Establishing a Genetic System for Studying Cannabis Domestication

Abstract

Cannabis represents a globally significant crop with extensive domestication history for fiber production, nutritional applications, and psychoactive compound biosynthesis. Despite economic and cultural importance, comprehensive understanding of evolutionary trajectory, genetic diversification mechanisms, and selective pressures remains fragmented across disciplinary boundaries. This dissertation employs an integrated genomic-economic analytical framework, combining population genetics, molecular chronometry, and quantitative economic analysis to resolve fundamental questions in Cannabis evolution and domestication. Chapter 1 establishes theoretical and historical context through comprehensive literature synthesis. This analysis delineates the multi-stage domestication process, traces historical biogeography and diversification patterns across Eurasia, and characterizes the biology of key agronomic traits under selection, including seed dehiscence mechanisms, sexual expression systems, flowering time phenology, and trichome density variation. Chapter 2 presents chromosome-scale reference genome assembly utilizing hybrid nanopore long-read and Illumina short-read sequencing technologies. Whole-genome sequencing of 96 F2 individuals and parental lines from hemp marijuana crosses enabled high-resolution genetic mapping to order and orient assembly contigs. Quantitative trait locus mapping identified a single locus on chromosome 7 explaining greater than 90% of variance in THC:CBD ratios. Population genomic analysis revealed that high-CBD phenotypes result from recent introgression of functional hemp-derived CBDAS alleles into high-potency marijuana genetic backgrounds, which typically possess non-functional THCAS alleles, demonstrating rapid evolutionary responses to changing regulatory frameworks. Chapter 3 constructed fossil-calibrated molecular chronograms for Cannabaceae utilizing comprehensive phylogenomic datasets. Rigorous re-evaluation of paleobotanical evidence established robust temporal frameworks for family-level evolution, estimating Cannabis-Humulus divergence at 35.6 (95% HPD: 33.94-38.30) million years ago while inferring ancestral genome sequences. This temporal framework and ancestral reconstruction provided calibration points for demographic inference and allele polarization in subsequent population analyses. Chapter 4 conducted population genomic analysis utilizing a comprehensive tissue library of approximately 2,000 herbarium specimens from 22 institutions, with collection dates spanning from Cesalpino's 16th-century material through the modern era, concentrated around the mid-20th century with notable wartime collection gaps. This temporal distribution minimizes confounding effects of recent anthropogenic globalization on genetic admixture patterns. Low-coverage whole-genome sequencing of 212 strategically selected individuals revealed ten major polymorphic chromosomal inversions exhibiting strong clinal variation across latitudinal gradients. These structural variants contain genes enriched for flowering time regulation and environmental stress response functions, displaying significant inter-inversion linkage disequilibrium patterns. Demographic analyses, maintained methodologically independent from selection-based inference frameworks, indicate these inversions function as supergenes facilitating local adaptation while maintaining ecological differentiation between populations. Chapter 5 quantifies selective pressures imposed by 20th-century prohibition regimes on drug-type Cannabis through integrated economic-evolutionary analysis. Application of the Alchian-Allen theorem to genomic datasets revealed strong positive correlation () between federal enforcement expenditure and THC potency evolution, demonstrating market-mediated adaptive responses to regulatory pressure. Economic analysis indicates that prohibition-induced artificial scarcity selected for increased potency per unit mass, consistent with theoretical predictions for quality-differentiated commodities under transport cost increases. This chapter documents extreme artificial selection on Cannabis reproductive systems, where estimated selection coefficients against male individuals approach 1.0 in elite cultivation practices, resulting in functionally unisexual populations maintained through clonal propagation and feminized seed production technologies. Collectively, this dissertation provides multi-scale analysis of Cannabis evolutionary dynamics. The research establishes refined evolutionary chronologies, identifies large-scale structural variants as primary drivers of adaptive differentiation, and quantifies intense recent selective pressures producing modern crop varieties through an integrated temporal-genomic analytical framework.