Variant Call File (VCF) for 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 versus drift and gene flow is lacking in many
important species such as Cannabis sativa (C.
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 FST, balancing selection,
and positive selection. Our analyses identified evidence for
sub-population structure and further support the Asian origin hypothesis
of this species. Feral plants sourced from the U.S. exhibited broad
regions on chromosomes 4 and 10 with high ?̅ST which may
indicate chromosomal inversions maintained at high frequency in this
sub-population. 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 versus domesticated
sub-populations. In the U.S. feral sub-population, we found six loci
related to stress response under balancing selection and one gene involved
in disease resistance under positive selection, suggesting local
adaptation to new climates and biotic interactions. In the marijuana
sub-population, 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.