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FISH mapping and molecular organization of the major repetitive sequences of tomato

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Abstract

This paper presents a bird’s-eye view of the major repeats and chromatin types of tomato. Using fluorescence in-situ hybridization (FISH) with Cot-1, Cot-10 and Cot-100 DNA as probes we mapped repetitive sequences of different complexity on pachytene complements. Cot-100 was found to cover all heterochromatin regions, and could be used to identify repeat-rich clones in BAC filter hybridization. Next we established the chromosomal locations of the tandem and dispersed repeats with respect to euchromatin, nucleolar organizer regions (NORs), heterochromatin, and centromeres. The tomato genomic repeats TGRII and TGRIII appeared to be major components of the pericentromeres, whereas the newly discovered TGRIV repeat was found mainly in the structural centromeres. The highly methylated NOR of chromosome 2 is rich in [GACA]4, a microsatellite that also forms part of the pericentromeres, together with [GA]8, [GATA]4 and Ty1-copia. Based on the morphology of pachytene chromosomes and the distribution of repeats studied so far, we now propose six different chromatin classes for tomato: (1) euchromatin, (2) chromomeres, (3) distal heterochromatin and interstitial heterochromatic knobs, (4) pericentromere heterochromatin, (5) functional centromere heterochromatin and (6) nucleolar organizer region.

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Authors and Affiliations

  1. Wageningen University, Laboratory of Genetics, 6703 BD, Wageningen, The Netherlands

    Song-Bin Chang, Dóra Szinay & Hans de Jong

  2. Department of Agronomy, National Taiwan University, Taipei, 10617, Taiwan

    Song-Bin Chang

  3. Department of Plant Science, College of Agriculture and Life Science, Seoul National University, Seoul, 151-921, Republic of Korea

    Tae-Jin Yang

  4. Wageningen University and Research Centre, Plant Research International, 6700 AA, Wageningen, The Netherlands

    Erwin Datema & Ben Vosman

  5. Departement van Moleculaire biologie, 191 NCMLS Radboud Universiteit, Nijmegen, 6500 HB, Nijmegen, The Netherlands

    Joke van Vugt

  6. Wageningen University, Laboratory of Plant Breeding, 6700 AA, Wageningen, The Netherlands

    Anja Kuipers & Evert Jacobsen

  7. Institute of Biophysics, Czech Academy of Sciences, 61265, Brno, Czech Republic

    Marie Meznikova

  8. Wageningen University, Centre for Biosystems Genomics, 6708 PB, Wageningen, The Netherlands

    René Klein Lankhorst & Hans de Jong

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  1. Song-Bin Chang
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  2. Tae-Jin Yang
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  11. Hans de Jong
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Correspondence to Hans de Jong.

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Chang, SB., Yang, TJ., Datema, E. et al. FISH mapping and molecular organization of the major repetitive sequences of tomato. Chromosome Res 16, 919–933 (2008). https://doi.org/10.1007/s10577-008-1249-z

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  • DOI: https://doi.org/10.1007/s10577-008-1249-z

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