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

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Abstract

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.

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Abbreviations

DAPI:

4′,6′-Diamidino-2-phenylindole

FISH:

Fluorescent in situ hybridization

GISH:

Genomic in situ hybridization

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Acknowledgments

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.

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Authors and Affiliations

  1. Laboratory of Plant Molecular Cytogenetics, Institute of Evolution, University of Haifa, Mount Carmel, Haifa, 31905, Israel

    Olga Raskina & Alexander Belyayev

  2. Laboratory of Systems Biology and Data Mining, Institute of Evolution, University of Haifa, Mount Carmel, Haifa, 31905, Israel

    Leonid Brodsky

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  1. Olga Raskina
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Correspondence to Olga Raskina.

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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)

High resolution image (TIFF 3677 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)

High resolution image (TIFF 3408 kb)

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Raskina, O., Brodsky, L. & Belyayev, A. Tandem repeats on an eco-geographical scale: outcomes from the genome of Aegilops speltoides . Chromosome Res 19, 607–623 (2011). https://doi.org/10.1007/s10577-011-9220-9

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