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Research Project: Management of Temperate-Adapted Fruit, Nut, and Specialty Crop Genetic Resources and Associated Information

Location: National Clonal Germplasm Repository

Title: An ultra-dense SNP linkage map for the octoploid, cultivated strawberry and its application in genetic research

Author
item Koehorst-van Putten, Herma - Wageningen University And Research Center
item Van Dijk, Thijs - Wageningen University And Research Center
item Bassil, Nahla
item Davis, Thomas - University Of New Hampshire
item Van De Weg, Eric - Wageningen University And Research Center

Submitted to: Eucarpia Fruit Breeding Symposium
Publication Type: Abstract Only
Publication Acceptance Date: 1/25/2015
Publication Date: N/A
Citation: N/A

Interpretive Summary: Strawberry cultivar development can be more efficient with the use of modern molecular resources. This study reports the development of one of the necessary molecular resources, a genetic “map” of the strawberry genome. This map contains the location of genetic markers on each of the seven chromosomes of strawberry. A new molecular genotyping tool that contains 90,000 markers was used to identify the genetic markers located on this map and to produce a very dense map. This map will be useful to breeders and to geneticists who study strawberry.

Technical Abstract: We will present an ultra-dense genetic linkage map for the octoploid, cultivated strawberry (Fragaria x ananassa) consisting of over 13K Axiom® based SNP markers and 150 previously mapped reference SSR loci. The high quality of the map is demonstrated by the short sizes of each of the 28 linkage groups despite holding hundreds of markers (some regions up to 75 SNP/cM). The map includes 17 gaps (>10 cM) that coincide with regions known to be commonly homozygous for the two mapping parents ‘Holiday’ and ‘Korona’. This high density and quality was achieved thanks to the availability of the strawberry 90K Axiom® IStraw90® SNP array and stringent data scrutinising, which included the graphical genotyping of each of the linkage maps, and the inclusion of fully informative bridge markers. The SNP markers were mostly of the classes Poly High Resolution (PHR) and No Minor Homozygosity (NMH) and a few hundred of the class Off target Variant (OTV). For the later segregation information from the non-fluorescing null alleles was used in addition to the two conventional “fluorescent alleles” of otherwise di-allelic SNP markers. We will describe the prospects of this map for further improvement of the physical reference map of Fragaria vesca ‘Hawaii 4’, for the examination of chromosomal re-arrangements among homoeologs, and for the building of haploblocks in coming pedigree-based association studies. This work was performed in the framework of the Dutch TTI-Green Genetics initiative with support from the USDA SCRI project RosBREED.