octoploids crossed with 2x and 4x F. vesca, Senanayake and Bringhurst suggested that the genomic formula should be AAA′A′BBBB, as higher bivalent numbers were observed in hexaploid than pentaploid hybrids. This indicated that the chromosome of F. vesca had at least partial homology with another set of octoploid chromosomes. Their guess was that the A genome was contributed by either F. vesca or F. viridis, and they had no idea about the origin of the A′ and B genomes. Bringhurst (1990) later suggested that the genome formula should be AAA′A′BBB′B′ to reflect his contention that the octoploids are completely diploidized with strict disomic inheritance. Noguchi et al. (1997) produced hybrids between F. iinumae and F. × ananassa that were highly fertile after chromosome doubling, suggesting that F. iinumae contributed a genome to the octoploids. Liu et al. (2016) using genomic in situ hybridization (GISH), found that octoploid-derived gametes carried seven chromosomes with hybridization affinities to F. vesca, while the remaining 21 chromosomes displayed varying affinities to F. iinumae.
Fig. 1.10. Genomic origin of the octoploid strawberry species proposed by Bringhurst (1990). Different letters represent highly divergent species, while those distinguished with a prime originated from much closer relatives.
The first phylogenetic studies utilizing the sequences of nuclear low-copy genes indicated that one of the octoploid subgenomes was closely related to F. vesca or F. mandshurica, and a second subgenome donor was F. iinumae (Rousseau-Gueutin et al., 2009; DiMeglio et al., 2014; Sargent et al., 2016), together forming a AAA′A′BBB′B′ genome structure. More recently, Tennessen et al. (2014), using sequenced regions anchored in the F. vesca map, came up with a more complex subgenome compliment of 2Av,2Bi,2B1,2B2. The Av genome was hypothesized to have come from a diploid F. vesca ancestor, the Bi from a diploid F. iinumae ancestor, and the B1, B2 ancestor from an F. iinumae-like autotetraploid. The divergence between homeologous chromosomes appeared to have been greatly augmented by interchromosomal rearrangements. Kamneva et al. (2017) using ‘haploSNPs’ found that one or more diploid ancestors, possibly related to F. viridis, F. bucharica or F. mandshurica, formed a hexaploid with F. iinumae (2Bi, 2B1, 2B2), which then introgressed with a diploid F. vesca-like species (2Av). Using sequences of 24 single-copy or low-copy nuclear genes, Yang and Davis (2017) found that at least five diploid ancestors contributed to the subgenomes of octoploids (F. vesca, F. iinumae, F. bucharica, F. viridis, and at least one additional allele contributor of unknown identity) and that the composition of the subgenomes was complex and not derived from a single ancestral source.
Edger et al. (2019) examined the species origin of the octoploid species by generating a near-complete chromosome scale assembly for the cultivated octoploid strawberry (F. × ananassa cv. Camarosa) and comparing it with 31 sequenced and de novo assembled transcriptomes of every described diploid Fragaria species, including 19,302 nuclear genes in the genome. Their analysis revealed that four species are in the ancestry of the octoploid strawberry: F. iinumae, F. nipponica, F. viridis and F. vesca ssp. bracheata. Because the range of F. viridis overlaps with that of the hexaploid F. moschata, they hypothesized that these were the evolutionary intermediates between the diploids and the wild octoploid species. This conclusion has been questioned based on methodological issues (Edger et al., 2020; Liston et al., 2020).
Edger et al. (2019) did not propose a genome formula for the octoploid strawberry but based on earlier crossibility studies, it could be represented by Bringhurst’s (1990) proposal of AAA′A′BBCC. F. vesca (AA) and F. viridis (A′A′) can be crossed with limited fertility so they warrant a similar letter designation. F. iinumae (BB) and F. nipponica (CC) cannot be crossed with any other diploid species so warrant separate letter designations.
Hardigan et al. (2019) employed whole-genome shotgun genotyping of interspecific segregating populations to identify 1.9 million subgenome variants spanning 3394 cM in F. chiloensis ssp. lucida, and 1.6 million subgenome variants spanning 2017 cM in F. × ananassa. Through comparative genetic mapping of these variants, they were able to show that the genomes of the wild octoploids are effectively diploidized as predicted by Bringhurst (1990) and completely collinear. This genetic structure has allowed for ‘unimpeded gene flow’ during the domestication and interspecific hybridization of the strawberry.
In comparisons of the nuclear and organelle genomes of the octoploids, it appears that F. vesca ssp. bracteata was the chloroplast donor of the octoploid strawberries, while both F. vesca ssp. bracteata and F. iinumae were the sources of the mitochondrial genomes, which subsequently recombined (Mahoney et al., 2010; Njuguna et al., 2013; Govindarajulu et al. 2015). Little is known about the origin of F. iturupensis, except it shares the same plastid donor as F. chiloensis and F. virginiana. A plastid genome phylogeny generated by Dillenberger (2018) found that the octoploid F. chiloensis is monophyletic, while all other polyploid taxa are para- or polyphyletic. F. cascadensis has biparental plastid inheritance and has four different plastid donors.
The tetraploid F. orientalis and hexaploid F. moschata likely represent a polyploid series (Harrison et al., 1997a; Njuguna et al., 2013). Based on the molecular studies of Lin and Davis (2000), Rousseau-Gueutin et al. (2009) and DiMeglio et al. (2014), F. orientalis appeared to be an allopolyploid derived from F. vesca and F. mandshurica, and F. moschata contains the additional genome of F. viridis. Based on the work of Edger et al. (2019), F. orientalis is more likely derived from F. vesca and F. nipponica. F. moschata crosses readily with F. viridis (Schiemann, 1937), F. nubicola (Ellis,
