Cannabis (Cannabis sativa L.) has recently been legalized in various countries, including Colombia, becoming a crop in high demand and with great commercial opportunities in both the national and international markets. However, despite this rapid growth in demand, it lacks the resources, genetic knowledge and associated genetic improvement tools that even minor crops currently enjoy. Due to the natural heterozygosity of the species and the still clandestine nature of the traditional market, there are no pure lines and the autochthonous varieties and seeds available are highly variable and heterogeneous, which is why, frequently, they present unpredictable agronomic performance and high variability in metabolomic content. Thus, most commercial production is based on the clonal propagation of elite heterozygous genotypes. This is labor intensive, representing about 40% of the production cost, and also promotes the persistence of plant pathogens such as viruses and fungi.

With legalization, formal cannabis research is expanding rapidly in the scientific community, but the limitations remain significant. For example, while several high-quality genomes have been published, all but one are modern hybrids which have undergone extensive hybridization, and therefore little is known of the contribution of the various landraces of the world. As well, as with most crops, disease pressure is a major constraint on production, and Cannabis has not yet benefitted from the careful introgression of resistance genes from wild relatives, as is common in breeding of tomato, lettuce, corn, and many others.

Thus, the time is ripe to accelerate the development of varieties and seed lines that are new, distinct, uniform, and stable, via the application of next-generation molecular techniques, in order to meet the demands of consumers and regulators, and develop an ecologically and economically sustainable production model. This research proposal aims to provide new knowledge and tools that can facilitate the genetic improvement of cannabis, by pursuing the following three specific objectives: 1, Sequencing and assembling high quality genomes of two Cannabis cultivars, Cherry Pie (CP) and Punto Rojo (PR); 2, cataloguing two important classes of genes, resistance genes of the canonical Nucleotide binding, Leucine rich Repeat type (NLRs) and terpene synthases (TPS), in these and other high-quality assemblies; and 3, using publicly available short read data to conduct a phylogenetic analysis, to include Cherry Pie, Punto Rojo, and a selection of other relevant cultivars, in order to clarify genetic relationships among them.