Dissecting genotype-environment interactions with functional implications for parental selection in cannabis breeding

Authors: HALPIN-MCCORMICK, ANNA - University Of Hawaii; THOMPSON, ROBERT - University Of Hawaii; CLARKE, ROBERT - Bioagronomics Group Consultants; Neyhart, Jeffrey; KANTAR, MICHAEL - University Of Hawaii

Submitted to: Journal of Heredity
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/6/2025
Publication Date: 7/13/2025
Citation: Halpin-Mccormick, A., Thompson, R., Clarke, R.C., Neyhart, J.L., Kantar, M.B. 2025. Dissecting genotype-environment interactions with functional implications for parental selection in cannabis breeding. Journal of Heredity. esaf048. https://doi.org/10.1093/jhered/esaf048.
DOI: https://doi.org/10.1093/jhered/esaf048

Interpretive Summary: Understanding the genetic basis of plant adaptation to environmental stress - such as extreme temperatures, drought, or excess rainfall - is crucial for improving crop breeding. Cannabis sativa has spread worldwide through both human cultivation and natural adaptation, allowing different populations to thrive in a variety of environments and providing a case study for exploring crop adaptation. In this study, we analyzed genetic data from 149 Cannabis samples to explore how different populations have adapted to their surroundings. We used a whole-genome approach to correlate genomic information with environmental conditions to understand local adaptation. We also examined how different genetic groups of Cannabis—such as those cultivated for fiber (hemp), medicinal or recreational use (drug-type), and wild-growing populations—respond to environmental stress. Our findings showed that wild drug-type Cannabis, often found in areas with seasonal monsoons, may have developed traits that help it withstand heavy rainfall and waterlogging. Additionally, a genetically diverse group known as the “basal” group exhibited broad adaptability, suggesting it could be a valuable resource for breeding plants with greater tolerance to environmental challenges. The environmental genomic selection method offered a rapid way to select parent plants while also providing insight into how different traits contribute to adaptation. This research supports breeders in creating Cannabis varieties that can thrive in a range of growing conditions, helping farmers and cultivators maintain stable production despite environmental uncertainties.

Technical Abstract: As seasonal weather variability continues to impact agricultural systems, identifying genetic factors that contribute to environmental adaptation will be essential for optimizing breeding strategies for the development of abiotic stress tolerant varieties. Through human cultivation and naturalization, Cannabis sativa has dispersed globally, adapting to a range of environmental conditions across geographic regions. We combined raw data from multiple public sources to conduct an Environmental Genomic Selection (EGS) analysis on 149 Cannabis sativa samples, to assess how different populations of Cannabis relate to their environmental conditions. Exploring Genomic Estimated Adaptive Values (GEAVs) across bioclimatic variables can facilitate the selection of parental material adapted for a specific condition. We further explore potential mechanisms of local adaptation by characterizing the individual marker effects which underlie these GEAV scores. To facilitate interpretation, we used previously described genetic groupings (Basal, Hemp-type, Drug-type feral, Drug-type). Distinct patterns emerged across population groups with the drug-type (Type I) group showing consistently narrow GEAV ranges, whereas the drug-type feral group showed a broader distribution, often having high GEAVs for precipitation variables. A key weather variable difference was seen in monthly average values, revealing a seasonal response to precipitation in drug-type feral samples. Exploring marker-effect differences between seasonal GEAVs indicated a response to seasonal precipitation in drug-type feral samples. As these samples are sourced from geographic regions that have seasonal monsoons, they may have traits conferring flood tolerance (water logging) that could be introgressed into other backgrounds. The basal group also exhibited broad GEAV ranges across several bioclimatic traits, indicating they may be a valuable genetic resource for introgression to enhance adaptation to different environments. These findings underscore the importance of incorporating diverse germplasm into breeding programs to improve Cannabis tolerance to changing environmental conditions. EGS provides a fast method to enable parental selection while gaining mechanistic information. Ultimately, we hope that such a strategy could support the development of abiotic stress tolerant Cannabis varieties tailored to both current and future environmental challenges.