SSAP Markers Based on a Novel Ty1-Copia Like Element Are a Powerful Tool for the Assessment of Genetic Diversity in Rye (Secale Cereale L.) Inbred Lines

Abstract

A partial sequence of a Ty1-copia retrotransposon was isolated from the genome of the rye (Secale cereale L.) inbred line L318 using degenerate primers targeted at the RNaseH sequence. Its putative 3’LTR region exhibited similarity to LTRs of known plant retrotransposons such as BARE-1, while no significant similarity to known rye retrotransposon sequences was found. A Sequence Specific Amplification Polymorphism (SSAP) protocol employing primer designed to correspond to the putative polypurine tract was developed and used for analysis of 30 rye inbred lines. Values of the parameters calculated to evaluate the efficiency of the method as well as the results of cluster analysis demonstrate that it is a powerful tool for genetic diversity analyses of rye.

Abbreviations

ISSR:

inter simple sequence repeat

LTR:

long terminal repeat

MI:

marker index

PIC:

polymorphic information content

SAMPL:

selective amplification of polymorphic microsatellite loci

SSAP:

sequence specific amplification polymorphism

SSR:

simple sequence repeat

References

  1. Acquardo, A., Portis, E., Mogila, A., Magurno, F., Lanteri, S. 2006. Retrotransposon-based S-SAP as a platform for the analysis of genetic variation and linkage in globe artichoke. Genome 49:1149–1159.

    Article  Google Scholar 

  2. Bartos, J., Paux, E., Kofler, R., Havránková, M., Kopecký, D., Suchánková, P., Safár, J., Simková, H., Town, C.D., Lelley, T., Feuillet, C., Dolezel, J. 2008. A first survey of the rye (Secale cereale) genome composition through BAC end sequencing of the short arm of chromosome 1R. BMC Plant Biol. 8:95.

    Article  Google Scholar 

  3. Bolibok, H., Rakoczy-Trojanowska, M., Hromada, A., Pietrzykowski, R. 2005. Efficiency of different PCR-based markers systems in assessing genetic diversity among winter rye (Secale cereale L.) inbred lines. Euphytica 146:109–116.

    CAS  Article  Google Scholar 

  4. Bolibok-Brbgoszewska, H., Heller-Uszymska, K., Wenzl, P., Uszymski, G., Kilian, A., Rakoczy-Trojanowska, M. 2009. DArT markers for the rye genome — genetic diversity and mapping. BMC Genomics 10:578.

    Article  Google Scholar 

  5. Chikmawati, T., Skovmand, B., Gustafson, J.P. 2005. Phylogenetic relationships among Secale species revealed by amplified fragment length polymorphisms. Genome 48:792–801.

    CAS  Article  Google Scholar 

  6. de la Puente, R., González, A.I., Ruiz, M.L., Polanco, C. 2008. Somaclonal variation in rye (Secale cereale L.) analyzed using polymorphic and sequenced AFLP markers. In Vitro Cell. Dev. Biol.-Plant 44:419–426.

    Article  Google Scholar 

  7. Ellis, T.H.N., Poyser, S.J., Knox, M.R., Vershinin, A.V., Ambrose, M.J. 1998. Polymorphism of insertion sites of Ty1-copia class retrotransposons and its use for linkage and diversity analysis in pea. Mol. Gen. Genet. 260:9–19.

    CAS  PubMed  Google Scholar 

  8. Flavell, R.B., Bennett, M.D., Smith, J.B., Smith, D.B. 1974. Genome size and the proportion of repeated nucleotide sequence DNA in plants. Biochem. Genet. 12:257–269.

    CAS  Article  Google Scholar 

  9. Galindo, L.M., Gaitán-Solís, E., Baccam, P., Thome, J. 2004. Isolation and characterization of Rnase LTR sequences of Ty1-copia retrotransposons in common bean (Phaseolus vulgaris L.). Genome 47:84–95.

    CAS  Article  Google Scholar 

  10. Ievina, B., Syed, N.H., Flavell, A.J., Ievinsh, G., Rostoks, N. 2010. Development of retrotransposon-based SSAP molecular marker system for study of genetic diversity in sea holly (Eryngium maritimum L.). Plant Genetic Resources: Characterisation and Utilisation 8:258–266.

    CAS  Article  Google Scholar 

  11. Isik, A., Parmaksiz, C., Coruh, C., Geylan-Su, Y.S., Cebeci, O., Beecher, B., Budak, H. 2007. Organellar genome analysis of rye (Secale cereale) representing diverse geographic regions. Genome 50:724–734.

    CAS  Article  Google Scholar 

  12. Konovalov, F.A., Goncharov, N.P., Goryunova, S., Shaturova, A., Proshlyakova, T., Kudryavtsev, A. 2010. Molecular markers based on LTR retrotransposons BARE-1 and Jeli uncover different strata of evolutionary relationships in diploid wheats. Mol. Genet. Genomics 283:551–563.

    CAS  Article  Google Scholar 

  13. Lou, Q., Chen, J. 2007. Ty1-copia retroptransposon-based SSAP marker development and its potential in the genetic study of cucurbits. Genome 50:802–810.

    CAS  Article  Google Scholar 

  14. Nagy, E.D., Lelley, T. 2003. Genetic and physical mapping of sequence-specific amplified polymorphic (SSAP) markers on the 1RS chromosome arm of rye in a wheat background. Theor. Appl. Genet. 107:1271–1277.

    CAS  Article  Google Scholar 

  15. Pearce, S.R., Harrison, G., Heslop-Harrison, P.J.S., Flavell, A.J., Kumar, A. 1997. Characterisation and genomic organization of Ty1-copia group retrotransposons in rye (Secale cereale). Genome 40:617–625.

    CAS  Article  Google Scholar 

  16. Pearce, S.R., Stuart-Rogers, C., Knox, M.R., Kumar, A., Ellis, T.H.N., Flavell, A.J. 1999. Rapid isolation of plant Ty1-copia group retrotransposon LTR sequences for molecular marker studies. Plant J. 19:711–717.

    CAS  Article  Google Scholar 

  17. Rohlf, F.J. 2001. NTSYS-pc Numerical Taxonomy and Multivariate Analysis System, Version 2.1. Exeter, Setauket, NY.

  18. Syed, N.H., Sureshsundar, A., Wilkinson, M.J., Bhau, B.S., Cavalcanti, J.J.V., Flavell, A.J. 2005. Ty1-copia retrotransposon-based SSAP marker development in cashew (Anacardium occidentale L.). Theor. Appl. Genet. 110:1195–1202.

    CAS  Article  Google Scholar 

  19. Tam, S.M., Mhiri, C., Vogelaar, A., Kerveld, M., Pearce, S.R., Grandbastien, M.A. 2005. Comparative analyses of genetic diversities within tomato and pepper collections detected by retrotrnsposon-based SSAP, AFLP and SSR. Theor. Appl. Genet. 110:819–831.

    CAS  Article  Google Scholar 

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Correspondence to H. Bolibok-Brbągoszewska.

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Bolibok-Brbągoszewska, H., Zabierzewska, N., Hromada-Judycka, A. et al. SSAP Markers Based on a Novel Ty1-Copia Like Element Are a Powerful Tool for the Assessment of Genetic Diversity in Rye (Secale Cereale L.) Inbred Lines. CEREAL RESEARCH COMMUNICATIONS 40, 204–209 (2012). https://doi.org/10.1556/CRC.40.2012.2.4

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Keywords

  • genetic diversity
  • molecular markers
  • retrotransposon
  • rye
  • SSAP
  • Secale cereale
  • Ty1-copia