Population genomics of a natural Cannabis sativa L. collection from Iran identifies novel genetic loci for flowering time, morphology, sex and chemotyping

Future breeding and selection of Cannabis sativa L. for drug production and industrial purposes require a source of germplasm with wide genetic variation, such as that found in wild relatives and progenitors of highly cultivated plants. Limited directional selection and breeding have occurred in this crop, especially informed by molecular markers. Here, we investigated the population genomics of a natural cannabis collection of male and female individuals from differing climatic zones in Iran. Using Genotyping-By-Sequencing (GBS), we sequenced 228 genotypes from 35 populations. The results obtained from GBS were used to perform association analysis identifying links between genotype and important phenotypes, including inflorescence characteristics, flowering time, plant morphology, tetrahydrocannabinol (THC) content, cannabidiol (CBD) content and sex. Approximately 23,266 significant SNPs of high quality were detected to establish associations between markers and traits, and population structure showed that Iranian cannabis plants fall into five groups. A comparison of Iranian samples from this study to global data suggests that the Iranian population is distinctive and, in general, is closer to marijuana than to hemp, although some populations in this collection are closer to hemp. The GWAS results showed that novel genetic loci, not previously identified, contribute to sex, yield and chemotype traits in cannabis and are worthy of further study.