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Development of the St/J and V Genome Specific Molecular Marker Based on 5s rDNA Polymorphism in Thinopyrum bessarabicum, Pseudoroegneria spicata, and Dasypyrum villosum

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Nontranscribed spacers (NTS) of 5S rDNA are often polymorphic in closely related species and even in the same genome. The polymorphism of 5S rDNA NTS was shown between genomes St, J, and V of Triticeae species Thinopyrum bessarabicum, Pseudoroegneria spicata, and Dasypyrum villosum, respectively. A molecular genetic marker was designed based on the 5S rDNA NTS polymorphism that allows identification of the St, J, and V genomes. We designed a pair of primers that correspond to the conserved regions of 5S rDNA NTS between the genomes studied. The PCR amplicon length is 158 bp, 171 bp, and 172 bp for V, St, and J genomes, respectively. The fragment of the St genome is characterized by the SmiM I restriction site that enables its differentiation from the J genome fragment that lacks this site. The developed marker showed its efficiency for verification of germplasm accessions and the study of allopolyploids.

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  1. Wicke, S., Costa, A., Muñoz, J., and Quandt, D., Restless 5S: The re-arrangement(s) and evolution of the nuclear ribosomal DNA in land plants, Mol. Phylogenet. Evol., 2011, vol. 61, no. 2, pp. 321–332.

    Article  CAS  PubMed  Google Scholar 

  2. Yang, Y.W., Tseng, P.F., Tai, P.Y., and Chang, Ch.J., Phylogenetic position of Raphanus in relation to Brassica species based on 5S rRNA spacer sequence data, Bot. Bull. Acad. Sin., 1998, vol. 39, no. 3, pp. 153–160.

    CAS  Google Scholar 

  3. Brown, G.R. and Carlson, J.E., Molecular cytogenetics of the genes encoding 18s-5.8s-26s rRNA and 5s rRNA in two species of spruce (Picea), Theor. Appl. Genet., 1997, vol. 95, nos. 1–2, pp. 1–9.

    Article  CAS  Google Scholar 

  4. Liu, Z.L., Zhang, D., Wang, X.Q., Ma, X.F., and Wang, X.R., Intragenomic and interspecific 5S rDNA sequence variation in five Asian pines, Am. J. Bot., 2003, vol. 90, no. 1, pp. 17–24.

    Article  CAS  PubMed  Google Scholar 

  5. Matyácek, R., Fulnecek, J., Lim, K.Y., Leitch, A.R., and Kovarik, A., Evolution of 5S rDNA unit arrays in the plant genus Nicotiana (Solanaceae), Genome, 2002, vol. 45, no. 3, pp. 556–562.

    Article  PubMed  Google Scholar 

  6. Baum, B.R., Edwards, T., and Johnson, D.A., Codependence of repetitive sequence classes in genomes: Phylogenetic analysis of 5S rDNA families in Hordeum (Triticeae: Poaceae), Genome, 2010, vol. 53, no. 3, pp. 180–202.

    Article  CAS  PubMed  Google Scholar 

  7. Bertea, C.M. and Gnavi, G., Restriction fragment length polymorphism of the 5S-rRNA-NTS region: A rapid and precise method for plant identification, in Plant DNA Fingerprinting and Barcoding. Methods in Molecular Biology, Sucher, N., Hennell, J., and Carles, M., Eds., 2012, vol. 862, pp. 89–101.

    Article  CAS  Google Scholar 

  8. Middleton, C.P., Senerchia, N., Stein, N., Akhunov, E.D., Keller, B., Wicker, T., and Kilian, B., Sequencing of chloroplast genomes from wheat, barley, rye and their relatives provides a detailed insight into the evolution of the Triticeae tribe, PLoS ONE, 2014, vol. 9, no. 3, p. e85761.

    Article  PubMed  PubMed Central  Google Scholar 

  9. Kroupin, P.Y., Divashuk, M.G., Belov, V.I., Glukhova, L.I., Aleksandrov, O.S., and Karlov, G.I., Comparative molecular cytogenetic characterization of partial wheat-wheatgrass hybrids, Russ. J. Genet., 2011, vol. 47, no. 4, pp. 432–437.

    Article  CAS  Google Scholar 

  10. Salina, E.A., Adonina, I.G., Badaeva, E.D., Kroupin, P.Y., Stasyuk, A.I., Leonova, I.N., Shishkina, A.A., Divashuk, M.G., Starikova, E.V., Khuat, T.M.L., Syukov, V.V., and Karlov, G.I., A Thinopyrum intermedium chromosome in bread wheat cultivars as a source of genes conferring resistance to fungal diseases, Euphytica, 2015, vol. 204, no. 1, pp. 91–101.

    Article  CAS  Google Scholar 

  11. Divashuk, M.G., Khuat, T.M.L., Kroupin, P.Yu., Kirov, I.V., Romanov, D.V., Kiseleva, A.V., Khrustaleva, L.I., Alexeev, D.G., Zelenin, A.S., Klimushina, M.V., Razumova, O.V., and Karlov, G.I., Variation in copy number of Ty3/Gypsy centromeric retrotransposons in the genomes of Thinopyrum intermedium and its diploid progenitors, PLoS ONE, 2016, vol. 11, no. 4, p. e0154241.

    Article  PubMed  PubMed Central  Google Scholar 

  12. Kocheshkova, A.A., Kroupin, P.Y., Bazhenov, M.S., Karlov, G.I., Pochtovyy, A.A., Upelniek, V.P., Belov, V.I., and Divashuk, M.G., Pre-harvest sprouting resistance and haplotype variation of ThVp-1 gene in the collection of wheat-wheatgrass hybrids, PLoS ONE, 2017, vol. 12, no. 11, p. e0188049.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Sibikeev, S.N., Badaeva, E.D., Gultyaeva, E.I., Druzhin, A.E., Shishkina, A.A., Dragovich, A.Y., Kroupin, P.Y., Karlov, G.I., Khuat, T.M., and Divashuk, M.G., Comparative analysis of Agropyron intermedium (Host) Beauv 6Agi and 6Agi2 chromosomes in bread wheat cultivars and lines with wheatwheatgrass substitutions, Russ. J. Genet., 2017, vol. 53, no. 3, pp. 314–324.

    Article  CAS  Google Scholar 

  14. Löve, A., Conspectus of the Triticeae, Fedd. Rep., 1984, vol. 95, nos 7-8, pp. 425–521.

    Google Scholar 

  15. Okito, P., Mott, I.W., Wu, Y., and Wang, R.R.C., A Y genome specific STS marker in Pseudoroegneria and Elymus species (Triticeae: Gramineae), Genome, 2009, vol. 52, no. 4, pp. 391–400.

    Article  CAS  PubMed  Google Scholar 

  16. Wei, J.Zh. and Wang, R.R.C., Genome-and speciesspecific markers and genome relationships of diploid perennial species in Triticeae based on RAPD analyses, Genome, 1995, vol. 38, no. 6, pp. 1230–1236.

    Article  CAS  PubMed  Google Scholar 

  17. Li, X.M., Lee, B.S., Mammadov, A.C., Koo, B.C., Mott, I.W., and Wang, R.R.C., CAPS markers specific to Eb, Ee and R genomes in the tribe Triticeae, Genome, 2007, vol. 50, no. 4, pp. 400–411.

    Article  CAS  PubMed  Google Scholar 

  18. Hu, L., Li, G., Zhan, H., Liu, C., and Yang, Z., New St-chromosome-specific molecular markers for identifying wheat–Thinopyrum intermedium derivative lines, J. Genet., 2014, vol. 93, no. 1, pp. 69–74.

    Article  Google Scholar 

  19. Zhang, J., Long, H., Pan, Z., Liang, J., Yu, S., Deng, G., and Yu, M., Characterization of a genome-specific Gypsy-like retrotransposon sequence and development of a molecular marker specific for Dasypyrum villosum (L.), J. Genet., 2013, vol. 92, no. 1, pp. 103–108.

    Article  PubMed  Google Scholar 

  20. Doyle, J.J., Doyle, J.L., and Hortoriun, L.B., Isolation of plant DNA from fresh tissue, Focus, 1990, vol. 12, no. 1, pp. 13–15.

    Google Scholar 

  21. GeneDoc: Analysis and visualization of genetic variation. Cited November 21, 2017.

  22. Chen, Q., Conner, R.L., Laroche, A., and Thomas, J.B., Genome analysis of Thinopyrum intermedium and Thinopyrum ponticum using genomic in situ hybridization, Genome, 1998, vol. 41, no. 4, pp. 580–586.

    Article  CAS  PubMed  Google Scholar 

  23. Mahelka, V., Kopecký, D., and Paštová, L., On the genome constitution and evolution of intermediate wheatgrass (Thinopyrum intermedium: Poaceae, Triticeae), BMC Evol. Biol., 2011, vol. 11, no. 1, p.127.

    Article  PubMed  PubMed Central  Google Scholar 

  24. Deng, C.L., Bai, L.L., Fu, S.L., Yin, W.B., Zhang, Y.X., Chen, Y.H., Wang, R.R.C., Zhang, X.Q., Han, F.P., and Hu, Z.M., Microdissection and chromosome painting of the alien chromosome in an addtition line of wheat–Thinopyrum intermedium, PLoS ONE, 2013, vol. 8, no. 8, p. e72564.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Khuat, Th.M.L., Divashuk, M.G., Kroupin, P.Yu., Nguyen, P.A., Kiseleva, A.V., and Karlov, G.I., Differences in ploidy level and genome constitution revealed by cytogenetic analysis of Pseudoroegneria germplasm accessions: Case study, Izv. Timiryazevsk. S-kh. Akad., 2015, no. 2, pp. 29–35.

    Google Scholar 

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Correspondence to O. S. Alexandrov.

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Original Russian Text © O.S. Alexandrov, M.G. Divashuk, G.I. Karlov, 2018, published in Vestnik Moskovskogo Universiteta, Seriya 16: Biologiya, 2018, Vol. 73, No. 1, pp. 22–28.

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Alexandrov, O.S., Divashuk, M.G. & Karlov, G.I. Development of the St/J and V Genome Specific Molecular Marker Based on 5s rDNA Polymorphism in Thinopyrum bessarabicum, Pseudoroegneria spicata, and Dasypyrum villosum. Moscow Univ. Biol.Sci. Bull. 73, 18–23 (2018).

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