Unraveling the complex hybrid ancestry and domestication history of cultivated strawberry

Cultivated strawberry (Fragaria × ananassa) is one of our youngest
domesticates, originating in early eighteenth-century Europe from
spontaneous hybrids between wild allo-octoploid species (F. chiloensis and
F. virginiana).  The improvement of horticultural traits by 300
years of breeding has enabled the global expansion of strawberry
production.  Here, we describe the genomic history of strawberry
domestication from the earliest hybrids to modern cultivars.  We
observed a significant increase in heterozygosity among interspecific
hybrids and a decrease in heterozygosity among domesticated descendants of
those hybrids.  Selective sweeps were found across the genome in
early and modern phases of domestication—59-76% of the selectively swept
genes originated in the three less dominant ancestral
subgenomes.  Contrary to the tenet that genetic diversity is
limited in cultivated strawberry, we found that the octoploid species
harbor massive allelic diversity and that F. × ananassa harbors as much
allelic diversity as either wild founder.  We identified 41.8M
subgenome-specific DNA variants among resequenced wild and domesticated
individuals.  Strikingly, 98% of common alleles and 73% of total
alleles were shared between wild and domesticated populations. 
Moreover, genome-wide estimates of nucleotide diversity were virtually
identical in F. chiloensis, F. virginiana, and F. × ananassa (π =
0.0059-0.0060).  We found, however, that nucleotide diversity and
heterozygosity were significantly lower in modern F. × ananassa
populations that have experienced significant genetic gains and have
produced numerous agriculturally important cultivars.