Genetic analysis of Cannabis flowering traits in differential environments

Cannabis sativa L. (Linnaeus) is a dioecious, highly heterozygous crop whose female inflorescences underpin the rapidly expanding medicinal and recreational markets. The emerging cannabis industry has necessitated the improvement of inflorescence traits relating to uniformity, quality, and yield under diverse growing conditions. Cannabis agronomic traits exhibit significant phenotypic variation due to both underlying genetic diversity and environmental heterogeneity. This dissertation describes research aimed at understanding how such traits are shaped and consists of two experimental chapters examining various aspects related to this. The first research chapter examines the mechanisms contributing to phenotypic variation in THC and CBD dominant varieties by evaluating key agronomic traits in two commercial environments. The first was a greenhouse with a controlled environment, while the second utilized a greenhouse in which aspects such as temperature fluctuations and humidity were not controlled. To support trait standardization a novel image-based phenotyping method was developed to quantify inflorescence size and compactness. This included the undesirable ‘foxtailing’ phenotype, characterized by elongated calyces and loose floral structures which was more prevalent in the less controlled environment. While environmental factors are a strong driver of most agronomic traits, it was found that individual inflorescence traits, such as inflorescence length and width of the individual buds that form part of the larger inflorescence showed both low phenotypic variability and low broad-sense heritability. Since low broad-sense heritability commonly indicates that the environment plays a dominant role in trait development, the absence of a significant influence of the environment on these traits reflect they are under genetic constraint. From this study, genotype-by-environment interactions were found to influence phenotypic expression of most traits, which complicates understanding the genetic architecture of inflorescence traits in cannabis. The second research chapter examined diverse drug-type cannabis populations to identify loci associated with phenotypic variation in inflorescence traits including apical inflorescence weight, apical inflorescence area, and apical inflorescence density. Population genetic analysis, using a custom genome-wide SNP panel, revealed that the genetic architecture of cannabis inflorescence yield may be population-specific with narrow-sense heritability estimates varying between populations. Furthermore, conducting a genome-wide association study (GWAS) identified loci that explained a relatively low percentage of phenotypic variance (0.04% to 5.32%) across the three traits, indicating that the traits are likely to conform to the infinitesimal model. Most candidate genes at these loci were related to cellular processes, with specific genes involved in gibberellin biosynthesis (linked to inflorescence weight); and chromatin remodelling, RNA processing, and cell cycle processes (linked to apical inflorescence area and density).

Grantor dc:publisher

Stellenbosch : Stellenbosch University

Year dc:date.issued

2026

Author dc:creator

• Gabriel, Casey Ashley

Advisors dc:contributor.advisor

• Lloyd, James Richard
• Rhode, Clint

Language dc:language.iso

en

Repository record dc:identifier.uri

https://scholar.sun.ac.za/handle/10019.1/136000

OAI identifier oai:identifier

oai:scholar.sun.ac.za:10019.1/136000