Diversity Arrays Technology (DArT) Platform for Genotyping and Mapping in Carrot (Daucus carota L.)

Carrot is one of the most important root vegetable crops grown worldwide on more than one million hectares. Its progenitor, wild Daucus carota, is a weed commonly occurring across continents in the temperate climatic zone. Diversity Array Technology (DArT) is a microarray-based molecular marker system allowing cost efficient high throughput genotyping of any organism and it does not require any prior knowledge on the genome sequence. We developed a DArT platform for carrot genotyping, based on genomic representations derived from a carrot diversity collection, including wild and cultivated accessions. The carrot DArT microarray comprised 7,680 clones. The platform was used to analyze the structure of genetic diversity of D. carota and to construct a genetic map of carrot. Analysis of diversity was performed with 900 high quality non-redundant markers. Three clusters were determined using STRUCTURE software, representing wild, Eastern cultivated, and Western cultivated gene pools. The genetic map of carrot was constructed using 819 non redundant DArT markers showing no segregation distortion. The map comprised nine linkage groups, of which eight contained from 35 to 101 markers, and the remaining linkage group (LG8) had only three markers. Comparative analysis of mapped loci and their frequency across wild and cultivated carrot gene pools is ongoing. These results provide a basis to concerted efforts towards development of high-throughput tools to characterize carrot genetic diversity and anchor the upcoming carrot genome sequence assembly.