A recently published study has provided one of the most detailed looks yet at the genetic diversity of Cannabis sativa, identifying four genetically distinct lineages and confirming the effectiveness of a rapid DNA-based test for determining plant sex long before flowering.
For the study, researchers at the Institute of Plant Breeding and Genetic Resources in Thessaloniki, Greece, examined 83 cannabis genotypes using a combination of 10 microsatellite markers and high-resolution melting (HRM) analysis. The plants represented a wide range of chemotypes — from low-THC fiber hemp to THC-rich marijuana — and were preserved in a germplasm collection for breeding purposes.
The genetic analysis revealed a more complex population structure than the traditional “hemp versus marijuana” divide. STRUCTURE modeling, supported by principal coordinate analysis and phylogenetic tree construction, showed that the samples fell into four distinct genetic clusters. These did not perfectly align with cannabinoid-based classifications, suggesting that breeding history and geographic origin are just as important as chemical composition in defining genetic relationships.
One group was dominated by European fiber-type hemp cultivars with low THC and high CBD or CBG, showing strong genetic conservation likely due to selective breeding for industrial traits. Another group contained almost exclusively high-THC marijuana accessions, reflecting long-term selection for psychoactive potency. A third group appeared to be hybrids, with mixed ancestry from hemp and marijuana types. The fourth cluster included European fiber hemp lines genetically distinct from the first hemp group, likely representing a separate breeding lineage.
Analysis of molecular variance found that 53% of genetic variation existed within individual plants, 38% among individuals within groups, and only 9% between hemp and marijuana populations. Hemp exhibited higher allelic diversity and more private alleles than marijuana, suggesting a broader genetic base. This is consistent with hemp’s long history of selection for multiple uses — fiber, grain, and seed oil — compared to marijuana’s narrower focus on THC production.
The study also applied HRM analysis using sex-linked SNP markers to determine plant gender. The test correctly identified 73 female and 10 male plants, matching traditional visual assessments at flowering. Early and accurate sex determination is critical for cannabinoid production, as male plants can reduce flower quality through pollination. The HRM method offers a rapid, inexpensive, and reliable way to screen seedlings, though it cannot detect hermaphroditism, which can occur later under stress.
The researchers conclude that recognizing the true genetic structure of cannabis — beyond chemotype — can improve breeding strategies, preserve genetic diversity, and optimize cultivar development. Meanwhile, the HRM sex identification tool could help cultivators save resources and improve efficiency.
By demonstrating that cannabis’ genetic diversity is far more nuanced than a simple legal classification, this work underscores the importance of integrating molecular profiling into future breeding and conservation efforts. It also highlights how modern DNA tools can solve one of cultivation’s most costly inefficiencies: waiting weeks to learn the sex of a plant.
Researchers say:
To conclude, this study contributes to understanding the genetic diversity and sex identification of C. sativa using microsatellite markers and HRM analysis. While not a genomic-scale study, the findings support the presence of structured diversity between hemp and marijuana groups. Most importantly, the use of HRM for sex identification offers a practical, rapid, and cost-effective method that can be implemented in-house with the appropriate equipment. Although no sex test is 100% accurate, this approach provides a useful tool for early screening, which can help reduce the allocation of resources to unwanted male plants and improve breeding efficiency.
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