Molecular characterization of rye cultivars


  • Želmí­ra Balážová Slovak University of Agriculture, Faculty of Biotechnology and Food Sciences, Department of Biochemistry and Biotechnology, Tr. A. Hlinku 2, 949 76 Nitra
  • Lenka Petrovičová Slovak University of Agriculture, Faculty of Biotechnology and Food Sciences, Department of Biochemistry and Biotechnology, Tr. A. Hlinku 2, 949 76 Nitra
  • Zdenka Gálová Slovak University of Agriculture, Faculty of Biotechnology and Food Sciences, Department of Biochemistry and Biotechnology, Tr. A. Hlinku 2, 949 76 Nitra
  • Martin Vivodí­k Vivodí­k Slovak University of Agriculture, Faculty of Biotechnology and Food Sciences, Department of Biochemistry and Biotechnology, Tr. A. Hlinku 2, 949 76 Nitra



Secale cereale L., polymorphism, microsatellite, PCR, dendrogram


The results of molecular analysis of 45 rye taxa (Secale cereale L.) represented by agricultural varieties originated from Central Europe and the Union of Soviet Socialist Republics (SUN) are presented. The genetic diversity of rye cultivars by 6 SSR markers was evaluated. Six specific microsatellite primer pairs produced 58 polymorphic alleles with an average of 9.7 alleles per locus. The number of alleles ranged from 6 (SCM2) to 14 (SCM86). Genetic polymorphism was characterized based on diversity index (DI), probability of identity (PI) and polymorphic information content (PIC). The diversity index (DI) of SSR markers ranged from 0.5478 (SCM2) to 0.887 (SCM86) with an average of 0.778. The lowest value of polymorphic information content was recorded for SCM2 (0.484) and the highest value for SCM86 (0.885) of PIC was detected in SCM86 with an average of 0.760.The dendrogram of genetic similarity was constructed, based on UPGMA algorithm. The hierarchical cluster analysis divided rye genotypes into 4 main clusters. The first cluster of 14 genotypes was subdivided in two subclusters (1a and 1b) where 50% of genotypes were Czechoslovak origin. The second cluster contained four genotypes were three (75%) of them had Czech or Czechoslovak origin. In the third subcluster separated three rye genotypes of different origin. The rest (24) of rye genotypes in the fourth cluster were divided into two subclusters (4a and 4b) where clearly separated group of Polish (4aa) and Czech and Czechoslovak (4ab) genotypes. Two genotypes of 4aa subcluster (Wojcieszyckie and Dankowskie Nowe) from Poland were genetically the closest. In the dendrogram alle genotypes were differentiated and clustering partially reflects geographic origin of studied rye genotypes. In this experiment, SSRs markers proved to be a high informative and usefull tool in genetic diversity research for the distinguishing and characterization of close related varieties.


Download data is not yet available.


Metrics Loading ...


Akhavan, A., Saeidi, H., Rahiminejad, M. R. 2009. Genetic diversity of Secale cereale L. in Iran as measured using microsatellites. Genetic Resources and Crop Evolution, vol. 57, no. 3, p. 415-422. DOI:

Altpeter, F., Konzun, V. 2007. Rye. Biotechnology in Agriculture and Forestry, vol. 59, p. 107-117. DOI:

Andersson, R., Fransson, G., Tietjen, M., Åman, P. 2009. Content and molecular-weight distribution of dietary fiber components in wholegrain rye flour and bread. Journal of Agricultural and Food Chemistry, vol. 57, no. 5, p.2004-2008. DOI:

Bassam, B. J., Caetano-Anolles, G., Gresshoff. P. M. 1991. Fast and sensitive silver staining of DNA in polyacrylamide gels. Analytical Biochemistry, vol. 196, no. 1, p. 80-83. DOI:

Bolibok, H., Rakoczy-Trojanowska, M., Hromada, A., Pietrzykowski, R. 2005. Efficiency of different PCR-based marker systems in assessing genetic diversity among winter rye (Secale cereale L.) inbred lines. Euphytica, vol. 146, no. 1, p. 109-116. DOI:

Botes, W. C., Bitalo D. 2013. Identification, evaluation and optimalization of a minimum simple sequence repeat marker set for triticale breeding. Journal of Apllied Biology and Biotechnology, vol. 1, no. 4, p.16-23.

Gailîte, A., Gaile, A., Gaile, I., Voronova, A., Veinberga, I., Kokare, A., Ruòìis, D. E. 2013. Genotypic assessment of the Latvian rye (Secale cereale L.) collection. Proceedings of the Latvian Academy of Sciences, vol. 67, p. 264-267. DOI:

Hackauf, B., Wehling, P. 2002. Identification of microsatellite polymorphisms in an expressed portion of the rye genome. Plant Breeding, vol. 121, no. 1, p. 17-25. DOI:

Huang, X. Q., Börner, A., Röder, M. S., Ganal, M. W. 2002. Assesing genetic diversity of wheat (Triticum aestivum L.) germplasm using microsatellite markers. Theoretical Applied Genetics, vol. 105, no. 4, p. 699-707. DOI:

Ignjatovic-Micic, D., Ristic, D., Babic, V., Andjelkovic, V., Vancetovic, J. 2015. A simple SSR analysis for genetic diversity estimation of maize landraces. Genetika, vol. 47, no. 1, p. 53-62. DOI:

Jenabi, T., Saeidi, H., Rahiminejad, M. R. 2011. Biodiversity of Secale strictum in Iran measured using microsatellites. Genetic Resources and Crop Evolution, vol. 58, no. 4, p. 497-505. DOI:

Jiang, S. K., Huang, C., Zhang, X. J., Wang, J. Y., Chen, W. F., Xu, Z. J. 2010. Development of Highly Informative Microsatellite (SSR) Marker Framework for Rice (Oryza sativa L.) Genotyping. Agricultural Sciences in China., vol. 9, no. 12, p. 1697-1704. DOI:

Khlestkina, E. K., Than, M. H. M., Pestsova, E. G., Röder, M. S., Malyshev, S. V., Korzun, V., Börner, A. 2004. Mapping of 99 new microsatellite-derived loci in rye (Secale cereale L.) including 39 expressed sequence tags. Theoretical Apllied Genetics., vol. 109, no. 4, p. 725-732. DOI:

Korzun, V., Malyshev, S., Voylokov, A. V., Börner, A. 2001. A genetic map of rye (Secale cereale L.) combining RFLP, isozyme, protein, microsatellite and gene loci. Theoretical and Applied Genetics, vol. 102, no. 5, p. 709-717. DOI:

Kuleung, C., Baenziger, P. S., Dweikat, I. 2004. Transferability of SSR markers among wheat, rye and triticale. Theoretical and Applied Genetics, vol. 108, no. 6, p. 1147-1150. DOI:

Maršálková, L., Židek, R., Pokoradi, J., Golian, J., Belej, Ľ. 2014. Genetic diversity and relatedness among seven red deer (Cervus Elaphus) populations. Potravinarstvo, vol. 8, no. 1, p. 15-19. DOI:

Ondroušková, J., Vyhnánek, T. 2013. Study of genetic variability of triticale varieties by SSR markers. Journal of Microbiology, Biotechnology and Food Sciences, vol. 2, p. 2366-2368.

Paetkau, D., Calvert, W., Stirling, I., Strobeck, C. 1995. Microsatellite analysis of population structure in Canadian polar bears., Molecular Ecology, vol. 4, no. 3, p. 347-354. PMid:7663752 DOI:

Persson, K., von Bothmer, B. 2002. Genetic diversity in landraces of rye (Secale cereale L.) from Northern part of Europe by using allozymes. Hereditas, vol. 136, no. 1, p. 29-38. DOI:

Röder, M. S., Plaschke, J., König, S. U., Börner, A., Sorrels, M. E., Tanksley, S. D., Ganal, M. 1995. Abundance, variability and chromosomal location of mocrosatellites in wheat. Molecular Genetics and Genomics, vol. 246, no. 3, p. 327-333. DOI:

Rosén, L. A. H., Östman, E. M., Shewry, P. R., Ward, J. L., Andersson, A. A. M., Piironen, V., Lampi, A. M., Rakszegi, M., Bedö, Z., Björck, I. M. E. 2011. Postprandial glycemia, insulinemia, and satiety responses in healthy subjects after whole grain rye bread made from different rye varieties. Journal of Agricultural and Food Chemistry, vol. 59, no. 22, p. 12139-12148. DOI:

Saal, B., Wricke, G. 1999. Development of simple sequence repeat markers in rye (Secale cereale L.). Genome, vol. 42, no. 5, p. 964-972. DOI:

Salem, K. F. M., El-Zanaty, A. M., Esmail, R. M. 2008. Assessing wheat (Triticum aestivum L.) genetic diversity using morphological characters and microsatellite markers. World Journal of Agricultural Sciences., vol. 4, no. 5, p. 538-544.

Shang, H. Y., Wei, M. Y., Wang, X. R., Zheng, Y. L. 2006. Genetic diversity and phylogenetic relationships in the rye genus Secale L. (rye) based on Secale cereale microsatellite markers. Genetics and Molecular Biology, vol. 29, no. 4, p. 685-691. DOI:

Targońska, M., Bolibok-Brągoszewska, H., Rakoczy-Trojanowska, M. 2015. Assessment of Genetic Diversity in Secale cereale Based on SSR Markers. Plant Journal Moecular Biology Report, p. 1-15. DOI:

Weber, J. L. 1990. Informativeness of human (dC-dA)n x (dG-dT)n polymorphism. Genomics, vol. 7, no. 4, p. 524-530. DOI:

Weir, B. S. 1990. Genetic data analysis. Sinauer Associated, Sunderland: Massachusetts, p. 445. PMCid:PMC249124

Žiarovská, J., Ražná, K., Labajová, M. 2013. Using of Inter Microsatellite Polymorphism to evaluate gamma-irradiated Amaranth mutants. Emirates Journal of Food and Agriculture, vol. 25, p. 673-681. DOI:




How to Cite

Balážová, Želmí­ra ., Petrovičová, L. ., Gálová, Z. ., & Vivodí­k, M. V. . (2016). Molecular characterization of rye cultivars. Potravinarstvo Slovak Journal of Food Sciences, 10(1), 54–58.

Most read articles by the same author(s)

<< < 1 2