Dissecting Genotype-Environment interactions with functional implications for parental selection in Cannabis Breeding

As climate 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 climate resilient varieties. Through human cultivation and naturalization, Cannabis sativa has dispersed globally, adapting to a range of environmental conditions across various climates and latitudes. 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 climate 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 this 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 environmental resilience. These findings underscore the importance of incorporating diverse germplasm into breeding programs to improve Cannabis resilience to changing environmental conditions. EGS provides a fast method to enable climate-conscious parental selection while gaining mechanistic information. Ultimately, we hope that such a strategy could support the development of climate-resilient Cannabis varieties tailored to both current and future environmental challenges.