An improved version of cultivated strawberry linkage map using the IStraw90 Axiom® Array for QTL analysis.

Strawberries are economically important fruits around the world. Fragaria x ananassa, the cultivated strawberry, is an allo-octoploid specie (2n=8x=56), their ploidy level difficult the application of marker assisted breeding. F. vesca has been considered as a diploid model organism. Berries, including strawberries, are known for their rich nutritional profile. Understanding the genetic bases controlling the production of phenolic and volatile compounds is extremely important for the selection of new varieties of cultivated strawberry with greater consumer acceptation.
The genetic map of a F2 population (CamarosaxDover) posses 192 loci distributed along the 28 expected linkage groups, representing each homeologous group with a high coverage (>70%) when compared to F. vesca genome. LC-MS analysis for polyphenol metabolites in full ripen fruits allowed the quantification of 22 metabolites and mapping 146 metabolic QTLs.
The IStraw90™ (International Strawberry 90K Axiom®) Affymetrix array developed by Rosbreed based on diploid and octoploide sequences was hybridized with 120 F2 individuals and parentals. The analysis of the results using GenotypeConsole and SNPolisher softwares shows a high quality of hybridization , with a >97% probe call rate for all individuals. For the 93937 valid SNPs : 75% were classified as MonoHighResolution, 9356 as NoMinorHomozygous, and 4939 as PolyHighResolution segregating in our population. The SNPs position in F.vesca and the SSR map allow to construct 4x7 homeologous groups with an increased resolution and higher coverage. Distribution of SNPs in homeologous groups will help the assembly of contigs and scaffolds of the genome draft sequence covering 154x of one population individual.