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

Abstract

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.

Allelic Variation ofMYB10is the Major Force Controlling Natural Variation of Skin and Flesh Color in Strawberry (Fragariaspp.) fruit

“…Within this population, seedlings with white or light pink skin are also characterized by white internal flesh. Using the second-generation high-density 50K SNP Array (FanaSNP) (Hardigan et al, 2020), a genome-wide association study (GWAS) was conducted to identify the chromosomal regions and specific SNPs associated with skin color in this breeding population.…”

“…However, to develop a more high-throughput assay for marker-assisted selection of white-or red-fleshed strawberries, we designed the KASP marker IFC-2. To identify homoeolog-specific primers that were not expected to amplify MYB10 homeologs in other sub-genomes or other off-target DNA sequences, the promoter fragments here described were aligned to those of 'Camarosa' and other octoploid accessions from Hardigan et al (2020). We identified an A/G SNP 20 bp upstream of the initial ATG and 966 bp downstream of the FaEnSpm-2 insertion (Supplemental Figure 9).…”

“…Total genomic DNA was isolated from leaf tissues using a modified CTAB method described by (Noh et al, 2018). A whole-genome SNP Genotyping was performed using the FanaSNP 50K Array (Hardigan et al, 2020). A general linear model (GLM), mixed linear model (MLM), and multi-locus mixedmodel (MLMM) were used for association tests using GAPIT v2 performed in R (Tang et al, 2016;Team, 2014;Liu et al, 2016).…”

A roadmap for research in octoploid strawberry

“…virginiana from North America [1][2][3][4][5] . Several additional wild octoploid subspecies have since been used as parents in breeding, creating an admixed population of F. × ananassa individuals with genomes that are mosaics of phylogenetically and demographically diverse progenitor genomes 4,[6][7][8][9][10][11][12][13] .…”

“…Although the chromosomes are architectural mosaics of the four diploid subgenome donors and their octoploid descendants, F. × ananassa is strongly allo-octoploid 6,9,14,22,23 . Because the F. × ananassa chromosomes are complex admixtures of genes with different phylogenetic histories via homoeologous exchanges 10,11,30 , Edger et al 10 developed a nomenclature that precludes oversimplified oneto-one assignments to a specific diploid progenitor.…”