limited understanding of its genomics and breeding potential.

We developed a cannabis pangenome by integrating 181 new and 12 previously released genomes, representing 156 biological samples from both male (XY) and female (XX) plants, covering varying chemotypes and photoperiod sensitivities from hemp, feral and marijuana plants. The pangenome includes 42 trio-phased and 36 haplotype-resolved, chromosome-scale assemblies, which enabled the identification of extensive genetic and structural diversity, highlighting potential breeding bottlenecks. Despite this diversity, we found cannabinoid synthase genes, which are the last step in the pathway, exhibit surprisingly low variation, even though they are embedded within highly variable regions containing non-functional paralogs and transposable elements. Additionally, we identified acyl-lipid thioesterase (ALT) gene variants that influence fatty acid chain length and are linked to the production of minor cannabinoids such as tetrahydrocannabinol varin (THCV) and cannabidiol varin (CBDV). The cannabis pangenome exposed unprecedented potential to develop novel cultivars tailored for emerging cannabinoid markets.

Learning Objectives:

  • The cannabis genome contains extensive genetic and structural diversity impacting breeding efforts

  • Even 200 genomes spanning diverse germplasm still does not capture all the diversity of the cannabis genome

  • The cannabis pangenome reveals unprecedented potential to develop novel cultivars tailored
BIO
Todd P. Michael, Ph.D. is a leading researcher specializing in genome sequencing and analysis, currently serving as a Research Professor at the Salk Institute for Biological Studies and an Adjunct Professor at the University of California, San Diego. With a distinguished career spanning several prestigious roles, including Professor and Director of Informatics at the J. Craig Venter Institute and Head of the Genome Center at Monsanto, Dr. Michael has established himself as a pioneer in the fields of plant genomics and bioinformatics. Dr. Michael earned his Ph.D. in Molecular and Cellular Biology from Dartmouth College under the mentorship of Dr. C. Robertson McClung, following a B.A. in Biology from the University of Virginia, where he was advised by Michael Timko. His postdoctoral work with renowned plant biologist Joanne Chory at the Salk Institute laid the groundwork for his prolific research career, during which he has authored over 100 publications, amassing more than 21,000 citations. Dr. Michael’s research has made significant contributions to understanding plant genome architecture, particularly through the study of unique and specialized plants that offer insights into adaptive strategies. His innovative work on pangenome tools and long-read sequencing technologies has advanced the understanding of how plant genomes are organized and how they adapt to specific environmental conditions. Dr. Michael's work continues to push the boundaries of our understanding of plant biology, with implications for agriculture, conservation, and climate resilience.

ATTENDANCE IS LIMITED. THE OPPORTUNITIES ARE NOT.

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