Detection genetic variability of secale cereale L. by scot markers

Authors

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

DOI:

https://doi.org/10.5219/726

Keywords:

Secale cereal, SCoT markers, genetic diversity

Abstract

Rye (Secale cereale L.) is our traditional cereal used for baking. The genetic variability of grown rye has been reduced by modern agronomic practices, which subsequently prompted the importance of search for species that could be useful as a gene pool for the improving of flour quality for human consumption or for other industrial uses. Therefore, the aim of this study was to detect genetic variability among the set of 45 rye genotypes using 8 SCoT markers. Amplification of genomic DNA of 45 genotypes, using SCoT analysis, yielded 114 fragments, with an average of 14.25 polymorphic fragments per primer. The most polymorphic primer was SCoT 36, where 21 polymorphic amplification products were detected. In contract the lowest polymorphic primer was SCoT 45 with 5 polymorphic products. Genetic polymorphism was characterized based on diversity index (DI), probability of identity (PI) and polymorphic information content (PIC). The hierarchical cluster analysis showed that the rye genotypes were divided into 2 main clusters. One rye genotype Motto, origin from Poland formed a separate subcluster (1b). Subscluster 2a included only genotype Valtické (CSK). In this experiment, SCoT proved to be a rapid, reliable and practicable method for revealing of polymorphism in the rye cultivars.

References

Akhavan, A., Saeidi, H., Rahiminejad, M. R. 2010. Genetic diversity of Secale cereale L. in Iran as measured using microsatellites. Genetic resources and crop evolution, vol. 57, no. 3, p. 415-422. https://doi.org/10.1007/s10722-009-9480-9

Alikhani, L., Rahmani, M. S., Shabanian, N., Badakhshan, H., Khadivi-Khub, A. 2014. Genetic variability and structure of Quercus brantii assessed by ISSR, IRAP and SCoT markers. Gene, vol. 552, no. 1, p. 176-183.. https://doi.org/10.1016/j.gene.2014.09.034 PMid:25241382

Alkimova, O. G., Mazurok, N. A., Potapova, T. A., Zakian, S. M., Heslop-Harrison, J. S., Vershinin, A. V. 2004. Diverse patterns of the tandem repeats organization in rye chromosomes. Chromosoma, vol. 113, no. 4, p. 42-52. https://doi.org/10.1007/s00412-004-0294-4

Amirmoradi, B., Talebi, R., Karami, E. 2012. Comparison of genetic variation and differentiation among annual Cicer species using start codon targeted (SCoT) polymorphism, DAMD-PCR, and ISSR markers. Plant systematics and evolution, vol. 298, no. 9, p. 1679-1688. https://doi.org/10.1007/s00606-012-0669-6

Andersen, J. R., Lübberstedt, T. 2003. Functional markers in plants. Trends in Plant Science, vol. 8, no. 11, p. 554-560. https://doi.org/10.1016/j.tplants.2003.09.010 PMid:14607101

Arya, L., Narayanan,R. K., Verma, M., Singh, A. K.,Gupta, V. 2014. Genetic diversity and population structure analyses of Morinda tomentosa Heyne, with neutral and gene based markers. Genetic resources and crop evolution, vol. 61, no. 8, 1469-1479. https://doi.org/10.1007/s10722-014-0168-4

Bartoš, J., Paux, E., Kofler, R., Havránková, M., Kopecký, D. 2008. A first survey of the rye (Secale cereale) genome composition through BAC end sequencing of the short arm of chromosome 1R. BMC Plant Biology, vol. 8, p. 1-12. https://doi.org/10.1186/1471-2229-8-95 PMid:18803819

Bauer, E., Schmutzer, T., Barilar, I., Mascher, M., Gundlach, H., Martis, M. M., Schmidt, M. 2016. Towards a whole‐genome sequence for rye (Secale cereale L.). The Plant Journal, vol. 89, no. 5, p. 853-869. https://doi.org/10.1111/tpj.13436 PMid:27888547

Bhattacharyya, P., Kumaria, S., Kumar, S., Tandon, P. 2013. Start Codon Targeted (SCoT) marker reveals genetic diversity of Dendrobium nobile Lindl., an endangered medicinal orchid species. Gene, vol. 529, no. 1, p. 21-26. https://doi.org/10.1016/j.gene.2013.07.096 PMid:23939470

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. https://doi.org/10.1007/s10681-005-0548-0

Collard, B. C.Y., Mackill, D. J. 2009. Start codon targeted (SCoT) polymorphism: a simple, novel DNA marker technique for generating gene-targeted markers in plants. Plant Molecular Biology Reproduction, vol. 27, no. 1, p. 86-93. https://doi.org/10.1007/s11105-008-0060-5

Gajera, H. P., Bambharolia, R. P., Domadiya, R. K., Patel, S. V., Golakiya, B.A. 2014. Molecular characterization and genetic variability studies associated with fruit quality of indigenous mango (Mangifera indica L.) cultivars. Plant Systematics and Evolution, vol. 300, no. 5, p. 1011-1020. https://doi.org/10.1007/s00606-013-0939-y

Gao, Y. H., Zhu, Y. Q., Tong, Z. K., Xu, Z. Y., Jiang, X. F., Huang, C. H. 2014. Analysis of genetic diversity and relationships among genus Lycoris based on start codon targeted (SCoT) marker. Biochemical Systematics and Ecology, vol. 57, 221-226. https://doi.org/10.1007/s11033-011-1329-6 PMid:22170600

Gorji, A. M., Poczai, P., Polgar, Z., Taller, J. 2011. Efficiency of arbitrarily amplified dominant markers (SCoT, ISSR and RAPD) for diagnostic fingerprinting in tetraploid potato. American journal of potato research, vol. 88, no. 3, p. 226-237. https://doi.org/10.1007/s12230-011-9187-2

Guo, D. L., Zhang, J. Y., Liu, C. H. 2012. Genetic diversity in some grape varieties revealed by SCoT analyses. Molecular biology reports, vol. 39, no. 5, p. 5307-5313. https://doi.org/10.1007/s11033-011-1329-6

Chikmawati, T., Skovmand, B., Gustafson, J. P. 2005. Phylogenetic relationships among Secale species revealed by amplified fragment length polymorphisms. Genome, vol. 48, no. 1, p. 792-801. https://doi.org/10.1139/g05-043 PMid:16391685

Joshi, C. P., Zhou, H., Huang, X., Chiang, V. L. 1997. Context sequences of translation initiation codon in plants. Plant Molecular Biology, vol. 35, no. 6, p. 993-1001. https://doi.org/10.1023/A:1005816823636 PMid:9426620

Luo, C., He, X. H., Chen, H., Hu, Y., Ou, S. J. 2012. Genetic relationship and diversity of Mangifera indica L.: revealed through SCoT analysis. Genetic resources and crop evolution, vol. 59, no. 7, p. 1505-1515. https://doi.org/10.1007/s10722-011-9779-1

Luo, C., He, X. H., Chen, H., Hu, Y., Ou, S. J. 2012. Genetic relationship and diversity of Mangifera indica L.: revealed through SCoT analysis. Genetic Resources of Crop Evolution, vol. 59, no. 1, p. 1505-1515. https://doi.org/10.1007/s10722-011-9779-1

Luo, C., He, X. H., Chen, H., Ou, S. J., Gao, M. P. 2010. Analysis of diversity and relationships among mango cultivars using Start Codon Targeted (SCoT) markers. Biochemical Systematics and Ecology, vol. 38, no. 6, p. 1176-1184. https://doi.org/10.1016/j.bse.2010.11.004

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. http://dx.doi.org/10.1111/j.1365-294x.1995.tb00227.x

Pakseresht, F., Talebi, R., Karami, E. 2013. Comparative assessment of ISSR, DAMD and SCoT markers for evaluation of genetic diversity and conservation of landrace chickpea (Cicer arietinum L.) genotypes collected from north-west of Iran. Physiology and Molecular Biology of Plants, vol. 19, no. 4, p. 563-574. https://doi.org/10.1007/s12298-013-0181-7 PMid:24431526

Persson, K., von Bothmer, R., Gullord, M., Gunnarsson, E. 2006. Phenotypic variation and relationships in landraces and improved varieties of rye (Secale cereale L.) from northern Europe. Genetic Resources Crop Evolution, vol. 53, no. 1, p. 857-866. https://doi.org/10.1007/s10722-004-6694-8

Rathore, N. S., Rai, M. K., Phulwaria, M., Rathore, N., Shekhawat, N. S. 2014. Genetic stability in micropropagated Cleome gynandra revealed by SCoT analysis. Acta physiologiae plantarum, vol. 36, no. 2, p. 555-559. https://doi.org/10.1007/s11738-013-1429-0

Reddy, P., Appel, R., Baum, B. R. 1990. Ribosomal DNA spacer-length variation in Secale ssp. (Poaceae). Plant Systematic Evolution, vol. 171, no. 4, p. 205-220. https://doi.org/10.1007/bf00940606

Saal, B., Wricke, G. 1999. Development of simple sequence repeat markers in rye (Secale cereale L.). Genome, vol. 42, no. 2, p. 964-972. https://doi.org/10.1139/gen-42-5-964 PMid:10584314

Sawant, S. V., Singh, P. K., Gupta, S. K., Madnala, R., Tuli, R. 1999. Conserved nucleotide sequences in highly expressed genes in plants. Journal of Genetics, vol. 78, no. 1, p. 123-131. https://doi.org/10.1007/bf02924562

Semagn, K., Bjornstad, A., Ndjiondjop, M. 2006. An overview of molecular marker methods for plants. African Journal of Biotechnology, vol. 5, no. 25, p. 2540-2568. https://doi.org/10.1007/7089_002

Shang, H., Wei, Y., Wang, X., Zheng, Y. 2006. Genetic diversity and phylogenetic relationships in the rye genus Secale L. (rye) based on Secale cereale microsatellite markers. Genetic Molecular Biology, vol. 29, no. 4, p. 685-691. https://doi.org/10.1590/s1415-47572006000400018

Schlegel, R., Meiz, G., Nestrowicz, R. 1987. A universal reference karyotype in rye, Secale cereale L. Theoretical Applied Genetic, vol. 74, no. 4, p. 820-826. https://doi.org/10.1007/bf00247563

Sujatha, M., Tarakeswari, M., Francis, G. 2013. Start codon targeted (SCoT) polymorphism in toxic and non-toxic accessions of Jatropha curcas L. and development of a codominant SCAR marker. Plant Science, vol. 207, no. 1, p. 117-127. https://doi.org/10.1016/j.plantsci.2013.02.013

Vences, F. J., Vaquero, F., Perez, de la Vega M. 1987. Phylogenetic relationship in Secale (Poaceae): an isozymatic study. Plant Systrmatic Evolution, vol. 157, no. 1, p. 33-47. https://doi.org/10.1007/bf00939179

Vivodík, M., Gálová, Z., Balážová, Ž. Petrovičová, L. 2016. Start codon targeted (scot) polymorphism reveals genetic diversity in European old maize (Zea mays L.) Genotypes. Potravinarstvo Slovak Journal of Food Sciences, vol. 10, no. 1, p. 563-569. https://doi.org/10.5219/660

Weber, J. L. 1990. Informativeness of human (dC-dA)n x (dG-dT)n polymorphism. Genomics, vol. 7, no. 4, p. 524-530. https://doi.org/10.1016/0888-7543(90)90195-z

Weir, B. S. 1990. Genetic data analysis. Sunderland, Massachusetts : Sinauer Associated, 1990, p. 445. ISBN 0878938710.

Xiong, F. Q., Zhong, R. C., Han, Z. Q., Jiang, J., He, L. Q., Zhuang, W. J., Tang, R. H. 2011. Start codon targeted polymorphism for evaluation of functional genetic variation and relationships in cultivated peanut (Arachis hypogaea L.) genotypes. Molecular Biology of Reproduction, vol. 38, no. 1, p. 3487-3494. https://doi.org/10.1007/s11033-010-0459-6

Xiong, F. Q., Tang, R. H., Chen, Z. L., Pan, L. H., Zhuang, W.J. 2009. SCoT: a novel gene targeted marker technique based on the translation start codon. Molecular Plant Breeding, vol. 7, no. 3, p. 635-638.

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Published

2017-04-11

How to Cite

Petrovičová, L. ., Balážová, Želmí­ra ., Vivodí­k, M. ., & Gálová, Z. . (2017). Detection genetic variability of secale cereale L. by scot markers. Potravinarstvo Slovak Journal of Food Sciences, 11(1), 197-202. https://doi.org/10.5219/726

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Vol. 11 No. 1 (2017): Potravinarstvo Slovak Journal of Food Sciences

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