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Physical mapping of rDNA and heterochromatin in chromosomes of 16 Coffea species: A revised view of species differentiation

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Abstract

The chromosome organization among 15 wild diploid Coffea species and cultivated tetraploid C. arabica was determined by fluorochrome banding (CMA, DAPI) and double fluorescence in-situ hybridization (FISH) of 5S and 18S rDNA achieved on the same chromosome plates. Two to five chromosome pairs (plus one putative chromosome B) are marked. Overall, there are two SAT-chromosome pairs for East African species and one for the Malagasy and the West and Central African species. 18S rDNA loci are telomeric and strongly marked the SAT-chromosome pairs. Generally, only one pericentromeric 5S rDNA locus characterized East African species, while an additional minor locus co-localized with the 18S rDNA-SAT locus for the Malagasy species and West and Central African species. A combination of rDNA FISH plus CMA and DAPI banding patterns enables identification of almost all the species, even those for which the genetic or botanical status is still being discussed. C. arabica clearly appears to be an allotetraploid species, including one genome from East Africa and one from West and Central Africa. However, since the minor 5S rDNA-SAT locus present in West/Central African genomes is not detected, two evolutionary hypotheses could be put forward for C. arabica. Considering only the diploid species, global trends are obvious in rDNA signal patterns, genome size variations, and geographic distribution of the species, but there are no clear evolutionary trends. However, complex interactions between these factors and environmental growing conditions exist, which have resulted in loss and gain of rDNA loci and probably also in copy repeat number variations in each rDNA family.

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Abbreviations

BAC:

bacterial artificial chromosome

CCD:

charge-coupled device camera

CMA:

chromomycin A3

DAPI:

4′,6 diamidino-2-phenylindole

FISH:

fluorescence in-situ hybridization

GISH:

genomic in-situ hybridization

HC:

heterochromatin

NOR:

nucleolar organizing region

SAT:

satellite chromosome with a secondary constriction

SC:

secondary constriction

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Acknowledgements

This work was financially supported by the Institut de Recherche pour le Développement (IRD, action incitative RubiComp) and the Centre National de Recherche Scientifique (CNRS). The authors thank Dr Spencer C. Brown from the Institut des Sciences du Végétal (CNRS, Gif-sur-Yvette, France) for his expert assistance in flow cytometry on the IFR87 Platform. We are most grateful to Pat Heslop-Harrison and the anonymous reviewers for their valuable comments and useful suggestions on earlier versions of the manuscript.

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  1. IRD, UMR DIAPC, 911 Av Agropolis, BP 64501, 34394, Montpellier cedex 5, France

    P. Hamon, V. Poncet, S. Hamon & A. de Kochko

  2. UMR 8079 UPS-CNRS-AgroParisTech, Bat. 360, 91405, Orsay cedex, France

    S. Siljak-Yakovlev & O. Robin

  3. University Mae Fah Luang, Chiang Raï, Thailand

    S. Srisuwan

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  1. P. Hamon
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  2. S. Siljak-Yakovlev
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  3. S. Srisuwan
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Correspondence to P. Hamon.

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Hamon, P., Siljak-Yakovlev, S., Srisuwan, S. et al. Physical mapping of rDNA and heterochromatin in chromosomes of 16 Coffea species: A revised view of species differentiation. Chromosome Res 17, 291–304 (2009). https://doi.org/10.1007/s10577-009-9033-2

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