Skip to main content
SpringerLink
Log in

DNA profiling of commercial pumpkin cultivars using simple sequence repeat polymorphisms

  • Research Report
  • Published:
Horticulture, Environment, and Biotechnology Aims and scope Submit manuscript

Abstract

Pumpkin (Cucurbita spp.) is a major vegetable crop grown worldwide. Three species, C. pepo, C. moschata, and C. maxima, are economically important cultivated pumpkins. To develop a core set of markers for DNA profiling and cultivar identification, we used a total of 300 SSRs consisting of 158 CMTp and 142 CMTm that were previously identified in C. pepo and C. moshata, respectively. Polymorphisms in these primers were tested using a subset of 22 cultivars selected from a collection of 160 commercial cultivars. A total of 12 CMTp and 28 CMTm markers were selected based on polymorphism and number of alleles, and these 40 markers were used to genotype all 160 cultivars. Of these, 29 markers (5 CMTp and 24 CMTm) accurately detected a total of 215 alleles with an average of 7.41 alleles per marker in our collection of pumpkin cultivars. Their PIC values ranged from 0.327 to 0.894 with an average of 0.674. Analysis of genetic similarity using the 29 SSR markers revealed that the 160 cultivars were divided into five major clusters representing C. maxima×C. moshata hybrids (cluster I), C. moshata (cluster II), C. maxima (cluster III), C. pepo (cluster IV), and C. ficifolia (cluster V). In clusters I-IV, the cultivars were further separated into 2-3 sub-clusters. In addition, we found that 29 SSR markers were able to differentiate all 160 cultivars. Results from our study will facilitate genetic study and protection of breeders’ intellectual property rights in pumpkins.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

Literature Cited

  • Anderson, J.A., G.A. Churchill, J.E. Autrique, S.D. Tanksley, and M.E. Sorrells. 1993. Optimizing parental selection for genetic-linkage maps. Genome 36:181–186.

    Article  PubMed  CAS  Google Scholar 

  • Bae, K.M., S.C. Sim, J.H. Hong, K.J. Choi, D.H. Kim, and Y.S. Kwon. 2015. Development of genomic SSR markers and genetic diversity analysis in cultivated radish (Raphanus sativus L.). Hortic. Environ. Biotechnol. 56:216–224.

    Article  CAS  Google Scholar 

  • Barbazuk, W.B., S.J. Emrich, H.D. Chen, L. Li, and P.S. Schnable. 2007. SNP discovery via 454 transcriptome sequencing. Plant J. 51:910–918.

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  • Blanca, J., J. Canizares, C. Roig, P. Ziarsolo, F. Nuez, and B. Pico. 2011. Transcriptome characterization and high throughput SSRs and SNPs discovery in Cucurbita pepo (Cucurbitaceae). BMC Genomics 12:104.

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  • Bundock, P.C., F.G. Eliott, G. Ablett, A.D. Benson, R.E. Casu, K.S. Aitken, and R.J. Henry. 2009. Targeted single nucleotide polymorphism (SNP) discovery in a highly polyploid plant species using 454 sequencing. Plant Biotechnol. J. 7:347–354.

    Article  PubMed  CAS  Google Scholar 

  • Collard, B.C.Y., M.Z.Z. Jahufer, J.B. Brouwer, and E.C.K. Pang. 2005. An introduction to markers, quantitative trait loci (QTL) mapping and marker-assisted selection for crop improvement: The basic concepts. Euphytica 142:169–196.

    Article  CAS  Google Scholar 

  • Esteras, C., P. Gomez, A.J. Monforte, J. Blanca, N. Vicente-Dolera, C. Roig, F. Nuez, and B. Pico. 2012. High-throughput SNP genotyping in Cucurbita pepo for map construction and quantitative trait loci mapping. BMC Genomics 13:80.

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  • FAO. 2015. Food and agriculture organization of the United Nations statistics division. http://faostat3.fao.org/.

  • Gong, L., H.S. Paris, M.H. Nee, G. Stift, M. Pachner, J. Vollmann, and T. Lelley. 2012. Genetic relationships and evolution in Cucurbita pepo (pumpkin, squash, gourd) as revealed by simple sequence repeat polymorphisms. Theor. Appl. Genet. 124:875–891.

    Article  PubMed  PubMed Central  Google Scholar 

  • Gong, L., G. Stift, R. Kofler, M. Pachner, and T. Lelley. 2008. Microsatellites for the genus Cucurbita and an SSR-based genetic linkage map of Cucurbita pepo L. Theor. Appl. Genet. 117:37–48.

    Article  CAS  Google Scholar 

  • Hamilton, J.P., C.N. Hansey, B.R. Whitty, K. Stoffel, A.N. Massa, A. Van Deynze, W.S. De Jong, D.S. Douches, and C.R. Buell. 2011a. Single nucleotide polymorphism discovery in elite north american potato germplasm. BMC Genomics 12:302.

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  • Hamilton, J.P., S. Sim, K. Stoffel, A. Van Deynze, C.R. Buell, and D.M. Francis. 2011b. Single nucleotide polymorphism discovery in cultivated tomato via sequencing by synthesis. The Plant Genome 5:17–29.

    Article  Google Scholar 

  • Hong, J.H., K.J. Choi, and Y.S. Kwon. 2014. Construction of DNA profile data base of strawberry cultivars using microsatellite markers. Korean J. Hortic. Sci. Technol. 32:853–863.

    Article  CAS  Google Scholar 

  • Honjo, M., T. Nunome, S. Kataoka, T. Yano, H. Yamazaki, M. Hamano, S. Yui, and M. Morishita. 2011. Strawberry cultivar identification based on hypervariable SSR markers. Breeding Sci. 61:420–425.

    Article  CAS  Google Scholar 

  • Hyten, D.L., S.B. Cannon, Q.J. Song, N. Weeks, E.W. Fickus, R.C. Shoemaker, J.E. Specht, A.D. Farmer, G.D. May, and P.B. Cregan. 2010. High-throughput SNP discovery through deep resequencing of a reduced representation library to anchor and orient scaffolds in the soybean whole genome sequence. BMC Genomics 11:38.

    Article  PubMed  PubMed Central  Google Scholar 

  • Kwon, Y.S., and K.J. Choi. 2013. Construction of a DNA profile database for commercial cucumber (Cucumis sativus L.) cultivars using microsatellite marker. Korean J. Hortic. Sci. Technol. 31:344–351.

    Article  CAS  Google Scholar 

  • Kwon, Y.S., and J.H. Hong. 2014. Use of microsatellite markers to identify commercial melon cultivars and for hybrid seed purity testing. Korean J. Hortic. Sci. Technol. 32:525–534.

    Article  CAS  Google Scholar 

  • Kwon, Y.S., J.H. Hong, and K.J. Choi. 2013. Construction of a microsatellite marker database of commercial pepper cultivars. Korean J. Hortic. Sci. Technol. 31:580–589.

    Article  CAS  Google Scholar 

  • Mcnally, K.L., K.L. Childs, R. Bohnert, R.M. Davidson, K. Zhao, V.J. Ulat, G. Zeller, R.M. Clark, D.R. Hoen, T.E. Bureau, R. Stokowski, D.G. Ballinger, K.A. Frazer, D.R. Cox, B. Padhukasahasram, C.D. Bustamante, D. Weigel, D.J. Mackill, R.M. Bruskiewich, G. Ratsch, C.R. Buell, H. Leung, and J.E. Leach. 2009. Genomewide SNP variation reveals relationships among landraces and modern varieties of rice. Proc. Natl. Acad. Sci. USA 106:12273–12278.

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  • Paris, H.S. 2000. History of the cultivar-groups of Cucurbita pepo. In: J. Janick (ed) Hortic. Rev. 25. John Wiley, New York, USA.

    Google Scholar 

  • Paris, H.S., N. Yonash, V. Portnoy, N. Mozees-Daube, G. Tzuri, and N. Katzir. 2003. Assessment of genetic relationships in Cucurbita pepo (Cucurbitaceae) using DNA markers. Theor. Appl. Genet. 106:971–978.

    PubMed  CAS  Google Scholar 

  • Rohlf, F.J., 2008. NTSYSpc: Numerical taxonomy system, ver. 2.20. Exeter Publishing, Ltd, Setauket, USA.

    Google Scholar 

  • Sim, S.C., M.D. Robbins, A. Van Deynze, A.P. Michel, and D.M. Francis. 2011. Population structure and genetic differentiation associated with breeding history and selection in tomato (Solanum lycopersicum L.). Heredity 106:927–935.

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  • Sneath, P.H.A., and R.R. Sokal. 1973. Numerical Taxonomy. W.H. Freeman and Company, San Francisco, USA.

    Google Scholar 

  • Varshney, R.K., A. Graner, and M.E. Sorrells. 2005. Genic microsatellite markers in plants: features and applications. Trends Biotechnol. 23:48–55.

    Article  PubMed  CAS  Google Scholar 

  • Wang, F.G., H.L. Tian, J.R. Zhao, H.M. Yi, L. Wang, and W. Song. 2011. Development and characterization of a core set of SSR markers for fingerprinting analysis of Chinese maize varieties. Maydica 56:7–17.

    Google Scholar 

  • Whitaker, T.W., and W.P. Bemis. 1964. Evolution in the genus cucurbita. Evolution 18:553–559.

    Article  Google Scholar 

  • Wu, T.Q., S.B. Luo, R. Wang, Y.J. Zhong, X.M. Xu, Y.E. Lin, X.M. He, B.J. Sun, and H.X. Huang. 2014. The first Illumina-based de novo transcriptome sequencing and analysis of pumpkin (Cucurbita moschata Duch.) and SSR marker development. Mol. Breeding 34:1437–1447.

    Article  CAS  Google Scholar 

  • Yadav, M., S. Jain, R. Tomar, G.B. Prasad, and H. Yadav. 2010. Medicinal and biological potential of pumpkin: an updated review. Nutr. Res. Rev. 23:184–90.

    Article  PubMed  CAS  Google Scholar 

  • Yi, S.I., K.M. Bae, Y.S. Kwon, and I.H. Cho. 2006. Development of oriental melon (Cucumis melo L.)-derived SSR markers using a PCR-based method and polymorphic application for the genotyping of commercial lines. Korean J. Genetics 28:317–324.

    CAS  Google Scholar 

  • Zhu, C., M. Gore, E.S. Buckler, and J. Yu. 2008. Status and prospects of association mapping in plants. The Plant Genome 1:5–20.

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Bioresources Engineering, Sejong University, Seoul, 05006, Korea

    Sung-Chur Sim

  2. Seed Testing & Research Center, Korea Seed & Variety Service, Ministry for Agriculture, Food & Rural Affairs, Gimcheon, 39660, Korea

    Jee-Hwa Hong

  3. Department of Genetic Engineering, Dong-A University, Busan, 49315, Korea

    Yong-Sham Kwon

Authors
  1. Sung-Chur Sim
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Jee-Hwa Hong
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Yong-Sham Kwon
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Yong-Sham Kwon.

Additional information

These authors contributed equally to this work.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Sim, SC., Hong, JH. & Kwon, YS. DNA profiling of commercial pumpkin cultivars using simple sequence repeat polymorphisms. Hortic. Environ. Biotechnol. 56, 811–820 (2015). https://doi.org/10.1007/s13580-015-0123-0

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s13580-015-0123-0

Additional key words

Search

Navigation