Article | 10. 2015 Vol. 33, Issue. 5
Use of Microsatellite Markers Derived from Genomic and Expressed Sequence Tag (EST) Data to Identify Commercial Watermelon Cultivars

Department of Genetic Engineering, College of Natural Resources & Life Science, Dong-A University1
Seed Test & Research Center, Korea Seed & Variety Service, Ministry for Agriculture, Food & Rural Affairs2

2015.10. 737:750


This study was carried out to construct a DNA profile database for 102 watermelon cultivars through the comparison of polymorphism level and genetic relatedness using genomic microsatellite (gMS) and expressed sequence tag (EST)-microsatellite (eMS) markers. Sixteen gMS and 10 eMS primers showed hyper-variability and were able to represent the genetic variation within 102 watermelon cultivars. With gMS markers, an average of 3.63 alleles per marker were detected with a polymorphism information content (PIC) value of 0.479, whereas with eMS markers, the average number of alleles per marker was 2.50 and the PIC value was 0.425, indicating that eMS detects a lower polymorphism level compared to gMS. Cluster analysis and Jaccard’s genetic distance coefficients using the unweighted pair group method with arithmetic average (UPGMA) based on the gMS, eMS, and combined data sets showed that 102 commercial watermelon cultivars could be categorized into 6 to 8 major groups corresponding to phenotypic traits. Moreover, this method was sufficient to identify 78 out of 102 cultivars. Correlation analysis with Mantel tests for those clusters using 3 data sets showed high correlation (r ≥ 0.80). Therefore, the microsatellite markers used in this study may serve as a useful tool for germplasm evaluation, genetic purity assessment, and fingerprinting of watermelon cultivars.

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