A Method of Genotyping By Pedigree-Based Training-Set for Identification of QTLs Associated with Cucumber Fruit Size

Large sets of genomic data are becoming available for cucumber (Cucumis sativus), yet there is no tool for whole genome genotyping. Creation of saturated genetic maps depends on development of good markers. The present cucumber genetic maps are based on several hundreds of markers. However they are not all assembled on one platform. We suggest a method for developing relatively fast and reliable genetic markers. Confident genotyping should rely on a training set. Based on extensive sequence data from two cucumber lines with highly divergent fruit types, Chinese Long 9930 (North China fresh market type) and GY14 (pickling type), we have designed a 45K SNP-array (Agilent technology) that includes a set of SNPs which has a pedigree-based training set. Combining this platform with RILs population from 9930xGY14 allows us to create a high density genetic map. The distance among markers is 0.22 cM on average with a total length of 854 cM.  Further, QTLs related to fruit size and shape (fruit and ovary length and diameter) were mapped in very high resolution on this saturated map (0.5cM or 100-300Kb). The tool is useful in the future for any cucumber segregating population and especially genome wide association studies which requires large amount of markers.