Horticulture, Environment, and Biotechnology

, Volume 56, Issue 6, pp 811–820

DNA profiling of commercial pumpkin cultivars using simple sequence repeat polymorphisms

Research Report

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.

Additional key words

genetic similarity molecular marker plant breeder rights polymorphism information content variety protection 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

Literature Cited

  1. 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.PubMedCrossRefGoogle Scholar
  2. 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.CrossRefGoogle Scholar
  3. 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.PubMedPubMedCentralCrossRefGoogle Scholar
  4. 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.PubMedPubMedCentralCrossRefGoogle Scholar
  5. 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.PubMedCrossRefGoogle Scholar
  6. 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.CrossRefGoogle Scholar
  7. 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.PubMedPubMedCentralCrossRefGoogle Scholar
  8. FAO. 2015. Food and agriculture organization of the United Nations statistics division. http://faostat3.fao.org/.Google Scholar
  9. 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.PubMedPubMedCentralCrossRefGoogle Scholar
  10. 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.CrossRefGoogle Scholar
  11. 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.PubMedPubMedCentralCrossRefGoogle Scholar
  12. 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.CrossRefGoogle Scholar
  13. 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.CrossRefGoogle Scholar
  14. 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.CrossRefGoogle Scholar
  15. 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.PubMedPubMedCentralCrossRefGoogle Scholar
  16. 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.CrossRefGoogle Scholar
  17. 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.CrossRefGoogle Scholar
  18. 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.CrossRefGoogle Scholar
  19. 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.PubMedPubMedCentralCrossRefGoogle Scholar
  20. 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
  21. 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.PubMedGoogle Scholar
  22. Rohlf, F.J., 2008. NTSYSpc: Numerical taxonomy system, ver. 2.20. Exeter Publishing, Ltd, Setauket, USA.Google Scholar
  23. 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.PubMedPubMedCentralCrossRefGoogle Scholar
  24. Sneath, P.H.A., and R.R. Sokal. 1973. Numerical Taxonomy. W.H. Freeman and Company, San Francisco, USA.Google Scholar
  25. Varshney, R.K., A. Graner, and M.E. Sorrells. 2005. Genic microsatellite markers in plants: features and applications. Trends Biotechnol. 23:48–55.PubMedCrossRefGoogle Scholar
  26. 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
  27. Whitaker, T.W., and W.P. Bemis. 1964. Evolution in the genus cucurbita. Evolution 18:553–559.CrossRefGoogle Scholar
  28. 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.CrossRefGoogle Scholar
  29. 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.PubMedCrossRefGoogle Scholar
  30. 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.Google Scholar
  31. 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.CrossRefGoogle Scholar

Copyright information

© Korean Society for Horticultural Science and Springer-Verlag GmbH 2015

Authors and Affiliations

  1. 1.Department of Bioresources EngineeringSejong UniversitySeoulKorea
  2. 2.Seed Testing & Research Center, Korea Seed & Variety ServiceMinistry for Agriculture, Food & Rural AffairsGimcheonKorea
  3. 3.Department of Genetic EngineeringDong-A UniversityBusanKorea

Personalised recommendations