A new Cannabis genome assembly associates elevated cannabidiol (CBD) with hemp introgressed into marijuana

Christopher J. Grassa, George D. Weiblen, Jonathan P. Wenger, Clemon Dabney, Shane G. Poplawski, S. Timothy Motley, Todd P. Michael, C. J. Schwartz

Research output: Contribution to journalArticlepeer-review

55 Scopus citations


Demand for cannabidiol (CBD), the predominant cannabinoid in hemp (Cannabis sativa), has favored cultivars producing unprecedented quantities of CBD. We investigated the ancestry of a new cultivar and cannabinoid synthase genes in relation to cannabinoid inheritance. A nanopore-based assembly anchored to a high-resolution linkage map provided a chromosome-resolved genome for CBDRx, a potent CBD-type cultivar. We measured cannabinoid synthase expression by cDNA sequencing and conducted a population genetic analysis of diverse Cannabis accessions. Quantitative trait locus mapping of cannabinoids in a hemp × marijuana segregating population was also performed. Cannabinoid synthase paralogs are arranged in tandem arrays embedded in long terminal repeat retrotransposons on chromosome 7. Although CBDRx is predominantly of marijuana ancestry, the genome has cannabidiolic acid synthase (CBDAS) introgressed from hemp and lacks a complete sequence for tetrahydrocannabinolic acid synthase (THCAS). Three additional genomes, including one with complete THCAS, confirmed this genomic structure. Only cannabidiolic acid synthase (CBDAS) was expressed in CBD-type Cannabis, while both CBDAS and THCAS were expressed in a cultivar with an intermediate tetrahydrocannabinol (THC) : CBD ratio. Although variation among cannabinoid synthase loci might affect the THC : CBD ratio, variability among cultivars in overall cannabinoid content (potency) was also associated with other chromosomes.

Original languageEnglish (US)
Pages (from-to)1665-1679
Number of pages15
JournalNew Phytologist
Issue number4
StatePublished - May 2021

Bibliographical note

Funding Information:
This work was supported by a David and Lucile Packard Fellowship (GDW), J. Craig Venter Institute (TPM), Sunrise Genetics Inc. and the Minnesota Department of Agriculture. Veronica Tonnell contributed DNA isolation for the mapping population. We thank Matthew Gibbs and Jason Schwartz for support from Sunrise Genetics Inc. and access to the FL germplasm. Timothy Gordon of Functional Remedies provided the high-CBDA material (CBDRx). We are grateful to the anonymous referees for questions and insights that prompted us to strengthen the manuscript.

Publisher Copyright:
© 2021 The Authors New Phytologist © 2021 New Phytologist Foundation


  • cannabidiol (CBD)
  • cannabinoids
  • domestication
  • hemp
  • marijuana
  • tetrahydrocannabinol (THC)


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