The first high-density sequence characterized SNP-based linkage map of olive (Olea europaea L. subsp. europaea) developed using genotyping by sequencing

A number of linkage maps have been previously developed in olive; however, these are mostly composed of markers that have not been characterized at the sequence level, supplemented with smaller numbers of microsatellite markers. In this investigation, we sought to develop a saturated linkage mapping resource for olive composed entirely of sequence characterized markers. We employed genotyping by sequencing to develop a map of a F2 population derived from the selfing of the cultivar Koroneiki. The linkage map contained a total of 23 linkage groups comprised of 1,597 tagged SNP markers in 636 mapping bins spanning a genetic distance of 1189.7 cM. An additional 6,658 segregating SNPs were associated with the 23 linkage groups identified but their marker order was not determined in this investigation. The SNP markers sequences were submitted to NCBI database. The linkage map produced will be an invaluable resource for the study of tree habit and vigour traits segregating in the progeny, and will assist to anchor and orientate sequencing scaffolds from future genome sequencing efforts.