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

●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 x marijuana segregating population was also performed.

●Cannabinoid synthase paralogs are arranged in tandem arrays embedded in long terminal repeat retrotransposons (LTR-RT) 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 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.