Genome-wide polymorphism and genic selection in feral and domesticated lineages of Cannabis sativa

A comprehensive understanding of the degree to which genomic variation is maintained by selection vs. drift and gene flow is lacking in many important species such as Cannabis sativa, one of the oldest known crops to be cultivated by humans worldwide. We generated whole genome resequencing data across diverse samples of feralized (escaped domesticated lineages) and domesticated lineages of C. sativa. We performed analyses to examine population structure, and genome-wide scans for F(ST), balancing selection, and positive selection. Our analyses identified evidence for subpopulation structure and further supported the Asian origin hypothesis of this species. Feral plants sourced from the United States exhibited broad regions on chromosomes 4 and 10 with high [Formula: see text] (ST), which may indicate chromosomal inversions maintained at high frequency in this subpopulation. Both our balancing and positive selection analyses identified loci that may reflect differential selection for traits favored by natural selection and artificial selection in feral vs. domesticated subpopulations. In the US feral subpopulation, we found 6 loci related to stress response under balancing selection and 1 gene involved in disease resistance under positive selection, suggesting local adaptation to new climates and biotic interactions. In the marijuana subpopulation, we identified the gene SMALLER TRICHOMES WITH VARIABLE BRANCHES 2 to be under positive selection, which suggests artificial selection for increased tetrahydrocannabinol yield. Overall, the data generated and results obtained from our study help to form a better understanding of the evolutionary history in C. sativa.