Skip to main content

Fat element—a new marker for chromosome and genome analysis in the Triticeae

Chromosome Research volume 18, pages 697–709 (2010)Cite this article

Abstract

Chromosomal distribution of the Fat element that was isolated from bacterial artificial chromosome (BAC) end sequences of wheat chromosome 3B was studied in 45 species representing eight genera of Poaceae (Aegilops, Triticum, Agropyron, Elymus, Secale, Hordeum, Avena and Triticale) using fluorescence in situ hybridisation (FISH). The Fat sequence was not present in oats and in two barley species, Hordeum vulgare and Hordeum spontaneum, that we investigated. Only very low amounts of the Fat element were detected on the chromosomes of two other barley species, Hordeum geniculatum and Hordeum chilense, with different genome compositions. The chromosomes of other cereal species exhibited distinct hybridisation patterns with the Fat probe, and labelling intensity varied significantly depending on the species or genome. The highest amount of hybridisation was detected on chromosomes of the D genome of Aegilops and Triticum and on chromosomes of the S genome of Agropyron. Despite the bioinformatics analysis of several BAC clones that revealed the tandem organisation of the Fat element, hybridisation with the Fat probe produces uneven, diffuse signals in the proximal regions of chromosomes. In some of the genomes we investigated, however, it also forms distinct, sharp clusters in chromosome-specific positions, and the brightest fluorescence was always observed on group 4 chromosomes. Thus, the Fat element represents a new family of Triticeae-specific, highly repeated DNA elements with a clustered–dispersed distribution pattern. These elements may have first emerged in cereal genomes at the time of divergence of the genus Hordeum from the last common ancestor. During subsequent evolution, the amount and chromosomal distribution of the Fat element changed due to amplification, elimination and re-distribution of this sequence. Because the labelling patterns that we detected were highly specific, the Fat element can be used as an accessory probe in FISH analysis for chromosome identification and investigation of evolutionary processes at the chromosomal level.

This is a preview of subscription content, access via your institution.

Access options

Buy single article

Instant access to the full article PDF.

43,34 €

Price includes VAT (Finland)
Tax calculation will be finalised during checkout.

Fig. 1
Fig. 2

Abbreviations

BAC:

bacterial artificial chromosomes

dUTP:

2’-dezoxyuridine-5'-triphosphate

FISH:

Fluorescence in situ hybridization

LTR:

long terminal repeat

PCR:

polymerase chain reaction

References

  • Abubakar M, Kimber G (1982) Chromosome-pairing regulators in the former genus Aegilops. Z Pflanzenzucht 89:130–138

    Google Scholar 

  • Ananiev EV, Vales MI, Phillips RL, Rines HW (2002) Isolation of A/D and C genome specific dispersed and clustered repetitive DNA sequences from Avena sativa. Genome 45:431–441

    CAS  Article  PubMed  Google Scholar 

  • Badaeva ED, Friebe B, Gill BS (1996) Genome differentiation in Aegilops. 1. Distribution of highly repetitive DNA sequences on chromosomes of diploid species. Genome 39:293–306

    CAS  Article  PubMed  Google Scholar 

  • Badaeva ED, Amosova AV, Muravenko OV et al (2002) Genome differentiation in Aegilops. 3. Evolution of the D-genome cluster. Plant Syst Evol 231:163–190

    CAS  Article  Google Scholar 

  • Badaeva ED, Amosova AV, Samatadze TE et al (2004) Genome differentiation in Aegilops. 4. Evolution of the U-genome cluster. Plant Syst Evol 246:45–76

    CAS  Article  Google Scholar 

  • Badaeva E, Dedkova O, Koenig J, Bernard S, Bernard M (2008) Analysis of introgression of Aegilops ventricosa Tausch. genetic material in a common wheat background using C-banding. Theor Appl Genet 117:803–811

    CAS  Article  PubMed  Google Scholar 

  • Bardsley D, Cuadrado A, Jack P et al (1999) Chromosome markers in the tetraploid wheat Aegilops ventricosa analysed by in situ hybridization. Theor Appl Genet 99:300–304

    Article  Google Scholar 

  • Bedbrook RJ, Jones J, O'Dell M, Thompson RJ, Flavell RB (1980) A molecular description of telomeric heterochromatin in Secale species. Cell 19:545–560

    CAS  Article  PubMed  Google Scholar 

  • Belyayev A, Raskina O, Nevo E (2001) Chromosomal distribution of reverse transcriptase-containing retroelements in two Triticeae species. Chromosome Res 9:129–136

    CAS  Article  PubMed  Google Scholar 

  • Belyayev A, Raskina O, Nevo E (2005) Variability of the chromosomal distribution of Ty3-gypsy retrotransposons in the populations of two wild Triticeae species. Cytogenet Genome Res 109:43–49

    CAS  Article  PubMed  Google Scholar 

  • Cabrera A, Friebe B, Jiang J, Gill BS (1995) Characterization of Hordeum chilense chromosomes by C-banding and in situ hybridization using highly repeated DNA probes. Genome 38:435–442

    CAS  PubMed  Google Scholar 

  • Charles M, Belcram H, Just J et al (2008) Dynamics and differential proliferation of transposable elements during the evolution of the B and A genomes of wheat. Genetics 180:1071–1086

    CAS  Article  PubMed  Google Scholar 

  • Chen Q, Conner RL, Laroche A, Thomas JB (1998) Genome analysis of Thinopyrum intermedium and Thinoryrum ponticum using genomic in situ hybridization. Genome 41:580–586

    CAS  Article  PubMed  Google Scholar 

  • Cuadrado A, Jouve N (2002) Evolutionary trends of different repetitive DNA sequences during speciation in the genus Secale. J Hered 93:339–345

    CAS  Article  PubMed  Google Scholar 

  • Dewey DR (1984) The genomic system of classification as a guide to intergeneric hybridization with the perennial Triticeae. In: Gustafson JP (ed) Gene manipulation in plant improvement. Plenum, New York, pp 209–280

    Google Scholar 

  • Dubkovsky J, Dvořák J (1994) Genome origin of Triticum cylindricum, Triticum triunciale, and Triticum ventricosum (Poaceae) inferred from variation in repeated nucleotide sequences: A methodological study. Am J Bot 81:1327–1335

    Article  Google Scholar 

  • Dubkovsky J, Dvořák J (1995) Genome identification of the Triticum crassum complex (Poaceae) with the restriction patterns of repeated nucleotide sequences. Am J Bot 182:131–140

    Article  Google Scholar 

  • Dvořák J, Dubkovsky J (1996) Genome analysis of polyploid species employing variation in repeated nucleotide sequences. In: Jauhar PP (ed) Methods in genome analysis in plants. CRC, Boca Raton, pp 133–145

    Google Scholar 

  • Dvořák J, Zhang HB (1992) Reconstruction of the phylogeny of the genus Triticum from variation in repeated nucleotide sequences. Theor Appl Genet 84:419–429

    Article  Google Scholar 

  • Feldman M (2001) Origin of cultivated wheat. In: Bonjean AP, Angus WJ (eds) The world wheat book: a history of wheat breeding. Intersept, London, pp 3–56

    Google Scholar 

  • Flavell RB (1986) Repetitive DNA and chromosome evolution in plants. Philos Trans R Soc Lond B Biol Sci 312:227–242

    CAS  Article  PubMed  Google Scholar 

  • Flavell RB, Bennett MD, Smith JB, Smith DB (1974) Genome size and the proportion of repeated sequence DNA in plants. Biochem Genet 12:257–269

    CAS  Article  PubMed  Google Scholar 

  • Flavell RB, Rimpau J, Smith DB (1977) Repeated sequence DNA relationships in four cereal genomes. Chromosoma 63:205–222

    CAS  Article  Google Scholar 

  • Flavell R, O'Dell M, Smith D (1979) Repeated sequence DNA comparisons between Triticum and Aegilops species. Heredity 42:309–322

    CAS  Article  Google Scholar 

  • Friebe BR, Tuleen NA, Gill BS (1999) Development and identification of a complete set of Triticum aestivum–Aegilops geniculata chromosome addition lines. Genome 42:374–380

    Article  Google Scholar 

  • Gerlach WL, Bedbrook JR (1979) Cloning and characterization of ribosomal RNA genes from wheat and barley. Nucleic Acids Res 7:1869–1885

    CAS  Article  PubMed  Google Scholar 

  • Gerlach WL, Dyer TA (1980) Sequence organization of the repeated units in the nucleus of wheat which contains 5S-rRNA genes. Nucleic Acids Res 8:4851–4865

    CAS  Article  PubMed  Google Scholar 

  • Grewal SIS, Moazed D (2003) Heterochromatin and epigenetic control of gene expression. Science 301:798–802

    CAS  Article  PubMed  Google Scholar 

  • Heslop-Harrison JS (2000) Comparative genome organization in plants: from sequence and markers to chromatin and chromosomes. Plant Cell 12:617–636

    CAS  Article  PubMed  Google Scholar 

  • Huang S, Sirikhachornkit A, Su X et al (2002) Genes encoding plastid acetyl-CoA carboxylase and 3-phosphoglycerate kinase of the Triticum/Aegilops complex and the evolutionary history of polyploid wheat. Proc Natl Acad Sci USA 99:8133–8138

    CAS  Article  PubMed  Google Scholar 

  • Irigoyen ML, Loarce Y, Linares C et al (2001) Discrimination of the closely related A and B genomes in AABB tetraploid species of Avena. Theor Appl Genet 103:1160–1166

    CAS  Article  Google Scholar 

  • Jaillon O, Aury J-M, Noel B et al (2007) The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449:463–467

    CAS  Article  PubMed  Google Scholar 

  • Jiang J, Gill BS, Wang G, Ronald PC, Ward DC (1995) Metaphase and interphase fluorescence in situ hybridization mapping of the rice genome with bacterial artificial chromosomes. Proc Natl Acad Sci USA 92:4487–4491

    CAS  Article  PubMed  Google Scholar 

  • Jones JDG, Flavell RB (1982a) The mapping of highly-repeated DNA families and their relationship to C-bands in chromosomes of Secale cereale. Chromosoma 86:595–612

    Article  Google Scholar 

  • Jones JDG, Flavell RB (1982b) The structure, amount and chromosomal localisation of defined repeated DNA sequences in species of the genus Secale. Chromosoma 86:613–641

    CAS  Article  Google Scholar 

  • Katsiotis A, Schmidt T, Heslop-Harrison JS (1996) Chromosomal and genomic organization of Ty1-copia-like retrotransposon sequences in the genus Avena. Genome 39:410–417

    CAS  Article  PubMed  Google Scholar 

  • Kimber G, Sallee PJ, Feiner MM (1988) The interspecific and evolutionary relationships of Triticum ovatum. Genome 30:218–221

    Article  Google Scholar 

  • Li W, Zhang P, Fellers JP, Friebe B, Gill BS (2004) Sequence composition, organization, and evolution of the core Triticeae genome. Plant J 40:500–511

    CAS  Article  PubMed  Google Scholar 

  • Lim KY, Matyasek R, Kovarik A, Fulnecek J, Leitch AR (2005) Molecular cytogenetics and tandem repeat sequence evolution in the allopolyploid Nicotiana rustica compared with diploid progenitors N. paniculata and N. undulata. Cytogenet Genome Res 109:298–309

    CAS  Article  PubMed  Google Scholar 

  • Linares C, Loarce Y, Serna AAF (2001) Isolation and characterization of two novel retrotransposons of the Ty1-copia group in oat genomes. Chromosoma 110:115–123

    CAS  Article  PubMed  Google Scholar 

  • Linc G, Friebe BR, Kynast RG et al (1999) Molecular cytogenetic analysis of Aegilops cylindrica Host. Genome 42:497–503

    CAS  Article  PubMed  Google Scholar 

  • Nagaki K, Kishii M, Tsujimoto H, Sasakuma T (1999) Tandem repetitive Afa-family sequences from Leymus racemosa and Psathyrostachys juncea (Poaceae). Genome 42:1258–1260

    CAS  Article  PubMed  Google Scholar 

  • Paterson AH, Bowers JE, Bruggmann R et al (2009) The Sorghum bicolor genome and the diversification of grasses. Nature 457:551–556

    CAS  Article  PubMed  Google Scholar 

  • Paux E, Roger D, Badaeva E et al (2006) Characterizing the composition and evolution of homoeologous genomes in hexaploid wheat through BAC-end sequencing on chromosome 3B. Plant J 48:463–474

    CAS  Article  PubMed  Google Scholar 

  • Paux E, Sourdille P, Salse J et al (2008) A physical map of the 1-gigabase bread wheat chromosome 3B. Science 322:101–104

    CAS  Article  PubMed  Google Scholar 

  • Rayburn AL, Gill BS (1986) Isolation of a D-genome specific repeated DNA sequence from Aegilops squarrosa. Plant Mol Biol Rep 4:104–109

    Article  Google Scholar 

  • Resta P, Zhang HB, Dubkovsky J, Dvořák J (1996) The origin of the genomes of Triticum biunciale, T. ovatum, T. neglectum, T. columnare, and T. rectum based on variation in repeated nucleotide sequences. Am J Bot 83:1556–1565

    CAS  Article  Google Scholar 

  • Schmidt T, Kubis S, Heslop-Harrison JS (1995) Analysis and chromosomal localization of retrotransposons in sugar beet (Beta vulgaris L.): LINEs and Ty1-copia-like elements as major components of the genome. Chromosome Res 3:335–345

    CAS  Article  PubMed  Google Scholar 

  • Schnable PS, Ware D, Fulton RS et al (2009) The B73 maize genome: complexity, diversity, and dynamics. Science 326:1112–1115

    CAS  Article  PubMed  Google Scholar 

  • Schneider A, Linc G, Molnar-Lang M (2003) Fluorescence in situ hybridization polymorphism using two repetitive DNA clones in different cultivars of wheat. Plant Breed 122:396–400

    CAS  Article  Google Scholar 

  • Schneider A, Molnár I, Molnár-Láng M (2008) Incorporation of Aegilops biuncialis chromosomes into wheat and their identification using fluorescent in situ hybridization. Acta Biol Szeged 52:133–137

    Google Scholar 

  • Sequencing Project International Rice G (2005) The map-based sequence of the rice genome. Nature 436:793–800

    Article  Google Scholar 

  • Sharma S, Raina SN (2005) Organization and evolution of highly repeated satellite DNA sequences in plant chromosomes. Cytogenet Genome Res 109:15–26

    CAS  Article  PubMed  Google Scholar 

  • Solano R, Hueros G, Fominaya A, Ferrer E (1992) Organization of repeated sequences in species of the genus Avena. Theor Appl Genet 83:602–607

    Article  Google Scholar 

  • Staton SE, Ungerer MC, Moore RC (2009) The genomic organization of Ty3/gypsy-like retrotransposons in Helianthus (Asteraceae) homoploid hybrid species. Am J Bot 96:1646–1655

    CAS  Article  Google Scholar 

  • Sun GL, Daley T, Ni Y (2007) Molecular evolution and genome divergence at RPB2 gene of the St and H genomes in Elymus species. Plant Mol Biol 64:645–655

    CAS  Article  PubMed  Google Scholar 

  • Taketa S, Ando H, Takeda K, Harrison GE, Heslop-Harrison JS (2000) The distribution, organization and evolution of two abundant and widespread repetitive DNA sequences in the genus Hordeum. Theor Appl Genet 100:169–176

    CAS  Article  Google Scholar 

  • The Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796–815

    Article  Google Scholar 

  • Thomas W, Stefan T, Andreas H et al (2009) A whole-genome snapshot of 454 sequences exposes the composition of the barley genome and provides evidence for parallel evolution of genome size in wheat and barley. Plant J 59:712–722

    Article  Google Scholar 

  • Vershinin AV, Schwarzacher T, Heslop-Harrison JS (1995) The large-scale genomic organization of repetitive DNA families at the telomeres of rye chromosomes. Plant Cell 7:1823–1833

    CAS  Article  PubMed  Google Scholar 

  • Yen Y, Kimber G (1990) The U genome in Triticum ovatum from Turkey. Cereal Res Commun 18:13–19

    Google Scholar 

  • Yen Y, Kimber G (1992) Genomic relationships on N-genome Triticum species. Genome 35:962–966

    Google Scholar 

  • Zhang HB, Dvorak J (1992) The genome origin and evolution of hexaploid Triticum crassum and Triticum syriacum determined from variation in repeated nucleotide sequences. Genome 35:806–814

    CAS  Google Scholar 

  • Zhang H-B, Dvořák J, Waines JG (1992) Diploid ancestry and evolution of Triticum kotschyi and T. peregrinum examined using variation in repeated nucleotide sequences. Genome 35:182–191

    CAS  Google Scholar 

  • Zhang P, Li W, Fellers J, Friebe B, Gill BS (2004) BAC-FISH in wheat identifies chromosome landmarks consisting of different types of transposable elements. Chromosoma 112:288–299

    CAS  Article  PubMed  Google Scholar 

Download references

Acknowledgements

The authors thank Drs. N.N. Chikida and I.G. Loskutov (Vavilov Institute of Plant Industry, VIR, St. Petersburg, Russia); Dr. B.S. Gill (Wheat Genetic and Genomics Resource Center, Kansas State University, USA); Dr. J. Konopka (ICARDA, Aleppo, Syria); Dr. S.N. Sibikeev (Agricultural Research Institute for South-East Region, Saratov, Russia); Drs. V.A. Pukhalskyi and V.P. Upelniek (Vavilov Institute of General Genetics, Moscow, Russia); Dr. S.V. Chebotar (Plant Breeding Institute, Odessa, Ukraine); Dr. L.A. Pershina (Institute of Cytology and Genetics, Novosibirsk, Russia); Dr. I.V. Iordanskaya (Scientific-Research Agricultural Institute of the Central Zone of Non-Chernozem Region, Moscow Region, Nemchinovka); and Dr. Hernandez P. (Institute for Sustainable Agriculture, Cordoba, Spain). This work was partially supported by grant of the Russian State Foundation for Basic Research (project number 08-04-00302).

Author information

Affiliations

  1. Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Street 32, Moscow, 119991, Russia

    Ekaterina D. Badaeva, Svyatoslav A. Zoshchuk, Natalia V. Zoshchuk & Alexander V. Zelenin

  2. INRA UBP UMR 1095, Genetics, Diversity and Ecophysiology of Cereals, 234 Avenue du Brézet, 63100, Clermont-Ferrand, France

    Etienne Paux, Georges Gay, Delphine Roger, Michel Bernard & Catherine Feuillet

Authors
  1. Ekaterina D. Badaeva
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Svyatoslav A. Zoshchuk
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Etienne Paux
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Georges Gay
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Natalia V. Zoshchuk
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Delphine Roger
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Alexander V. Zelenin
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Michel Bernard
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Catherine Feuillet
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Ekaterina D. Badaeva.

Additional information

Responsible Editor: Pat Heslop-Harrison.

Electronic supplementary materials

Below is the link to the electronic supplementary material.

ESM 1

(JPEG 6554 kb)

ESM 2

(JPEG 2277 kb)

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Badaeva, E.D., Zoshchuk, S.A., Paux, E. et al. Fat element—a new marker for chromosome and genome analysis in the Triticeae. Chromosome Res 18, 697–709 (2010). https://doi.org/10.1007/s10577-010-9151-x

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10577-010-9151-x

Key Words

  • Fat sequence
  • Fluorescence in situ hybridisation (FISH)
  • chromosome
  • genome
  • cereal
  • evolution