Biologia Plantarum

, Volume 55, Issue 3, pp 577–580 | Cite as

Comparison of genomic SSR and EST-SSR markers for estimating genetic diversity in cucumber

  • J. Hu
  • L. Wang
  • J. LiEmail author
Brief Communication


Thirteen genomic microsatellite (gSSR) and sixteen expressed sequence tag (EST)-SSR (eSSR) markers were compared to estimate genetic diversity among 29 cucumber (Cucumis sativus L.) accessions. gSSR markers detected mean 4.46 alleles with a mean polymorphic information content (PIC) of 0.664, against eSSR markers with mean 3.38 alleles and a mean PIC of 0.397. gSSRs amplified more null alleles than eSSRs. Genetic diversity within the accession set was estimated by construction of dendrograms using gSSR or eSSR data. There was a clear consistency between gSSR and eSSR trees in terms of positioning of most cucumber germplasms. gSSR markers could separate various types of cucumber germplasms on the whole, although clustering of some accessions was not based on their geographical origins in eSSR tree. eSSR markers identified an independent sub-cluster containing five accessions resistant to downy mildew, suggesting a probable relationship between eSSRs and disease-resistance trait in cucumber. The Mantel test between gSSR and eSSR matrices revealed a good fit correlation (r = 0.836). The general dendrogram constructed using the combined data of gSSRs and eSSRs was similar to those obtained separately with each marker.

Additional key words

Cucumis sativus dendrograms polymorphic information content 



Europe greenhouse, Europe open-field

north China

occident processing and south China accessions, respectively


expressed sequence tag microsatellite


expressed sequence tag


genomic microsatellite


polymorphic information content


unweighted pair group method using arithmetic averages


wild species


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This work is supported by National Key Technology R & D Program (No. 2009BADB8B02). We are grateful to Prof. Jiancan Feng, College of Horticulture, Henan Agricultural University, for his assistance in the laboratory work on this project.


  1. Anderson, J.A., Churchill, G.A., Autrique, J.E., Tanksley, S.D., Sorrells, M.E.: Optimizing parental selection for genetic linkage maps. — Genome 36: 181–186, 1993.PubMedCrossRefGoogle Scholar
  2. Chabane, K., Ablett, G.A., Cordeiro, G.M., Valkoun, J., Henry, R.J.: EST versus genomic derived microsatellite markers for genotyping wild and cultivated barley. — Genet. Resour. Crop Evol. 52: 903–909, 2005.CrossRefGoogle Scholar
  3. Cho, Y.G., Ishii, T., Temnykh, S., Chen, X., Lipovich, L., McCouch, S.R., Park, W.D., Cartinhour, N.A.S.: Diversity of microsatellites derived from genomic libraries and GenBank sequences in rice (Oryza sativa L.). — Theor. appl. Genet. 100: 713–722, 2000.CrossRefGoogle Scholar
  4. Creste, S., Neto, A.T., Figueira, A.: Detection of single sequence repeat polymorphisms in denaturing polyacrylamide sequencing gels by silver staining. — Plant mol. Biol. Rep. 19: 229–306, 2001.CrossRefGoogle Scholar
  5. Danin-Poleg, Y., Reis, N., Tzuri, G., Katzir, N.: Development and characterization of microsatellite markers in Cucumis. — Theor. appl. Genet. 102: 61–72, 2001.CrossRefGoogle Scholar
  6. Dijkhuizen, A., Kennard, W., Havey, M.J., Staub J.E.: RFLP variation and genetic relationships in cultivated cucumber. — Euphytica 90: 79–87, 1996.Google Scholar
  7. Gupta, P.K., Rustgi, S., Sharma, S., Singh, R., Kumar, N., Balyan, H.S.: Transferable EST-SSR markers for the study of polymorphism and genetic diversity in bread wheat. — Mol. Genet. Genomics 270: 315–323, 2003.PubMedCrossRefGoogle Scholar
  8. Hu, J.B., Li, J.W., Zhou, X.Y.: Analysis of cytoplasmic variation in a cucumber germplasm collection using chloroplast microsatellite markers. — Acta Physiol. Plant. 31: 1085–1089, 2009.CrossRefGoogle Scholar
  9. Hu, J.B., Zhou, X.Y., Li, J.W.: Development of novel EST-SSR markers for cucumber (Cucumis sativus) and their transferability to related species. — Sci. Hort. 125: 534–538, 2010.CrossRefGoogle Scholar
  10. Jaccard, P.: Nouvelles recherches sur la distribution florale. — Bul. Soc. Vaudoise Sci. Nat. 44: 223–270, 1908.Google Scholar
  11. Murray, M.G., Thompson, W.F.: Rapid isolation of high molecular weight plant DNA. — Nucl. Acids Res. 8: 4321–4325, 1980.PubMedCrossRefGoogle Scholar
  12. Pitrat, M., Chauvet, M., Foury, C.: Diversity, history, and production of cultivated cucurbits. — Acta Hort. 492: 21–28, 1999.Google Scholar
  13. Rohlf, F.J.: NTSYS-pc: Numerical Taxonomy and Multivariate Analysis System, Version 2.1. — Exeter Publications, New York 2000.Google Scholar
  14. Scott, K.D., Eggler, P., Seaton, G., Rossetto, M., Ablett, E.M., Lee, L.S., Henry, R.J.: Analysis of SSRs derived from grape ESTs. — Theor. appl. Genet. 100: 723–726, 2000.CrossRefGoogle Scholar
  15. Sikdar, B., Bhattacharya, M., Mukherjee, A., Banerjee, A., Ghosh, E., Ghosh, B., Roy, S.C.: Genetic diversity in important members of Cucurbitaceae using isozyme, RAPD and ISSR markers. — Biol. Plant. 54: 135–140, 2010.CrossRefGoogle Scholar
  16. Staub, J.E., Chung, S.M., Fazio, G.: Conformity and genetic relatedness estimation in crop species having a narrow genetic base: the case of cucumber (Cucumis sativus L.). — Plant Breed. 124: 44–53, 2005.CrossRefGoogle Scholar
  17. Varshney, R.K., Graner, A., Sorrells, M.W.: Genic microsatellite markers in plants: features and applications. — Trends Biotechnol. 23: 48–55, 2005.PubMedCrossRefGoogle Scholar
  18. Watcharawongpaiboon, N., Chunwongse, J.: Development and characterization of microsatellite markers from an enriched genomic library of cucumber (Cucumis sativus). — Plant Breed. 127: 74–81, 2008.Google Scholar
  19. Zhuang, F.Y., Chen, J.F., Staub, J.E., Qian, C.T.: Assessment of genetic relationships among Cucumis spp. by SSR and RAPD marker analysis. — Plant Breed. 123: 167–172, 2008.CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2011

Authors and Affiliations

  1. 1.Open Key Laboratory of Horticultural Plant Physiology and Genetic Improvement, High School of Henan Province; Key Laboratory of Fruit Plant and Cucurbit, Henan Province; College of HorticultureHenan Agricultural UniversityZhengzhouP.R. China

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