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United States Department of Agriculture

Agricultural Research Service

Research Project: Genetic Enhancement of Allium, Cucumis, and Daucus Germplasm

Location: Vegetable Crops Research Unit

Title: A method of genotyping by pedigree-based training-set for identification of QTLs associated with cucumber fruit size

Authors
item Ophir, Ron -
item Rubinstein, Mor -
item Eshed, Ravit -
item Katzir, Nurit -
item Colle, Marivi -
item Grumet, Rebecca -
item Yang, Luming -
item Weng, Yiqun
item Sherman, Amir -

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: December 1, 2013
Publication Date: January 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.

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.

Last Modified: 10/24/2014
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