Genome Synteny Has Been Conserved Among the Octoploid Progenitors of Cultivated Strawberry Over Millions of Years of Evolution

Allo-octoploid cultivated strawberry
(Fragaria × ananassa) originated through a combination
of polyploid and homoploid hybridization, domestication of an
interspecific hybrid lineage, and continued admixture of wild species over
the last 300 years. While genes appear to flow freely between the
octoploid progenitors, the genome structures and diversity of the
octoploid species remain poorly understood. The complexity and absence of
an octoploid genome frustrated early efforts to study chromosome
evolution, resolve subgenomic structure, and develop a single coherent
linkage group nomenclature. Here, we show that
octoploid Fragaria species harbor millions of
subgenome-specific DNA variants. Their diversity was sufficient to
distinguish duplicated (homoeologous and paralogous) DNA sequences and
develop 50K and 850K SNP genotyping arrays populated with co-dominant,
disomic SNP markers distributed throughout the octoploid genome.
Whole-genome shotgun genotyping of an interspecific segregating population
yielded 1.9M genetically mapped subgenome variants in 5,521 haploblocks
spanning 3,394 cM
in F. chiloensis subsp. lucida, and
1.6M genetically mapped subgenome variants in 3,179 haploblocks spanning
2,017 cM in F. × ananassa. These studies provide a dense
genomic framework of subgenome-specific DNA markers for seamlessly
cross-referencing genetic and physical mapping information and unifying
existing chromosome nomenclatures. Using comparative genomics, we show
that geographically diverse wild octoploids are effectively diploidized,
nearly completely collinear, and retain strong macro-synteny with diploid
progenitor species. The preservation of genome structure among
allo-octoploid taxa is a critical factor in the unique history of garden
strawberry, where unimpeded gene flow supported its origin and
domestication through repeated cycles of interspecific hybridization.