Genetic architecture of phenological, morphological, and phytochemical traits in Cannabis landraces

Despite its long history of cultivation and diverse applications, Cannabis sativa remains underexplored at the genomic level, particularly in landrace populations that harbor untapped genetic diversity. In this study, we investigated the genetic architecture of 145 Iranian cannabis landrace accessions, including both male and female plants, using 233K common SNPs and genome-wide association studies (GWAS). Our analysis revealed three genetically distinct subpopulations shaped by geography, climate, and traditional cultivation practices. We identified 91 significant genomic regions associated with 40 phenological, morphological, and phytochemical traits, including 15 key loci with pleiotropic effects linked to multiple traits, including flowering time, plant architecture, biomass accumulation, and cannabinoid biosynthesis. These findings highlight the complex interplay between developmental and metabolic pathways in cannabis. The high heritability of most traits and rapid linkage disequilibrium decay underscore the potential of these landraces for high-resolution mapping and genetic improvement. This work provides a valuable genomic resource for marker-assisted selection, supporting the development of improved cultivars with tailored cannabinoid profiles and agronomic traits.