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ARS Home » Midwest Area » Madison, Wisconsin » Vegetable Crops Research » Research » Publications at this Location » Publication #301017
Title: A method of genotyping by pedigree-based training-set for identification of QTLs associated with cucumber fruit size

Author
item OPHIR, RON - Agricultural Research Organization, Volcani Center
item RUBINSTEIN, MOR - Agricultural Research Organization, Volcani Center
item ESHED, RAVIT - Agricultural Research Organization, Volcani Center
item KATZIR, NURIT - Newe Ya'Ar Research Center
item COLLE, MARIVI - Michigan State University
item GRUMET, REBECCA - Michigan State University
item YANG, LUMING - University Of Wisconsin
item Weng, Yiqun
item SHERMAN, AMIR - Agricultural Research Organization, Volcani Center

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: 12/1/2013
Publication Date: 1/12/2014
Citation: Ophir, R., Rubinstein, M., Eshed, R., Katzir, N., Colle, M., Grumet, R., Yang, L., Weng, Y., Sherman, A. 2014. A method of genotyping by pedigree-based training-set for identification of QTLs associated with cucumber fruit size [abstract]. Plant and Animal Genome Conference. Paper No. W237.

Interpretive Summary:

Technical Abstract: 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 Gy14 × 9930 cross 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 (0.5 cM 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.