Molecular Genetics and Genomics

, Volume 271, Issue 1, pp 91–97 | Cite as

Retrotransposon-based molecular markers for linkage and genetic diversity analysis in wheat

  • R. A. Queen
  • B. M. Gribbon
  • C. James
  • P. Jack
  • A. J. Flavell
Original Paper


Retrotransposon-based molecular markers have been developed to study bread wheat ( Triticum aestivum) and its wild relatives. SSAP (Sequence-Specific Amplification Polymorphism) markers based on the BARE-1/ Wis-2-1A retrotransposons were assigned to T. aestivum chromosomes by scoring nullisomic-tetrasomic chromosome substitution lines. The markers are distributed among all wheat chromosomes, with the lowest proportion being assigned the D wheat genome. SSAP markers for BARE-1/ Wis-2-1A and three other wheat retrotransposons, Thv19 , Tagermina and Tar1, are broadly distributed on a wheat linkage map. Polymorphism levels associated with these four retrotransposons vary, with BARE-1/ Wis-2-1A and Thv19 both showing approximately 13% of bands polymorphic in a mapping population, Tagermina showing approximately 17% SSAP band polymorphism and Tar1 roughly 18%. This suggests that Tagermina and Tar1 have been more transpositionally active in the recent evolutionary past, and are potentially the more useful source of molecular markers in wheat. Lastly, BARE-1 / Wis-2-1A markers have also been used to characterise the genetic diversity among a set of 35 diploid and tetraploid wheat species including 26 Aegilops and 9 Triticum accessions. The SSAP-based diversity tree for Aegilops species agrees well with current classifications, though the Triticum tree shows several significant differences, which may be associated with polyploidy in this genus.


Retrotransposon Transposable element  Triticum aestivum  copia 


  1. Casa AM, Brouwer C, Nagel A, Wang L, Zhang Q, Kresovich S, Wessler SR (2000) The MITE family Heartbreaker ( Hbr): molecular markers in maize. Proc Natl Acad Sci USA 97:10083–10089CrossRefPubMedGoogle Scholar
  2. Ellis THN, Poyser SJ, Knox MR, Vershinin AV, Ambrose MJ (1998) Ty1- copia class retrotransposon insertion site polymorphism for linkage and diversity analysis in pea. Mol Gen Genet 260:9–19PubMedGoogle Scholar
  3. Flavell AJ, Dunbar E, Anderson R, Pearce SR, Hartley R, Kumar A (1992a) Ty1- copia group retrotransposons are ubiquitous and heterogeneous in higher plants. Nucleic Acids Res 20:3639–3644PubMedGoogle Scholar
  4. Flavell AJ, Smith DB, Kumar A (1992b) Extreme heterogeneity of Ty- copia group retrotransposons in plants. Mol Gen Genet 231:233–242PubMedGoogle Scholar
  5. Gribbon BM, Pearce SR, Kalendar, R Schulman AH, Paulin L, Jack P, Kumar A, Flavell AJ (1999) Phylogeny and transpositional activity of Ty1- copia group retrotransposons in cereal genomes. Mol Gen Genet 261:883–891PubMedGoogle Scholar
  6. Kalendar R, Grob T, Regina M, Suoniemi A, Schulman A (1999) IRAP and REMAP: two new retrotransposon-based fingerprinting techniques. Theor Appl Genet 98:704–711Google Scholar
  7. Kellogg EA, Appels R, Mason-Gamer RJ (1996) When genes tell different stories: the diploid genera of Triticeae (Gramineae). Syst Bot 21:321–347Google Scholar
  8. Konieczny A, Voytas DF, Cummings MP, Ausubel FM (1991) A superfamily of Arabidopsis thaliana retrotransposons. Genetics 127:801–809PubMedGoogle Scholar
  9. Kubis SE, Heslop-Harrison JS, Desel C, Schmidt T (1998) The genomic organization of non-LTR retrotransposons (LINEs) from three Beta species and five other angiosperms. Plant Mol Biol 36:821–831CrossRefPubMedGoogle Scholar
  10. Lane BG, Bernier F, Dratewka-Kos E, Shafai R, Kennedy TD, Caron P, Munro JR, Vaughan T, Walters D, Altomare F (1991) Homologies between members of the germin gene family in hexaploid wheat and similarities between these wheat germins and certain Physarum spherulins. J Biol Chem 266:10461–10469PubMedGoogle Scholar
  11. Manninen I, Schulman A (1993) BARE-1, a copia -like retroelement in barley ( Hordeum vulgare L.) Plant Mol Biol: 22:829–846Google Scholar
  12. Matsuoka Y, Tsunewaki K (1997) Presence of wheat retrotransposons in Gramineae species and the origin of wheat retrotransposon families. Genes Genet Systems 72:335–343CrossRefGoogle Scholar
  13. Moore G, Lucas H, Batty N, Flavell RB (1991) A family of retrotransposons and associated genomic variation in wheat. Genomics 10:461–468PubMedGoogle Scholar
  14. Pearce SR, Harrison G, Li D, Heslop-Harrison JS, Kumar A, Flavell AJ (1996) The Ty1- copia group retrotransposons in Vicia species: copy number, sequence heterogeneity and chromosomal localisation. Mol Gen Genet 250:305–315CrossRefPubMedGoogle Scholar
  15. Pearce SR, Harrison G, Heslop-Harrison JS, Flavell AJ, Kumar A (1997) Characterisation and genomic organisation of Ty1- copia group retrotransposons in rye ( Secale cereale) Genome 40:617–625Google Scholar
  16. Pearce SR, Knox MR, Ellis THN, Flavell AJ, Kumar A (2000) Pea Ty1-copia group retrotransposons: transpositional activity and use as markers to study genetic diversity in Pisum. Mol Gen Genet 263:898–907PubMedGoogle Scholar
  17. Porceddu A, Albertini E, Barcaccia G, Marconi G, Bertoli FB, Veronesi F (2002) Development of S-SAP markers based on an LTR-like sequence from Medicago sativa L. Mol Genet Genomics 267:107–114PubMedGoogle Scholar
  18. SanMiguel P, Tikhonov A, Jin Y-K, Motchoulskaia N, Zakharov D, Melake-Berhan A, Springer PS, Edwards KJ, Lee M, Avramova Z, Bennetzen JL (1996) Nested retrotransposons in the intergenic regions of the maize genome. Science 274:765–768PubMedGoogle Scholar
  19. SanMiguel P, Gaut BS, Tikhonov A, Nakijama Y and Bennetzen JL (1998) The paleontology of intergene retrotransposons of maize. Nat Genet 20:43–45PubMedGoogle Scholar
  20. Sasanuma T, Miyashita NT, Tsunewaki K (1996) Wheat phylogeny determined by RFLP analysis of nuclear DNA. 3. Intra- and interspecific variations of five Aegilops sitopsis species. Theor Appl Genet 92:928–934CrossRefGoogle Scholar
  21. Stam P, van Coijen JW (1993) Joinmap (version 2.0): software for the calculation of genetic linkage maps. CPRO-DLO, Wageningen (available at
  22. Suoniemi A, Tanskanen J, Schulman AH (1998) Gypsy -like retrotransposons are widespread in the plant kingdom. Plant J 13:699–705PubMedGoogle Scholar
  23. Swofford DL (1998) PAUP: Phylogenetic Analysis Using Parsimony. Sinauer Associates, Sunderland, Mass.Google Scholar
  24. Van Deynze AE, Dubcovsky J, Gill KS, Nelson JC, Sorrells ME, Dvorak J, Gill BS, Lagudah ES, McCouch SR and Appels R (1995) Molecular-genetic maps for group 1 chromosomes of Triticeae species and their relation to chromosomes in rice and oat. Genome 38:45–59Google Scholar
  25. Van Slageren MW (1994) Wild wheats: a monograph of Aegilops L. and Amblyopyrum (Jaub & Spach) Eig Wageningen Agric Univ PapGoogle Scholar
  26. Voytas DF, Cummings MP, Konieczny A, Ausubel FM, Rodermel SR (1992) copia -like retrotransposons are ubiquitous among plants. Proc Natl Acad Sci USA 89:7124–7128PubMedGoogle Scholar
  27. Wang G-Z, Miyashita NT, Tsunewaki K (1997) Plasmon analyses of Triticum (wheat) and Aegilops: PCR-single-strand conformational polymorphism (PCR-SSCP) analyses of organellar DNAs Proc Natl Acad Sci USA 94:14570–14577Google Scholar
  28. Waugh R, McLean K, Flavell AJ, Pearce SR, Kumar A, Thomas BT, Powell W (1997) Genetic distribution of BARE-1 retrotransposable elements in the barley genome revealed by sequence-specific amplification polymorphisms (S-SAP). Mol Gen Genet 253:687–694CrossRefPubMedGoogle Scholar
  29. Yu GX, Wise RP (2000) An anchored AFLP- and retrotransposon-based map of diploid Avena. Genome 43:736–749CrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2004

Authors and Affiliations

  • R. A. Queen
    • 1
  • B. M. Gribbon
    • 1
  • C. James
    • 2
  • P. Jack
    • 2
  • A. J. Flavell
    • 1
  1. 1.Plant Research UnitUniversity of Dundee at SCRIDundeeUK
  2. 2.Monsanto plcCambridgeUK

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