Triticeae Genome Structure and Evolution

Part of the Plant Genetics and Genomics: Crops and Models book series (PGG, volume 7)


Repeated nucleotide sequences are by far the largest component of Triticeae genomes, accounting for about 90% of the nuclear DNA. Tandem repeated sequences play an important role in chromosome function during mitosis and meiosis. Interspersed repeated sequences fill the intergenic regions. The most remarkable attribute of this component is its unprecedented rate of turnover, which is in stark contrast to the stability of gene content. The term “gene order paradox” is coined to reflect this dichotomy. A model is proposed postulating the existence of two strata in Triticeae genomes, “conservative” and “dynamic” to account for this paradox and its evolutionary causes. Numerous aspects of gene content in Triticeae genomes, such as the location of single-copy genes, multi-gene loci, gene deletions and duplications, gene density, restriction fragment length polymorphism and single nucleotide polymorphism, location of novel and lineage-specific genes, and the level of synteny, correlate with recombination rate and gene location on the centromere-telomere axis. Special attention is devoted to the discussion of gene distribution along chromosomes. It is pointed out that evidence for the existence of gene-rich islands is weak. A model accounting for correlation between gene density and recombination rate is proposed. It is suggested that the vast amounts of repeated sequences in Triticeae genomes play a role in the evolution of new genes and in adaptation.


Bacterial Artificial Chromosome Wheat Chromosome Subtelomeric Region Triticeae Species Ectopic Recombination 



The author is grateful to Patrick E. McGuire and Karin R. Deal for reading the manuscript and making valuable suggestions.


  1. Akhunov, E.D., Akhunov, A.R., Linkiewicz, A.M., Dubcovsky, J., Hummel, D., Lazo, G., Chao, S., Anderson, O.D., David, J., Qi, L.L., Echalier, B., Gill, B.S., Miftahudin, Gustafson, J.P., La Rota, M., Sorrells, M.E., Zhang, D., Nguyen, H.T., Kalavacharla, V., Hossain, K., Kianian, S., Peng, J., Lapitan, N.L.V., Wennerlind, E.J., Nduati, V., Anderson, J.A., Sidhu, D., Gill, K., McGuire, P.E., Qualset, C.O. and Dvořák, J. (2003a) Synteny perturbations between wheat homoeologous chromosomes by locus duplications and deletions correlate with recombination rates along chromosome arms. Proc. Natl. Acad. Sci. USA 100, 10836–10841.Google Scholar
  2. Akhunov, E.D., Goodyear, J.A., Geng, S., Qi, L.-L., Echalier, B., Gill, B.S., Miftahudin, Gustafson, J.P., Lazo, G., Chao, S., Anderson, O.D., Linkiewicz, A.M., Dubcovsky, J., La Rota, M., Sorrells, M.E., Zhang, D., Nguyen, H.T., Kalavacharla, V., K., H., Kianian, S.F., Peng, J., Lapitan, N.L.V., Gonzalez-Hernandez, J.L., Anderson, J.A., Choi, D.-W., Close, T.J., Dilbirligi, M., Gill, K.S., Walker-Simmons, M.K., Steber, C., McGuire, P.E., Qualset, C.O. and Dvořák, J. (2003b) The organization and rate of evolution of the wheat genomes are correlated with recombination rates along chromosome arms. Genome Res. 13, 753–763.Google Scholar
  3. Akhunov, E.D., Akhunova, A.R. and Dvořák, J. (2005) BAC libraries of Triticum urartu, Aegilops speltoides and Ae. tauschii, the diploid ancestors of polyploid wheat. Theor. Appl. Genet. 111, 1617–1622.PubMedCrossRefGoogle Scholar
  4. Akhunov, E.D., Akhunova, A.R. and Dvořák, J. (2007a) Mechanisms and rates of birth and death of dispersed duplicated genes during the evolution of a multigene family in diploid and tetraploid wheats. Mol. Biol. Evol. 24, 539–550.Google Scholar
  5. Akhunov, E.D., Akhunova, A.R., Saini, B., Grishina, I., Morrell, P.L., Toleno, D., Clegg, M.T. and Dvořák, J. (2007b) Genetic diversity of diploid ancestors of wheat. Plant and Animal Genome XV, San Diego, CA, pp. 168.Google Scholar
  6. Alkhimova, O.G., Mazurok, N.A., Potapova, T.A., Zakian, S.M., Heslop-Harrison, J.S. and Vershinin, A.V. (2004) Diverse patterns of the tandem repeats organization in rye chromosomes. Chromosoma 113, 42–52.PubMedCrossRefGoogle Scholar
  7. Amor, D.J., Kalitsis, P., Sumer, H. and Choo, K.H.A. (2004) Building the centromere: from foundation proteins to 3D organization. Trends in Cell Biol. 14, 359–368.CrossRefGoogle Scholar
  8. Anamthawat-Jonsson, K., Schwarzacher, T., Leitch, A.R., Bennett, M.D. and Heslop-Harrison, J.S. (1990) Discrimination between closely related species using genomic DNA as a probe. Theor. Appl. Genet. 79, 721–728.CrossRefGoogle Scholar
  9. Anamthawat-Jonsson, K. and Heslop-Harrison, J.S. (1993) Isolation and characterization of genome-specific DNA sequences in Triticeae species. Mol. Gen. Genet. 240, 151–158.PubMedCrossRefGoogle Scholar
  10. Appels, R., Driscoll, C. and Peacock, W.J. (1978) Heterochromatin and highly repeated DNA sequences in rye (Secale cereale). Chromosoma 70, 67–89.CrossRefGoogle Scholar
  11. Appels, R., Gerlach, W.L., Dennis, E.S., Swift, H. and Peacock, W.J. (1980) Molecular and chromosomal organization of DNA sequences coding for the ribosomal RNAs in cereals. Chromosoma 78, 293–311.CrossRefGoogle Scholar
  12. Appels, R., Dennis, E.S., Smyth, D.R. and Peacock, W.J. (1981) Two repeated DNA-sequences from the heterochromatic regions of rye (Secale cereale) chromosomes. Chromosoma 84, 265–277.CrossRefGoogle Scholar
  13. Appels, R. and Dvořák, J. (1982) The wheat ribosomal DNA spacer: its structure and variation in populations and among species. Theor. Appl. Genet. 63, 337–348.CrossRefGoogle Scholar
  14. Appels, R. and Moran, L.B. (1984) Molecular analysis of alien chromatin introduced into wheat. In: P.J. Gustafson (Ed.), Stadler Genetics Symposia. University of Missouri, Columbia, MO, pp. 529–557.Google Scholar
  15. Appels, R. and Honeycutt, R.L. (1986) rDNA: evolution over a billion years. In: S.K. Dutta (Ed.), DNA Systematics. CRC Press, Florida, pp. 81–135.Google Scholar
  16. Appels, R., Reddy, P., McIntyre, C.L., Moran, L.B., Frankel, O.H. and Clarke, B.C. (1989) The molecular-cytogenetic analysis of grasses and its application to studying relationships among species Triticeae. Genome 31, 122–133.PubMedCrossRefGoogle Scholar
  17. Aragon-Alcaide, L., Miller, T., Schwarzacher, T., Reader, S. and Moore, G. (1996) A cereal centromeric sequence. Chromosoma 105, 261–268.PubMedCrossRefGoogle Scholar
  18. Arumuganathan, K. and Earle, E.D. (1991) Nuclear DNA content of some important plant species. Plant Mol. Biol. Rep. 9, 208–218.CrossRefGoogle Scholar
  19. Bedbrook, J.R., Jones, J., O'Dell, M., Thompson, R.D. and Flavell, R.B. (1980) A molecular description of telomeric heterochromatin in Secale species. Cell 19, 545–560.PubMedCrossRefGoogle Scholar
  20. Belostotsky, D.A. and Ananiev, E.V. (1990) Characterization of relic DNA from barley genome. Theor. Appl. Genet. 80, 374–380.CrossRefGoogle Scholar
  21. Bennett, M.D. (1972) Nuclear DNA content and minimum generation time in herbaceous plants. Proc. Royal Soc. Lond. B 181, 109–135.CrossRefGoogle Scholar
  22. Bennett, M.D. and Smith, J.B. (1976) Nuclear DNA amounts in angiosperms. Phil. Trans. Royal Soc. Lond. Ser. B, Biol. Sci. 274, 227–274.CrossRefGoogle Scholar
  23. Bennett, M.D., Gustafson, J.P. and Smith, J.B. (1977) Variation in nuclear DNA in genus Secale. Chromosoma 61, 149–176.CrossRefGoogle Scholar
  24. Bennetzen, J.L. and Kellogg, E.A. (1997) Do plants have a one-way ticket to genomic obesity? Plant Cell 9, 1509–1514.PubMedCrossRefGoogle Scholar
  25. Bernard, P., Maure, J.F., Partridge, J.F., Genier, S., Javerzat, J.P. and Allshire, R.C. (2001) Requirement of heterochromatin for cohesion at centromeres. Science 294, 2539–2542.PubMedCrossRefGoogle Scholar
  26. Blackburn, E.H. (1986) Structure and formation of telomeres in Holotrichous Ciliates. Internatl. Rev. Cytol. 99, 29–47.CrossRefGoogle Scholar
  27. Brandes, A., Roder, M.S. and Ganal, M.W. (1995) Barley telomeres are associated with two different types of satellite DNA-sequences. Chromosome Res. 3, 315–320.PubMedCrossRefGoogle Scholar
  28. Bureau, T.E. and Wessler, S.R. (1994) Mobile inverted-repeat elements of the tourist family are associated with the genes of many cereal grasses. Proc. Natl. Acad. Sci. USA 91, 1411–1415.PubMedCrossRefGoogle Scholar
  29. Castilho, A. and Heslop-Harrison, J.S. (1995) Physical mapping of 5S and 18S-25S rDNA and repetitive DNA sequences in Aegilops umbellulata. Genome 38, 91–96.PubMedCrossRefGoogle Scholar
  30. Chantret, N., Salse, J., Sabot, F., Rahman, S., Bellec, A., Laubin, B., Dubois, I., Dossat, C., Sourdille, P., Joudrier, P., Gautier, M.F., Cattolico, L., Beckert, M., Aubourg, S., Weissenbach, J., Caboche, M., Bernard, M., Leroy, P. and Chalhoub, B. (2005) Molecular basis of evolutionary events that shaped the hardness locus in diploid and polyploid wheat species (Triticum and Aegilops). Plant Cell 17, 1033–1045.PubMedCrossRefGoogle Scholar
  31. Cheng, Z.J. and Murata, M. (2003) A centromeric tandem repeat family originating from a part of Ty3/gypsy retroelement in wheat and its relatives. Genetics 164, 665–672.PubMedGoogle Scholar
  32. Cheung, W.Y., Money, T.A., Abbo, S., Devos, K.M., Gale, M.D. and Moore, G. (1994) A family of related sequences associated with (TTTAGGG)n repeats are located in the interstitial regions of wheat chromosomes. Mol. Gen. Genet. 245, 349–354.PubMedCrossRefGoogle Scholar
  33. Cohen, S., Yacobi, K. and Segal, D. (2003) Extrachromosomal circular DNA of tandemly repeated genomic sequences in Drosophila. Genome Res. 13, 1133–1145.PubMedCrossRefGoogle Scholar
  34. Conrad, M.N., Lee, C.Y., Wilkerson, J.L. and Dresser, M.E. (2007) MPS3 mediates meiotic bouquet formation in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 104, 8863–8868.PubMedCrossRefGoogle Scholar
  35. Crosby, A.R. (1957) Nucleolar activity of lagging chromosomes in wheat. Amer. J. Bot. 44, 813–822.CrossRefGoogle Scholar
  36. Cuadrado, A., Schwarzacher, T. and Jouve, N. (2000) Identification of different chromatin classes in wheat using in situ hybridization with simple sequence repeat oligonucleotides. Theor. Appl. Genet.101, 711–717.CrossRefGoogle Scholar
  37. Cuadrado, A. and Jouve, N. (2007) The nonrandom distribution of long clusters of all possible classes of trinucleotide repeats in barley chromosomes. Chromos. Res. 15, 711–720.CrossRefGoogle Scholar
  38. Dennis, E.S., Gerlach, W.L. and Peacock, W.J. (1980) Identical polypyrimidine-polypurine satellite DNAs in wheat and barley. Heredity 44, 344–366.CrossRefGoogle Scholar
  39. Devos, K.M., Brown, J.K.M. and Bennetzen, J.L. (2002) Genome size reduction through illegitimate recombination counteracts genome expansion in Arabidopsis. Genome Res. 12, 1075–1079.PubMedCrossRefGoogle Scholar
  40. Devos, K.M., Ma, J.X., Pontaroli, A.C., Pratt, L.H. and Bennetzen, J.L. (2005) Analysis and mapping of randomly chosen bacterial artificial chromosome clones from hexaploid bread wheat. Proc. Natl. Acad. Sci. USA 102, 19243–19248.PubMedCrossRefGoogle Scholar
  41. Dubcovsky, J. and Dvořák, J. (1995) Ribosomal RNA loci: nomads in the Triticeae genomes. Genetics 140, 1367–1377.PubMedGoogle Scholar
  42. Dubcovsky, J., Luo, M.C., Zhong, G.Y., Bransteitter, R., Desai, A., Kilian, A., Kleinhofs, A. and Dvořák, J. (1996) Genetic map of diploid wheat, Triticum monococcum L., and its comparison with maps of Hordeum vulgare L. Genetics 143, 983–999.PubMedGoogle Scholar
  43. Dubcovsky, J. and Dvořák, J. (2007) Genome plasticity a key factor in the success of polyploid wheat under domestication. Science 316, 1862–1866.PubMedCrossRefGoogle Scholar
  44. Dvořák, J. and Fowler, D.B. (1978) Cold hardiness potential of triticale and tetraploid rye. Crop Sci. 17, 477–478.CrossRefGoogle Scholar
  45. Dvořák, J. and Appels, R. (1982) Chromosomal and nucleotide sequence differentiation in genomes of polyploid Triticum species. Theor. Appl. Genet. 63, 349–360.CrossRefGoogle Scholar
  46. Dvořák, J. and Chen, K.-C. (1984) Distribution of nonstructural variation between wheat cultivars along chromosome arm 6Bp: evidence from the linkage map and physical map of the arm. Genetics 106, 325–333.PubMedGoogle Scholar
  47. Dvořák, J., Lassner, M.W., Kota, R.S. and Chen, K.C. (1984a) The distribution of the ribosomal RNA genes in the Triticum speltoides and Elytrigia elongata genomes. Can. J. Genet. Cytol. 26, 628–632.Google Scholar
  48. Dvořák, J., McGuire, P.E. and Mendlinger, S. (1984b) Inferred chromosome morphology of the ancestral genome of Triticum. Plant Syst. Evol. 144, 209–220.Google Scholar
  49. Dvořák, J. and Appels, R. (1986) Investigation of homologous crossing over and sister chromatid exchange in the wheat Nor-2 locus coding for rRNA and Gli-B2 locus coding for gliadins. Genetics 113, 1037–1056.PubMedGoogle Scholar
  50. Dvořák, J., Zhang, H.B., Kota, R.S. and Lassner, M. (1989) Organization and evolution of the 5S ribosomal RNA gene family in wheat and related species. Genome 32, 1003–1016.CrossRefGoogle Scholar
  51. Dvořák, J. and Zhang, H.B. (1990) Variation in repeated nucleotide sequences sheds light on the phylogeny of the wheat B and G genomes. Proc. Natl. Acad. Sci. USA 87, 9640–9644.PubMedCrossRefGoogle Scholar
  52. Dvořák, J., Luo, M.-C. and Yang, Z.-L. (1998) Restriction fragment length polymorphism and divergence in the genomic regions of high and low recombination in self-fertilizing and cross-fertilizing Aegilops species. Genetics 148, 423–434.PubMedGoogle Scholar
  53. Dvořák, J., Akhunov, A.D., Akhunov, A.R., Luo, M.C., Linkiewicz, A.M., Dubcovsky, J., Hummel, D., Lazo, G., Chao, S., Anderson, O.D., David, J., Qi, L.L., Echalier, B., Gill, B.S., Miftahudin, Gustafson, J.P., La Rota, M., Sorrells, M.E., Zhang, D., Nguyen, H.T., Kalavacharla, V., Hossain, K., Kianian, S.F., Peng, J.H., Lapitan, N.L.V., Wennerlind, E.J., Nduati, V., Anderson, J.A., Sidhu, D., Gill, K.S., Choi, D.-W., Close, T.J., McGuire, P.E. and Qualset, C.O. (2003) New insights into the organization and evolution of wheat genomes. In: N.E. Pogna, M. Romano, E.A. Pogna and G. Galterio (Eds.), 10th Inernational Wheat Genetics Symposium. SIMI, Rome, Italy, pp. 261–264.Google Scholar
  54. Dvořák, J., Yang, Z.-L., You, F.M. and Luo, M.C. (2004) Deletion polymorphism in wheat chromosome regions with contrasting recombination rates. Genetics 168, 1665–1675.PubMedCrossRefGoogle Scholar
  55. Dvořák, J. and Akhunov, E.D. (2005) Tempos of deletions and duplications of gene loci in relation to recombination rate during diploid and polyploid evolution in the Aegilops-Triticum alliance. Genetics 171, 323–332.PubMedCrossRefGoogle Scholar
  56. Dvořák, J., Akhunov, E.D., Akhunov, A.R., Deal, K.R. and Luo, M.C. (2006) Molecular characterization of a diagnostic DNA marker for domesticated tetraploid wheat provides evidence for gene flow from wild tetraploid wheat to hexaploid wheat. Mol. Biol. Evol. 23, 1386–1396.Google Scholar
  57. Echenique, V.C., Stamova, B., Volters, P., Lazo, G.R., Carollo, V.L. and Dubcovsky, J. (2002) Frequencies of Ty1-copia and Ty3-gypsy retroelements within the Triticeae EST databases. Theor. Appl. Genet. 104, 840–844.PubMedCrossRefGoogle Scholar
  58. Fajkus, J., Sykorova, E. and Leitch, A.R. (2005) Telomeres in evolution and evolution of telomeres. Chromos. Res. 13, 469–479.CrossRefGoogle Scholar
  59. Finnegan, D.J. (1985) Transposable elements in eukaryotes. Internatl. Rev. Cytol. 93, 281–326.CrossRefGoogle Scholar
  60. Flavell, R.B., Bennett, M.D., Smith, J.B. and Smith, D.B. (1974) Genome size and the proportion of repeated nucleotide sequence DNA in plants. Biochem. Gen. 12, 257–269.CrossRefGoogle Scholar
  61. Friebe, B., Tuleen, N., Jiang, J. and Gill, B.S. (1993) Standard karyotype of Triticum longissimum and its cytogenetic relationship with T. aestivum. Genome 36, 731–742.PubMedCrossRefGoogle Scholar
  62. Fukui, K.N., Suzuki, G., Lagudah, E.S., Rahman, S., Appels, R., Yamamoto, M. and Mukai, Y. (2001) Physical arrangement of retrotransposon-related repeats in centromeric regions of wheat. Plant Cell Physiol. 42, 189–196.PubMedCrossRefGoogle Scholar
  63. Gale, M.D. and Devos, K.M. (1998) Comparative genetics in the grasses. Proc. Natl. Acad. Sci. USA 95, 1971–1974.PubMedCrossRefGoogle Scholar
  64. Gerlach, W.L., Appels, R., Dennis, E.S. and Peacock, W.J. (1979) Evolution and analysis of wheat genomes using highly repeated DNA sequences. In: S. Ramanujam (Ed.), Fifth International Wheat Genetics Symposium. Indian Society of Genetics and Plant Breeding, Indian Agricultural Research Institute, New Delhi, India, pp. 81–91.Google Scholar
  65. Gerlach, W.L., Miller, T.E. and Flavell, R.B. (1980) The nucleolus organizers of diploid wheats revealed by in situ hybridization. Theor. Appl. Genet. 58, 97–100.CrossRefGoogle Scholar
  66. Gill, B.S. and Kimber, G. (1974) Giemsa C-banding and the evolution of wheat. Proc. Natl. Acad. Sci. USA 71, 4086–4090.PubMedCrossRefGoogle Scholar
  67. Gill, K.S., Gill, B.S. and Endo, T.R. (1993) A chromosome region-specific mapping strategy reveals gene-rich telomeric ends in wheat. Chromosoma 102, 374–381.CrossRefGoogle Scholar
  68. Greenblatt, I.M. and Brink, R.A. (1962) Twin mutations in medium variegated pericarp maize. Genetics 47, 489–501.PubMedGoogle Scholar
  69. Grewal, S.I.S. and Klar, A.J.S. (1997) A recombinationally repressed region between mat2 and mat3 loci shares homology to centromeric repeats and regulates directionality of mating-type switching in fission yeast. Genetics 146, 1221–1238.PubMedGoogle Scholar
  70. Grewal, S.I.S. and Moazed, D. (2003) Heterochromatin and epigenetic control of gene expression. Science 301, 798–802.PubMedCrossRefGoogle Scholar
  71. Harper, L., Golubovskaya, I. and Cande, W.Z. (2004) A bouquet of chromosomes. J. Cell Sci. 117, 4025–4032.PubMedCrossRefGoogle Scholar
  72. Houben, A., Schroeder-Reiter, E., Nagaki, K., Nasuda, S., Wanner, G., Murata, M. and Endo, T.R. (2007) CENH3 interacts with the centromeric retrotransposon cereba and GC-rich satellites and locates to centromeric substructures in barley. Chromosoma 116, 275–283.PubMedCrossRefGoogle Scholar
  73. Huang, S., Sirikhachornkit, A., Su, X., Faris, J., Gill, B.S., Haselkorn, R. and Gornicki, P. (2002) Genes encoding plastid acetyl-CoA carboxylase and 3-phopshoglycerate kinase of the Triticum/Aegilops complex and the evolutionary history of polyploid wheat. Proc. Natl. Acad. Sci. USA 99, 8133–8138.PubMedCrossRefGoogle Scholar
  74. Hudakova, S., Michalek, W., Presting, G.G., Ten Hoopen, R., Dos Santos, K., Jasencakova, Z. and Schubert, I. (2001) Sequence organization of barley centromeres. Nucl. Acid Res. 29, 5029–5035.CrossRefGoogle Scholar
  75. Jakob, S.S., Meister, A. and Blattner, F.R. (2004) The considerable genome size variation of Hordeum species (Poaceae) is linked to phylogeny, life form, ecology, and speciation rates. Mol. Biol. Evol. 21, 860–869.Google Scholar
  76. Jiang, J. and Gill, B.S. (1994) New 18S-26S ribosomal RNA gene loci: chromosomal landmarks for the evolution of polyploid wheats. Chromosoma 103, 179–185.PubMedCrossRefGoogle Scholar
  77. Jiang, N., Bao, Z., Zhang, X., Eddy, S.R. and Wessler, S.R. (2004) Pack-MULE transposable elements mediate gene evolution in plants. Nature 30, 569–573.CrossRefGoogle Scholar
  78. Jones, J.D.G. and Flavell, R.B. (1982a) The structure, amount and chromosomal localization of defined repeated DNA-sequences in species of the genus Secale. Chromosoma 86, 613–641.Google Scholar
  79. Jones, J.D.G. and Flavell, R.B. (1982b) The mapping of highly-repeated DNA families and their relationship to C-bands in chromosomes of Secale cereale. Chromosoma 86, 595–612.Google Scholar
  80. Juretic, N., Hoen, D.R., Huynh, M.L., Marrison, P.M. and Bureau, T.E. (2006) The evolutionary fate of MULE-mediated duplications of host gene fragments in rice. Genome Res. 15, 1292–1297.CrossRefGoogle Scholar
  81. Kanazin, V., Ananiev, E. and Blake, T. (1993) The genetics of 5S rRNA encoding multigene families in barley. Genome 36, 1023–1028.PubMedCrossRefGoogle Scholar
  82. Kapitonov, V.V. and Jurka, J. (2001) Rolling-circle transposons in eukaryotes. Proc. Natl. Acad. Sci. USA 98, 8714–8719.PubMedCrossRefGoogle Scholar
  83. Katsiotis, A., Hagidimitriou, M. and Heslop-Harrison, J.S. (1997) The close relationship between the A and B genomes in Avena L. (Poaceae) determined by molecular cytogenetic analysis of total genomic, tandemly and dispersed repetitive DNA sequences. Annals Bot. 79, 103–109.CrossRefGoogle Scholar
  84. Khrustaleva, L.I., de Melo, P.E., van Heusden, A.W. and Kik, C. (2005) The integration of recombination and physical maps in a large-genome monocot using haploid genome analysis in a trihybrid Allium population. Genetics 169, 1673–1685.PubMedCrossRefGoogle Scholar
  85. Kilian, A., Kudrna, D. and Kleinhofs, A. (1999) Genetic and molecular characterization of barley chromosome telomeres. Genome 42, 412–419.CrossRefGoogle Scholar
  86. Kilian, B., Özkan, H., Deusch, O., Effgen, S., Brandolini, A., Kohl, J., Martin, W. and Salamini, F. (2007) Independent wheat B and G genome origins in outcrossing Aegilops progenitor haplotypes. Mol. Biol. Evol. 24, 217–227.Google Scholar
  87. Kishii, M., Nagaki, K., Tsujimoto, H. and Sasakuma, T. (1999) Exclusive localization of tandem repetitive sequences in subtelomeric heterochromatin regions of Leymus racemosus (Poaceae, Triticeae). Chromosome Res. 7, 519–529.PubMedCrossRefGoogle Scholar
  88. Kishii, M., Nagaki, K. and Tsujimoto, H. (2001) A tandem repetitive sequence located in the centromeric region of common wheat (Triticum aestivum) chromosomes. Chromos. Res. 9, 417–428.CrossRefGoogle Scholar
  89. Kishii, M. and Tsujimoto, H. (2002) Genus-specific localization of the TaiI family of tandem-repetitive sequences in either the centromeric or subtelomeric regions in Triticeae species (Poaceae) and its evolution in wheat. Genome 45, 946–955.PubMedCrossRefGoogle Scholar
  90. Kunzel, G., Korzun, L. and Meister, A. (2000) Cytologically integrated physical restriction fragment length polymorphism maps for the barley genome based on translocation breakpoints. Genetics 154, 397–412.PubMedGoogle Scholar
  91. Lassner, M. and Dvořák, J. (1986) Preferential homogenization between adjacent and alternate subrepeats in wheat rDNA. Nucl. Acid. Res. 14, 5499–5512.CrossRefGoogle Scholar
  92. Lassner, M., Anderson, O. and Dvořák, J. (1987) Hypervariation associated with a 12-nucleotide direct repeat and inferences on intragenomic homogenization of ribosomal RNA gene spacer based on the DNA sequence of a clone from the wheat Nor-D3 locus. Genome 29, 770–781.CrossRefGoogle Scholar
  93. Lawrence, G.J. and Appels, R. (1986) Mapping the nucleolus organizing region, seed protein loci and isozyme loci on chromosome 1R in rye. Theor. Appl. Genet. 71, 742–749.CrossRefGoogle Scholar
  94. Leitch, A.R., Mosgoller, W., Shi, M. and Heslop-Harrison, J.S. (1992) Different patterns of rDNA organization at interphase in nuclei of wheat and rye. J. Cell Sci. 101, 751–757.PubMedGoogle Scholar
  95. Leitch, I.J. and Heslop-Harrison, J.S. (1992) Physical mapping of the 18S-5.8S-26S rRNA genes in barley by in situ hybridization. Genome 35, 1013–1018.CrossRefGoogle Scholar
  96. Li, W., Zhang, P., Fellers, J.P., Friebe, B. and Gill, B.S. (2004) Sequence composition, organization, and evolution of the core Triticeae genome. Plant J. 40, 500–511.PubMedCrossRefGoogle Scholar
  97. Linde-Laursen, I. and Baden, C. (1994) Comparison of the Giemsa C-banded karyotypes of the three subspecies of Psathyrostachys fragilis, subspp. villosus (2x), secaliformis (2x, 4x), and fragilis (2x) (Poaceae), with notes on chromosome pairing. Pl. Syst. Evol. 191, 183–198.Google Scholar
  98. Longwell, A.C. and Svihla, G. (1960) Specific chromosomal control of the nucleolus and of cytoplasm in wheat. Exp. Cell Res. 20, 294–312.CrossRefGoogle Scholar
  99. Löve, A. (1984) Conspectus of the Triticeae. Feddes Repertorium 95, 425–521.Google Scholar
  100. Lukaszewski, A.J. and Curtis, C.A. (1993) Physical distribution of recombination in B-genome chromosomes of tetraploid wheat. Theor. Appl. Genet. 84, 121–127.Google Scholar
  101. Luo, M.C., Thomas, C., Deal, K.R., You, F.M., Anderson, O.D., Gu, Y.G., Li, W., Kuraparthy, V., Gill, B.S., McGuire, P.E. and Dvořák, J. (2003) Construction of contigs of Ae. tauschii genomic DNA fragments cloned in BAC and BiBAC vectors. In: N.E. Pogna, M. Romano, E.A. Pogna and G. Galterio (Eds.) 10th International Wheat Genetics Symposium. Institute Sperimentale per la Cerealicoltura, Roma, Italy, pp. 293–296.Google Scholar
  102. Luo, M.C., Deal, K.R., Young, Z.L. and Dvořák, J. (2005) Comparative genetic maps reveal extreme crossover localization in the Aegilops speltoides chromosomes. Theor. Appl. Genet. 111, 1098–1106.PubMedCrossRefGoogle Scholar
  103. Mao, L., Devos, K.M., Zhu, L. and Gale, M.D. (1997) Cloning and genetic mapping of wheat telomere-associated sequences. Mol. Gen. Genet. 254, 584–591.PubMedCrossRefGoogle Scholar
  104. Metzlaff, M., Troebner, W., Baldauf, F., Schlegel, R. and Cullum, J. (1986) Wheat specific repetitive DNA-sequences – construction and characterization of 4 different genomic clones. Theor. Appl. Genet. 72, 207–210.CrossRefGoogle Scholar
  105. Miller, J.T., Dong, F.G., Jackson, S.A., Song, J. and Jiang, J.M. (1998) Retrotransposon-related DNA sequences in the centromeres of grass chromosomes. Genetics 150, 1615–1623.PubMedGoogle Scholar
  106. Miller, T.E., Hutchinson, J. and Reader, S.M. (1983) The identification of the nucleolus organiser chromosomes of diploid wheat. Theor. Appl. Genet. 65, 145–147.CrossRefGoogle Scholar
  107. Morgante, M. (2006) Plant genome organisation and diversity: the year of the junk! Curr. Opin. Biotech. 17, 168–173.CrossRefGoogle Scholar
  108. Mukai, Y., Endo, T.R. and Gill, B.S. (1991) Physical mapping of the 18S.26S rRNA multigene family in common wheat: identification of a new locus. Chromosoma 100, 71–78.CrossRefGoogle Scholar
  109. Nagaki, K., Tsujimoto, H., Isono, K. and Sasakuma, T. (1995) Molecular characterization of a tandem repeat, Afa family, and distribution among Triticeae. Genome 38, 479–486.PubMedCrossRefGoogle Scholar
  110. Nagaki, K., Tsujimoto, H. and Sasakuma, T. (1998a) Dynamics of tandem repetitive Afa-family sequences in Triticeae, wheat-related species. J. Mol. Evol. 47, 183–189.Google Scholar
  111. Nagaki, K., Tsujimoto, H. and Sasakuma, Y. (1998b) H genome specific repetitive sequence, pEt2, of Elymus trachycaulus in part of Afa family of Triticeae. Genome 41, 134–136.Google Scholar
  112. Nagaki, K., Kishii, M., Tsujimoto, H. and Sasakuma, T. (1999) Tandem repetitive Afa-family sequences from Leymus racemosus and Psathyrostachys juncea (Poaceae). Genome 42, 1258–1260.PubMedGoogle Scholar
  113. Nasuda, S., Hudakova, S., Schubert, I., Houben, A. and Endo, T.R. (2005) Stable barley chromosomes without centromeric repeats. Proc. Natl. Acad. Sci. USA 102, 9842–9847.PubMedCrossRefGoogle Scholar
  114. Ohno, S. (1980) So much 'junk' DNA in our genome. Brookhaven Symp. Biol. 23, 604–607.Google Scholar
  115. Orgel, L.E. and Crick, F.H.C. (1980) Selfish DNA – the ultimate parasite. Nature 284, 604–607.PubMedCrossRefGoogle Scholar
  116. Pandita, T.K., Hunt, C.R., Sharma, G.G. and Yang, Q. (2007) Regulation of telomere movement by telomere chromatin structure. Cell. Mol. Life Sci. 64, 131–138.PubMedCrossRefGoogle Scholar
  117. Paux, E., Roger, D., Badaeva, E., Gay, G., Bernard, M., Sourdille, P. and Feuillet, C. (2006) Characterizing the composition and evolution of homoeologous genomes in hexaploid wheat through BAC-end sequencing on chromosome 3B. Plant J. 48, 463–474.PubMedCrossRefGoogle Scholar
  118. Peacock, W.J., Gerlach, W.L. and Dennis, E.S. (1981) Molecular aspects of wheat evolution: repeated DNA sequences. In: L.T. Evans and W.J. Peacock (Eds.), Wheat Science-Today and Tomorrow. Cambridge University Press, Cambridge, pp. 41–60.Google Scholar
  119. Pedersen, C., Rasmussen, S.K. and LindeLaursen, I. (1996) Genome and chromosome identification in cultivated barley and related species of the Triticeae (Poaceae) by in situ hybridization with the GAA-satellite sequence. Genome 39, 93–104.PubMedCrossRefGoogle Scholar
  120. Pestsova, E.G., Goncharov, N.P. and Salina, E.A. (1998) Elimination of a tandem repeat of telomeric heterochromatin during the evolution of wheat. Theor. Appl. Genet. 97, 1380–1386.CrossRefGoogle Scholar
  121. Presting, G.G., Malysheva, L., Fuchs, J. and Schubert, I.Z. (1998) A TY3/GYPSY retrotransposon-like sequence localizes to the centromeric regions of cereal chromosomes. Plant J. 16, 721–728.PubMedCrossRefGoogle Scholar
  122. Prieto, P., Martin, A. and Cabrera, A. (2004) Chromosomal distribution of telomeric and telomeric-associated sequences in Hordeum chilense by in situ hybridization. Hereditas 141, 122–127.PubMedCrossRefGoogle Scholar
  123. Ramakrishna, W., Dubcovsky, J., Park, Y.J., Busso, C., Embereton, J., SanMiguel, P. and Bennetzen, J.L. (2002) Different types and rates of genome evolution detected by comparative sequence analysis of orthologus segments from four cereal genomes. Genetics 162, 1389–1400.PubMedGoogle Scholar
  124. Rayburn, A.L. and Gill, B.S. (1986) Isolation of a D-genome specific repeated DNA sequence from Aegilops squarrosa. Plant Mol. Biol. Report. 4, 102–109.CrossRefGoogle Scholar
  125. Rayburn, A.L. and Gill, B.S. (1987) Molecular analysis of the D-genome of the Triticeae. Theor. Appl. Genet. 73, 385–388.CrossRefGoogle Scholar
  126. Roder, M.S., Lapitan, N.L.V., Sorrells, M.E. and Tanksley, S.D. (1993) Genetic and physical mapping of barley telomeres. Mol. Gen. Genet. 238, 294–303.PubMedGoogle Scholar
  127. Sabot, F., Guyot, R., Wicker, T., Chantret, N., Laubin, B., Chalhoub, B., Leroy, P., Sourdille, P. and Bernard, M. (2005) Updating of transposable element annotations from large wheat genomic sequences reveals diverse activities and gene associations. Mol. Genet. Genom. 274, 119–130.CrossRefGoogle Scholar
  128. Šafář, J., Bartoš, J., Janda, J., Bellec, A., Kubaláková, M., Valárik, M., Pateyron, S., Weiserová, J., Tušková, J., Čihalíková, J., Vrána, J., Šimková, H., Faivre-Rampant, P., Sourdille, P., Caboche, M., Bernard, M., Doležel, J. and Chalhoub, B. (2004) Dissecting large and complex genomes: flow sorting and BAC cloning of individual chromosomes from bread wheat. Plant J. 39, 960–968.PubMedCrossRefGoogle Scholar
  129. Saghai-Maroof, M.A., Soliman, K.M., Jorgensen, R.A. and Allard, R.W. (1984) Ribosomal DNA spacer-length polymorphism in barley: Mendelian inheritance, chromosomal location, and population dynamics. Proc. Natl. Acad. Sci. USA 81, 8014–8018.PubMedCrossRefGoogle Scholar
  130. Salina, E.A., Lim, K.Y., Badaeva, E.D., Shcherban, A.B., Adonina, I.G., Amosova, A.V., Samatadze, T.E., Vatolina, T.Y., Zoshchuk, S.A. and Leitch, A.R. (2006) Phylogenetic reconstruction of Aegilops section Sitopsis and the evolution of tandem repeats in the diploids and derived wheat polyploids. Genome 49, 1023–1035.PubMedCrossRefGoogle Scholar
  131. Sandhu, D., Champoux, J.A., Bondareva, S.N. and Gill, K.S. (2001) Identification and physical localization of useful genes and markers to a major gene-rich region on wheat group 1S chromosomes. Genetics 157, 1735–1747.PubMedGoogle Scholar
  132. Sandhu, D. and Gill, K.S. (2002) Gene-containing regions of wheat and the other grass genomes. Plant Physiol. 128, 803–811.PubMedCrossRefGoogle Scholar
  133. SanMiguel, P., Tikhonov, A., Jin, Y.-K., Moutchoulskaia, N., Zakharov, D., Melake-Berhan, A., Springer, P.S., Edvards, K.J., Lee, M., Avramova, Z. and Bennetzen, J.L. (1996) Nested retrotransposons in the intergenic regions of the maize genome. Science 274, 765–768.PubMedCrossRefGoogle Scholar
  134. Scherthan, H. (2007) Telomere attachment and clustering during meiosis. Cellular Mol. Life Sci. 64, 117–124.CrossRefGoogle Scholar
  135. Schwarzacher, T. and Heslop-Harrison, J.S. (1991) In situ hybridization to plant telomeres using synthetic oligomers. Genome 34, 317–323.CrossRefGoogle Scholar
  136. Schweizer, D. and Loidl, J. (1987) A model for heterochromatin dispersion and the evolution of C-band patterns. Chromos. Today 9, 61–74.Google Scholar
  137. See, D.R., Brooks, S., Nelson, J.C., Brown-Guedira, G., Friebe, B. and Gill, B.S. (2006) Gene evolution at the ends of wheat chromosomes. Proc. Natl. Acad. Sci. USA 103, 4162–4167.PubMedCrossRefGoogle Scholar
  138. Smith, D.B. and Flavell, R.B. (1975) Characterisation of the wheat genome by renaturation kinetics. Chromosoma 50, 223–242.CrossRefGoogle Scholar
  139. Sorrells, M.E., La Rota, C.M., Bermudez-Kandianis, C.E., Greene, R.A., Kantety, R., Munkvold, J.D., Miftahudin, Mahmoud, A., Gustafson, J.P., Qi, L.L., Echalier, B., Gill, B.S., Matthews, D., Lazo, G., Chao, S., Anderson, O.D., Edwards, H., Linkiewicz, A.M., Dubcovsky, J., Akhunov, E.D., Dvořák, J., Zhang, D., Nguyen, H.T., Peng, J., Lapitan, N.L.V., Gonzalez-Hernandez, J.L., Anderson, J.A., Hossain, K.G., Kalavacharla, V., Kianian, S.F., Choi, D.W., Close, T.J., Dilbirligi, M., Gill, K.S., Steber, C., Walker-Simmons, M.K., McGuire, P.E. and Qualset, C.O. (2003) Comparative DNA sequence analysis of wheat and rice genomes. Genome Res. 13, 1818–1827.PubMedGoogle Scholar
  140. Taketa, S., Ando, H., Takeda, K., Harrison, G.E. and Heslop-Harrison, J.S. (2000) The distribution, organization and evolution of two abundant and widespread repetitive DNA sequences in the genus Hordeum. Theor. Appl. Genet. 100, 169–176.CrossRefGoogle Scholar
  141. Thompson, P.E. (1964) Evidence on the basis of the centromere effect in the large autosomes of Drosophila melanogaster. Genetics 49, 761–769.PubMedGoogle Scholar
  142. Van't Hof, J. and Sparrow, A.H. (1963) A relationship between DNA content, nuclear volume, and minimum mitotic cycle time. Proc. Natl. Acad. Sci. USA 49, 897–902.Google Scholar
  143. Van Schaik, N.W. and Brink, R.A. (1959) Transpositions of modulator, a component of the variegated pericarp allele in maize. Genetics 44, 725–738.PubMedGoogle Scholar
  144. Vershinin, A.V., Schwarzacher, T. and Heslop-Harrison, J.S. (1995) The large-scale genomic organization of repetitive DNA families at the telomeres of rye chromosomes. Plant Cell 7, 1823–1833.PubMedCrossRefGoogle Scholar
  145. Vershinin, A.V. and Heslop-Harrison, J.S. (1998) Comparative analysis of the nucleosomal structure of rye, wheat and their relatives. Plant Mol. Biol. 36, 149–161.PubMedCrossRefGoogle Scholar
  146. Vicient, C.M., Suoniemi, A., Anamthawat-Jónsson, K., Tanskanen, J., Beharav, A., Nevo, E. and Schulman, A.H. (1999) Retrotransposon BARE-1 and its role in genome evolution in the genus Hordeum. Plant Cell 11, 1769–1784.PubMedCrossRefGoogle Scholar
  147. Vogel, K.P., Arumuganathan, R. and Jensen, K.B. (1999) Nuclear DNA content of perennial grasses of the Triticeae. Crop Sci. 39, 661–667.CrossRefGoogle Scholar
  148. Werner, J.E., Kota, R.S., Gill, B.S. and Endo, T.R. (1992) Distribution of telomeric repeats and their role in the healing of broken chromosome ends in wheat. Genome 35, 844–848.CrossRefGoogle Scholar
  149. Wicker, T., Stein, N., Albar, L., Feuillet, C., Schlagenhauf, E. and Keller, B. (2001) Analysis of a contiguous 211 kb sequence in diploid wheat (Triticum monococcum L.) reveals multiple mechanisms of genome evolution. Plant J. 26, 307–316.PubMedCrossRefGoogle Scholar
  150. Wicker, T., Guyot, R., Yahiaoui, N. and Keller, B. (2003a) CACTA transposons in Triticeae. A diverse family of high-copy repetitive elements. Plant Phys. 132, 52–63.Google Scholar
  151. Wicker, T., Yahiaoui, N., Guyot, R., Schlagenhauf, E., Liu, Z.D., Dubcovsky, J. and Keller, B. (2003b) Rapid genome divergence at orthologous low molecular weight glutenin loci of the A and Am genomes of wheat. Plant Cell 15, 1186–1197.Google Scholar
  152. Wicker, T., Zimmermann, W., Perovic, D., Paterson, A.H., Ganal, M., Graner, A. and Stein, N. (2005) A detailed look at 7 million years of genome evolution in a 439 kb contiguous sequence at the barley Hv-eIF4E locus: recombination, rearrangements and repeats. Plant J. 41, 184–194.PubMedCrossRefGoogle Scholar
  153. Wicker, T., Sabot, F., Hua-Van, A., Bennetzen, J.L., Capy, P., Chalhoub, B., Flavell, A., Leroy, P., Morgante, M., Panaud, O., Paux, E., SanMiguel, P. and Schulman, A.H. (2007) A unified classification system for eukaryotic transposable elements. Nat. Rev. Genet. 8, 973–982.PubMedCrossRefGoogle Scholar
  154. Xin, Z.-Y. and Appels, R. (1988) Occurence of rye (Secale cereale) 350-family DNA sequences in Agropyron and other Triticeae. Plant Syst. Evol. 160, 65–76.Google Scholar
  155. Zhang, H.B. and Dvořák, J. (1990) Isolation of repeated DNA sequences from Lophopyrum elongatum for detection of Lophopyrum chromatin in wheat genomes. Genome 33, 283–293.CrossRefGoogle Scholar

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© Springer Science+Business Media, LLC 2009

Authors and Affiliations

  1. 1.Department of Plant SciencesUniversity of CaliforniaDavisUSA

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