Advertisement

Euphytica

, Volume 137, Issue 2, pp 193–201 | Cite as

Genetic relationships of Brassica vegetables determined using database derived simple sequence repeats

  • Muhammet Tonguç
  • Phillip D. Griffiths
Article

Abstract

Sequence databases were screened to identify simple sequence repeats (SSRs) in Brassica oleracea sequences. A total of 512 B. oleracea DNA sequences were screened and 43 potential SSRs were identified. Thirty-six primer pairs were designed to amplify target sequences. Of the 36 primer pairs, six failed to amplify fragments of expected sizes, and 17 primer pairs failed to generate polymorphisms. Thirteen SSRs were used to assess genetic similarity between 54 B. oleracea cultivars, belonging to 3 variteal groups (cabbage, cauliflower, and broccoli). Pairwise genetic similarities were calculated for cultivars, and a dendrogram of relationships was produced. All cabbage cultivars were distinguished from each other and clustered in two separate groups. Five cauliflower cultivars could not be distinguished with SSR markers used in the study. Three broccoli cultivars clustered with cauliflower cultivars, and two cauliflower cultivars grouped with broccoli cultivars. The varietal group with the narrowest genetic variation in the study was cauliflower (B. oleracea var. botrytis) followed by broccoli (B. oleracea var. italica) and cabbage (B. oleracea var. capitata) groups. Polymorphism information content (PIC) values and number of alleles produced per marker ranged between 0.25 to 0.86 and 1 to 8, respectively, for database derived SSR markers.

Brassica oleracea, broccoli cabbage cauliflower microsatellite 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Akkaya, M.S., A.A. Bhagwat & P.B. Cregan, 1992. Length poly-morphisms of simple sequence repeat DNA in soybean. Genetics 132: 1131–1139.Google Scholar
  2. Becker, J. & M. Heun, 1995. Barley microsatellites: allele variation and mapping. Plant Mol Biol 27: 835–845.Google Scholar
  3. Broun, P. & S.D. Tanksley, 1996. Characterization and genetic map-ping of simple sequence repeats in tomato genome. Mol Gen Genet 250: 39–49.Google Scholar
  4. Brown, S.M., M.S. Hopkins, S.E. Mitchell, M.L. Senior, T.Y. Wang, R.R. Duncan, F. Gonzales-Candales & S. Kresovich, 1996. Multi-ple methods for the identification of polymorphic simple sequence repeats (SSRs) in sorghum [Sorghum bicolor (L.) Moench]. Theor Appl Genet 93: 190–198.Google Scholar
  5. Chin, E.C.L., M.L. Senior, H. Shu & J.S.C. Simith, 1996. Maize simple repetitive DNA sequences: Abundance and allele varia-tion. Genome 39: 866–873.Google Scholar
  6. Cho, Y.G., T. Ishii, S. Temnykh, X. Chen, L. Lipovich, S.R. McCouch, W.D. Park, N. Ayres & S. Cartinhour, 2000. Diversity of microsatellites derived from genomic libraries and GenBank.201 sequences in rice (Oryza sativa L.). Theor Appl Genet 100: 713– 722.Google Scholar
  7. Doyle, J. & J. Doyle, 1990. Isolation of plant DNA from fresh tissue. Focus 12: 13–15.Google Scholar
  8. Eujayl, I., M. Sorrels, M. Baum, P. Walters & W. Powell, 2001. Assessment of genoypic variation among cultivated durum wheat based on EST-SSRS and genomic SSRS. Euphytica 119: 39–43.Google Scholar
  9. GenStat, 1997. GenStat 5 Release 4.1. Downers Grove, II.Google Scholar
  10. Gupta, P.K. & R.K. Varshney, 2000. The development and use of microsatellite markers for genetic analysis and plant breeding with emphasis on bread wheat. Euphytica 113: 163–185.Google Scholar
  11. Hokanson, S.C., A.K. Szewc-McFadden, W.F. Lamboy & J.R. McFerson, 1998. Microsatellite (SSR) markers reveal genetic identities, genetic diversity and relationships in a Malus x domes-tica borkh; Core subset collection. Theor Appl Genet 97: 671– 683.Google Scholar
  12. Kresovich, S., A.K. Szewc-McFadden, S.M. Bliek & J.R. McFerson, 1995. Abundance and characterization of simple-sequence re-peats (SSRs) isolated from a size-fractionated genomic library of Brassica napus L. (rapeseed). Theor Appl Genet 91: 206–211.Google Scholar
  13. Lamboy, W.F. & J.G. Alpha, 1998. Simple sequence repeats (SSRs) for DNA fingerprinting germplasm accessions of grape (Vitis L.) species. J Am Hort Sci 123: 182–188.Google Scholar
  14. Maughan, P.J., M.A. Saghai-Maroof & G.R. Buss, 1995. Microsatel-lite and amplified length polymorphisms in cultivated and wild soybean. Genome 38: 715–728.Google Scholar
  15. Morgante, M., M. Hanafey & W. Powell, 2002. Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes. Nature Genet 30: 194–200.Google Scholar
  16. Pillen, K., A. Binder, B. Kreuzkam, L. Ramsay, R. Waugh, J. Forster & J. Leon, 2000. Mapping new EMBL-derived barley microsatel-lites and their use in differentiating German barley cultivars. Theor Appl Genet 101: 652–660.Google Scholar
  17. Plaschke, J., M.W. Ganal & M.S. Roder, 1995. Detection of genetic diversity in closely related bread wheat using microsatellite mark-ers. Theor Appl Genet 91: 1001–1007.Google Scholar
  18. Plieske, J. & D. Struss, 2001. Microsatellite markers for genome analysis in Brassica. I.: Development in Brassica napus and abundance in Brassicaceae species. Theor Appl Genet 102: 689– 694.Google Scholar
  19. Powell, W., G.C. Machray & J. Provan, 1996. Polymorphism revealed by simple sequence repeats. Trends Plant Sci 1: 215–222.Google Scholar
  20. Prasad, M., R.K. Varshney, J.K. Roy, H.S. Balyan & P.K. Gupta, 2000. The use of microsatellites for detecting DNA polymor-phism, genotype identification and genetic diversity in wheat. Theor Appl Genet 100: 584–592.Google Scholar
  21. Rozen, S. & H.J. Skaletsky, 2000. Primer 3 on the www for general users and for biologist programmers. In: S. Krawetz & S. Mis-ener (Eds.), Bioinformatics Methods and Protocols: Methods in Molecular Biology, pp. 365–386. Humana Press, Totowa, NJ.Google Scholar
  22. Russel, J., J. Fuller, G. Young, B. Thomas, G. Taramino, M. Maculay, R. Waugh & W. Powell, 1997. Discriminating between barley genotypes using microsatellite markers. Genome 40: 442–450.Google Scholar
  23. Saghai-Maroof, M.A., R.M. Biyaschev, G.P. Yang, Q. Zhang & R.W. Allard, 1994. Extraordinary polymorphic microsatellite DNA in barley: Species diversity, chromosomal locations, and population dynamics. Proc Natl Acad Sci USA 91: 5466–5470.Google Scholar
  24. Sambrook, J., E.F. Frithsch & T. Maniatis, 1989. Molecular cloning: A laboratory manual. Cold Springs Harbor Lab. Press, New York.Google Scholar
  25. Senior, M.L., J.P. Murphy, M.M. Goodman & C.W. Stuber, 1998. Utility of SSRs for determining genetic similarities and relation-ships in maize using an agarose gel system. Crop Sci 38: 1088– 1098.Google Scholar
  26. Smulders, M.J.M., G. Bredemeijer, W. Rus-Kortekaas, P. Arens & B. Vosman, 1997. Use of short microsatellites from database se-quences to generate polymorphisms among Lycopersicon escu-lentum cultivars and accessions of other Lycopersicon species. Theor Appl Genet 97: 264–272.Google Scholar
  27. Sneath, P.H.A. & R.R. Sokal, 1973. Numerical taxonomy. W.H. Fre-man Co., San Francisco, CA.Google Scholar
  28. Struss, D. & J. Plieske, 1998. The use of microsatellite markers for detection of genetic diversity in barley populations. Theor Appl Genet 97: 307–315.Google Scholar
  29. Szewc-McFadden, A.K., S. Kresovich, S.M. Bliek, S.E. Mitchell & J.R. McFerson, 1996. Identification of polymorphic, conserved simple sequence repeats (SSRs) in cultivated Brassica species. Theor Appl Genet 93: 534–538.Google Scholar
  30. Tautz, D. & C. Schlotterer, 1994. Simple sequences. Curr Opin Genet 15: 99–102.Google Scholar
  31. Temnykh, S., G. DeClerk, A. Lukashova, L. Lipovich, S. Cartinhour & S.R. McCouch, 2001. Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): Frequency, length variation, transposon associations, and genetic marker potential. Genome Res 11: 1441–1452.Google Scholar
  32. Weber, J.L. & P.E. May, 1989. Abundant class of human DNA poly-morphisms which can be typed using the polymerase chain reac-tion. Am J Hum Genet 44: 388–396.Google Scholar
  33. Yang, H., M.W. Sweetingham, W.A. Cowling & P.M.C. Simith, 2001. DNA fingerprinting based on microsatellite-anchored fragment length polymorphisms, and isolation of sequence-specific PCR markers in lupin (Lupinus angustifolius L.). Mol Breed 7: 203–209.Google Scholar

Copyright information

© Kluwer Academic Publishers 2004

Authors and Affiliations

  • Muhammet Tonguç
    • 1
  • Phillip D. Griffiths
    • 1
  1. 1.Department of Horticultural SciencesCornell University, NYSAES, Hedrick HallGenevaU.S.A

Personalised recommendations