Social Network Analysis of the Genealogy of Strawberry: Retracing the Wild Roots of Heirloom and Modern Cultivars

Abstract

The widely recounted story of the origin of cultivated strawberry (Fragaria × ananassa) oversimplifies the complex interspecific hybrid ancestry of the highly admixed populations from which heirloom and modern cultivars have emerged. To develop deeper insights into the three century long domestication history of strawberry, we reconstructed the genealogy as deeply as possible---pedigree records were assembled for 8,851 individuals, including 2,656 cultivars developed since 1775. The parents of individuals with unverified or missing pedigree records were accurately identified by applying exclusion analysis to array-genotyped single nucleotide polymorphisms. We identified 187 wild octoploid and 1,171 F. × ananassa founders in the genealogy, from the earliest hybrids to modern cultivars. The pedigree networks for cultivated strawberry are exceedingly complex labyrinths of ancestral interconnections formed by diverse hybrid ancestry, directional selection, migration, admixture, bottlenecks, overlapping generations, and recurrent hybridization with common ancestors that have unequally contributed allelic diversity to heirloom and modern cultivars. Fifteen to 333 ancestors were predicted to have transmitted 90% of the alleles found in country-, region-, and continent-specific populations. Using parent-offspring edges in the global pedigree network, we found that selection cycle lengths over the last 200 years of breeding have been extraordinarily long (16.0-16.9 years/generation) but decreased to a present-day range of 6.0-10.0 years/generation. Our analyses uncovered conspicuous differences in the ancestry and structure of North American and European populations and shed light on forces that have shaped phenotypic diversity in F. × ananassa.

Unraveling the Complex Hybrid Ancestry and Domestication History of Cultivated Strawberry

“…2020 ). We suspect that this perception stems from the observation that a disproportionate fraction of the alleles found in certain domesticated populations have flowed through a small number of common ancestors ( Sjulin and Dale 1987 ; Dale, Sjulin, and others 1990 ; Pincot et al. 2020 ).…”

“…We examined this question in greater depth in the present study and in companion studies where we comparatively genetically mapped the genomes of F. chiloensis , F. virginiana , and F. × ananassa , identified DNA variants across the octoploid genome, developed high-density single nucleotide polymorphism (SNP) arrays using DNA sequences anchored to the octoploid reference genome, and reconstructed and analyzed the genealogy of cultivated strawberry from early hybrids to modern cultivars ( Hardigan et al. 2020 ; Pincot et al. 2020 ).…”

“…2020 ). From the latter analysis, we identified 1,438 founders in the ancestry of F. × ananassa ( Pincot et al. 2020 ).…”

Diversification, Spread, and Admixture of Octoploid Strawberry in the Western Hemisphere

“…Additionally, the ability to easily hybridize or duplicate genomes allows for experimental manipulation of ploidy level for ecological studies (Wei et al, 2020). The cultivated garden strawberry Fragaria × ananassa is unusual for a domesticated crop in that it is a homoploid hybrid of two wild octoploids and has a very recent domestication history (<300 years) that is well documented, so the progenitor species and populations are well known (Darrow, 1966; Pincot et al, 2021; Hardigan et al, 2020b).…”

“…F. virginiana is distributed across North America, whereas F. chiloensis is only distributed along the coast of Western North America from Alaska to Southern California as well as Hawaii and the Chilean coast in South America (Staudt, 1988, 1999, 2008). It was these two species, Fragaria virgniana from North America and Fragaria chiloensis from South America, that would result in the spontaneous hybrid formation of the cultivated strawberry F. × ananassa throughout Europe in the 18th century after being transported from the Western hemisphere (Darrow, 1966; Pincot et al, 2021). Their wide range, including sympatry in North America where natural hybrids have been previously observed (Dillenberger et al, 2018), and role as progenitors to an important agricultural crop has produced great interest from evolutionary biologists and ecologists as well as plant breeders.…”