Chromosome Research

, Volume 19, Issue 5, pp 607–623 | Cite as

Tandem repeats on an eco-geographical scale: outcomes from the genome of Aegilops speltoides

  • Olga Raskina
  • Leonid Brodsky
  • Alexander Belyayev


The chromosomal pattern of tandem repeat fractions of repetitive DNA is one of the most important characteristics of a species. In the present research, we aimed to detect and evaluate the level of intraspecific variability in the chromosomal distribution of species-specific Spelt 1 and Aegilops-Triticum-specific Spelt 52 tandem repeats in Aegilops speltoides and in closely related diploid and polyploid species. There is a distinct eco-geographical gradient in Spelt 1 and Spelt 52 blocks abundance in Ae. speltoides. In marginal populations, the number of Spelt 1 chromosomal blocks could be 12–14 times lower than in the center of the species distribution. Also, in related diploid species, the abundance of Spelt 52 correlates with evolutionary proximity to Ae. speltoides. Finally, the B- and G-genomes of allopolyploid wheats have Spelt 1 chromosomal distribution patterns similar to those of the types of Ae. speltoides with poor and rich contents of Spelt 1, respectively. The observed changes in numbers of blocks of Spelt 1 and Spelt 52 tandem repeats along the eco-geographical gradient may due to their depletion in the marginal populations as a result of increased recombination frequency under stressful conditions. Alternatively, it may be accumulation of tandem repeats in conducive climatic/edaphic environments in the center of the species’ geographical distribution. Anyway, we observe a bidirectional shift of repetitive DNA genomic patterns on the population level leading to the formation of population-specific chromosomal patterns of tandem repeats. The appearance of a new chromosomal pattern is considered an important factor in promoting the emergence of interbreeding barriers.


Aegilops B-chromosomes Eco-geographical gradient Heterochromatin Tandem repeats Triticum 





Fluorescent in situ hybridization


Genomic in situ hybridization



We thank Hanan Sela for his help in collecting plant material. We are most grateful to Moshe Feldman and Estella Nazarova for kindly supplying seeds. We thank anonymous reviewers for the helpful comments. This work is supported by the Israel Science Foundation under grant number 723/07.

Supplementary material

10577_2011_9220_MOESM1_ESM.doc (44 kb)
ESM 1  (DOC 44.0 kb)
10577_2011_9220_Fig7_ESM.jpg (29 kb)
Fig. 7

a The bi-partite clustering of genotypes based on 28 Spelt 1 tandem repeats features (counts of blocks in 28 chromosome arms of the diploid genome). 1 Central and intermediate populations; 2 marginal populations. This clustering unites clusters I (intermediate populations) and C (central populations) of Fig. 2a, and separates them from cluster M (marginal populations). Such a clustering corresponds to the first discrimination function of LDA (supplementary Table 4). b The clustering silhouette widths for individual genotypes (dark blue bars) and predicted classes (yellow bars) for the bi-partite clustering according to Spelt 1 blocks features (JPEG 28 kb)

10577_2011_9220_MOESM2_ESM.tif (3.6 mb)
High resolution image (TIFF 3677 kb)
10577_2011_9220_Fig8_ESM.jpg (29 kb)
Fig. 8

a The bi-partite clustering of genotypes that is based on twenty eight Spelt 52 tandem repeats features. 1 Marginal and intermediate populations; 2 central populations. This clustering united clusters M and I of Fig. 2a and separated them from cluster C. Such a clustering corresponded to the second discrimination function of LDA. b The clustering silhouette widths for individual genotypes (dark blue bars) and predicted classes (yellow bars) for the bi-partite clustering according to the Spelt 52 tandem repeats features. (JPEG 29 kb)

10577_2011_9220_MOESM3_ESM.tif (3.3 mb)
High resolution image (TIFF 3408 kb)


  1. Anamthawat-Jonsson K, Heslop-Harrison JS (1993) Isolation and characterization of genome-specific DNA sequences in Triticeae species. Mol Gen Genet 240:151–158PubMedCrossRefGoogle Scholar
  2. Anderson JA, Ogihara Y, Sorrels ME, Tanksley SD (1992) Development of a chromosomal arm map for wheat based on RFLP markers. Theor Appl Genet 83:1035–1043Google Scholar
  3. Ankory H, Zohary D (1962) Natural hybridization between Aegilops sharonensis and Ae. longissima: a morphological and cytological study. Cytologia 27:314–324Google Scholar
  4. Badaeva ED, Zoshchuk SA, Paux E, Gay G, Zoshchuk NV, Roger D, Zelenin AV, Bernard M, Feuillet C (2010) Fat element - a new marker for chromosome and genome analysis in the Triticeae. Chromosome Res 18:697–709PubMedCrossRefGoogle Scholar
  5. Badaeva ED, Friebe B, Gill BS (1996) Genome differentiation in Aegilops. 2. Physical mapping of 5S and 18S–26S ribosomal RNA gene families in diploid species. Genome 39:1150–1158PubMedCrossRefGoogle Scholar
  6. Baum B, Bailey G (2001) The 5S rRNA gene sequence variation in wheats and some polyploid wheat progenitors (Poaceae: Triticeae). Genet Resour Crop Evol 48:35–51CrossRefGoogle Scholar
  7. Belyayev A, Raskina O (1998) Heterochromatin discrimination in Aegilops speltoides by simultaneous genomic in situ hybridization. Chromosome Res 6:559–565PubMedCrossRefGoogle Scholar
  8. Belyayev A, Raskina O, Korol A, Nevo E (2000) Coevolution of A and B genomes in allotetraploid Triticum dicoccoides. Genome 43:1021–1026PubMedGoogle Scholar
  9. Belyayev A, Kalendar R, Brodsky L, Nevo E, Schulman AH, Raskina O (2010) Transposable elements in a marginal plant population: temporal fluctuations provide new insights into genome evolution of wild diploid wheat. Mobile DNA 1:6PubMedCrossRefGoogle Scholar
  10. Carchilan M, Kumke K, Mikolajewski S, Houben A (2009) Rye B chromosomes are weakly transcribed and might alter the transcriptional activity of A chromosome sequences. Chromosoma 118:607–616PubMedCrossRefGoogle Scholar
  11. Cebria A, Navarro ML, Puertas MJ (1994) Genetic control of B chromosome transmission in Aegilops speltoides (Poaceae). Amer J Bot 81:1502–1507CrossRefGoogle Scholar
  12. Da Cunha AB, Dobzhansky T (1954) A further study of chromosomal polymorphism in Drosophila willistoni in its relation to the environment. Evolution 8:119–134CrossRefGoogle Scholar
  13. Daud HM, Gustafson JP (1996) Molecular determination of a B genome progenitor of wheat (Triticum aestivum) using a genome-specific repetitive DNA sequence. Genome 39:543–548PubMedCrossRefGoogle Scholar
  14. Devos KM (2010) Grass genome organization and evolution. Curr Opin Plant Biol 13:139–145PubMedCrossRefGoogle Scholar
  15. Devos KM, Dubcovsky J, Dvořák J, Chinoy CN, Gale MD (1995) Structural evolution of wheat chromosomes 4A, 5A, and 7B and its impact on recombination. Theor Appl Genet 91:282–288CrossRefGoogle Scholar
  16. Dvořák J, Zhang HB (1990) Variation in repeated nucleotide sequences sheds light on the origin of the wheat B and G genomes. Proc Natl Acad Sci USA 87:9640–9644PubMedCrossRefGoogle Scholar
  17. Dvořák J, Zhang HB (1992) Reconstruction of the phylogeny of the genus Triticum from variation in repeated nucleotide sequences. Theor Appl Genet 84:419–429CrossRefGoogle Scholar
  18. Feldman M, Kislev M (1977) Aegilops searsii, a new species of section Sitopsis (Platystachys). Israel J Bot 26:190–201Google Scholar
  19. Feldman M, Levy AA (2005) Allopolyploidy - a shaping force in the evolution of wheat genomes. Cytogenet Gen Res 109:250–258CrossRefGoogle Scholar
  20. Flavell RB, Gale M, O’Dell M, Murphy G, Moore G, Lucas H (1993) Molecular organization of genes and repeats in the large cereal genomes and implications for the isolation of genes by chromosome walking. Chromosomes Today 11:199–214Google Scholar
  21. Gerlach WL, Bedbrook JR (1979) Cloning and characterization of ribosomal RNA genes from wheat and barley. Nucleic Acids Res 7:1869–1885PubMedCrossRefGoogle Scholar
  22. Giorgi D, D’Ovidio R, Tanzarella OA, Ceoloni C, Porceddu E (2003) Isolation and haracterization of S genome specific sequences from Aegilops sect. Sitopsis species Genome 46:478–489Google Scholar
  23. Grant V (1981) Plant speciation, 2nd edn. Columbia University Press, New YorkGoogle Scholar
  24. Hoffmann AA, Sgrò CM, Weeks AR (2004) Chromosomal inversion polymorphisms and adaptation. Trends Ecol Evol 19:482–488PubMedCrossRefGoogle Scholar
  25. Jiang J, Gill BS (1994a) New 18S-26S ribosomal RNA gene loci: chromosomal landmarks for the evolution of polyploid wheats. Chromosoma 103:179–185PubMedCrossRefGoogle Scholar
  26. Jiang J, Gill BS (1994b) Different species-specific chromosome translocations in Triticum timopheevii and T. turgidum support diphyletic origin of polyploid wheats. Chromosome Res 2:59–64PubMedCrossRefGoogle Scholar
  27. Jones N, Houben A (2003) B chromosomes in plants: escapees from the A chromosome genome? Trends Plant Sci 8:417–423PubMedCrossRefGoogle Scholar
  28. Jones RN, González-Sánchez M, González-Garciía M, Vega JM, Puertas MJ (2008a) Chromosomes with a life of their own. Cytogenet Genome Res 120:265–280PubMedCrossRefGoogle Scholar
  29. Jones RN, Viegas W, Houben A (2008b) A century of B chromosomes in plants: so what? Ann Bot 101:767–775PubMedCrossRefGoogle Scholar
  30. Kimber G, Feldman M (1987) Wild Wheat, an Introduction. College of Agriculture University Missouri, ColumbiaGoogle Scholar
  31. King IP, Pordie KA, Liu CJ, Reader SM, Pittaway TS, Orford SE, Miller TE (1994) Detection of interchromosomal translocations within the Triticeae by RFLP analysis. Genome 37:882–887PubMedCrossRefGoogle Scholar
  32. Kirkpatrick M, Barton N (2006) Chromosome inversions, local adaptation and speciation. Genetics 173:419–434PubMedCrossRefGoogle Scholar
  33. Lamb JC, Birchler JA (2006) Retroelement genome painting: cytological visualization of retroelement expansions in the genera Zea and Tripsacum. Genetics 173:1007–1021PubMedCrossRefGoogle Scholar
  34. Lamb JC, Yu W, Han F, Birchler JA (2007) Plant chromosomes from end to end: telomeres, heterochromatin and centromeres. Curr Opin Plant Biol 10:116–122PubMedCrossRefGoogle Scholar
  35. Levin DA (2002) The role of chromosomal change in plant evolution. Oxford University Press, New YorkGoogle Scholar
  36. Lewis H (1962) Catastrophic selection as a factor in speciation. Evolution 16:257–271CrossRefGoogle Scholar
  37. Lewis H, Raven PH (1958) Rapid evolution in Clarkia. Evolution 12:319–336CrossRefGoogle Scholar
  38. Lippman Z, Gendrel AV, Black M, Vaughn MW, Dedhia N, McCombie WR, Lavine K, Mittal V, May B, Kasschau KD, Carrington JC, Doerge RW, Colot V, Martienssen R (2004) Role of transposable elements in heterochromatin and epigenetic control. Nature 430:471–476PubMedCrossRefGoogle Scholar
  39. Liu CJ, Atkinson MD, Chinoy CN, Devos KM, Gale MD (1992) Nonhomoeologous translocations between group 4, 5, and 7 chromosomes within wheat and rye. Theor Appl Genet 83:305–312CrossRefGoogle Scholar
  40. Lynch M, Conery JS (2003) The origins of genome complexity. Science 302:1401–1404PubMedCrossRefGoogle Scholar
  41. Maestra B, Naranjo T (1999) Structural chromosome differentiation between Triticum timopheevii and T. turgidum and T. aestivum. Theor Appl Genet 98:744–750CrossRefGoogle Scholar
  42. Maestra B, Naranjo T (2000) Genome evolution in Triticeae. Chromosomes Today 13:155–167Google Scholar
  43. Martienssen R (2008) Great leap forward? Transposable elements, small interfering RNA and adaptive Lamarckian evolution. New Phytol 179:570–572PubMedCrossRefGoogle Scholar
  44. Mayr E (1942) Systematics and the origin of species. Columbia University Press, New YorkGoogle Scholar
  45. Mendelson D, Zohary D (1972) Behavior and transmission of supernumerary chromosomes in Aegilops speltoides. Heredity 29:329–339CrossRefGoogle Scholar
  46. Miyashita NT, Mori N, Tsunewaki K (1994) Molecular variation in chloroplast DNA regions in ancestral species of wheat. Genetics 137:883–889PubMedGoogle Scholar
  47. Mori N, Liu YG, Tsunewaki K (1995) Wheat phylogeny determined by RFLP analysis of nuclear DNA. 2. Wild tetraploid wheat. Theor Appl Genet 90:129–134CrossRefGoogle Scholar
  48. Naranjo T (1990) Chromosome structure of durum wheat. Theor Appl Genet 79:397–400CrossRefGoogle Scholar
  49. Puertas MJ (2002) Nature and evolution of B chromosomes in plants: a non-coding but information-rich part of plant genomes. Cytogenet Genome Res 96:198–205PubMedCrossRefGoogle Scholar
  50. Raskina O, Belyayev A, Nevo E (2002) Repetitive DNAs of wild emmer wheat Triticum dicoccoides and their relation to S-genome species: molecular-cytogenetic analysis. Genome 45:391–401PubMedCrossRefGoogle Scholar
  51. Raskina O, Belyayev A, Nevo E (2004a) Activity of the En/Spm-like transposons in meiosis as a base for chromosome repatterning in a small, isolated, peripheral population of Aegilops speltoides Tausch. Chromosome Res 12:153–161PubMedCrossRefGoogle Scholar
  52. Raskina O, Belyayev A, Nevo E (2004b) Quantum speciation in Aegilops: Molecular cytogenetic evidence from rDNA cluster variability in natural populations. Proc Natl Acad Sci USA 101:14818–14823PubMedCrossRefGoogle Scholar
  53. Rieseberg L, Willis JH (2007) Plant Speciation. Science 317:910–914PubMedCrossRefGoogle Scholar
  54. Riley R, Unrau J, Chapman V (1958) Evidence on the origin of the B genome of wheat. J Heredity 49:91–98Google Scholar
  55. Rodrígues S, Maestra B, Perera E, Díez M, Naranjo T (2000a) Pairing affinities of the B- and G-genome chromosomes of polyploid wheats with those of Aegilops speltoides. Genome 43:814–819Google Scholar
  56. Rodrígues S, Perera E, Maestra B, Díez M, Naranjo T (2000b) Chromosome structure of Triticum timopheevii relative to T. turgidum. Genome 43:923–930Google Scholar
  57. Salina EA, Pestsova EG, Vershinin AV (1997) Spelt1 - new family of cereal tandem repeats. Russian J Genet 33:352–357Google Scholar
  58. Salina EA, Numerova OM, Ozkan H, Feldman M (2004) Alterations in subtelomeric tandem repeats during early stages of allopolyploidy in wheat. Genome 47:860–867PubMedCrossRefGoogle Scholar
  59. Salina EA, Lim YL, Badaeva ED, Shcherban AB, Adonina IG, Amosova AV et al (2006) Phylogenetic reconstruction of Aegilops section Sitopsis and the evolution of tandem repeats in the diploids and derived wheat polyploids. Genome 49:1023–1035PubMedCrossRefGoogle Scholar
  60. Sarkar P, Stebbins GL (1956) Morphological evidence concerning the origin of the B genome in wheat. Am J Bot 43:297–304CrossRefGoogle Scholar
  61. Sears E (1941) Amphidiploids in the seven-chromosome Triticina. Univ Missouri Agric Exper Sta Res Bull 336:1–46Google Scholar
  62. Sharma S, Raina SN (2005) Organization and evolution of highly repeated satellite DNA sequences in plant chromosomes. Cytogenet Genome Res 109:15–26PubMedCrossRefGoogle Scholar
  63. 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 94:14570–14577PubMedCrossRefGoogle Scholar
  64. Zarchi Y, Hillel J, Simchen G (1974) Supernumerary chromosomes and chiasma distribution in Triticum speltoides. Heredity 33:173–180CrossRefGoogle Scholar
  65. Zohary M (1970) Botany. In: Amiran DHK, Elster J, Gilead M, Rosenan N, Kadmon N, Parah U (eds) Atlas of Israel. Elsevier, AmsterdamGoogle Scholar
  66. Zohary D, Imber D (1963) Genetic dimorphism in fruit types in Aegilops speltoides. Heredity 18:223–231CrossRefGoogle Scholar
  67. Zohary D, Harlan JR, Vardi A (1969) The wild diploid progenitors of wheat and their breeding value. Euphytica 18:58–65Google Scholar
  68. Zoshchuk SA, Badaeva ED, Zoshchuk NV, Adonina IG, Shcherban AB, Salina EA (2007) Intraspecific divergence in wheats of the Timopheevi group as revealed by in situ hybridization with tandem repeats of the Spelt1 and Spelt52 families. Russian J Genet 43:771–781CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2011

Authors and Affiliations

  • Olga Raskina
    • 1
  • Leonid Brodsky
    • 2
  • Alexander Belyayev
    • 1
  1. 1.Laboratory of Plant Molecular Cytogenetics, Institute of EvolutionUniversity of HaifaHaifaIsrael
  2. 2.Laboratory of Systems Biology and Data Mining, Institute of EvolutionUniversity of HaifaHaifaIsrael

Personalised recommendations