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Patterns of genetic diversity and linkage disequilibrium in a highly structured Hordeum vulgare association-mapping population for the Mediterranean basin

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Abstract

Population structure and genome-wide linkage disequilibrium (LD) were investigated in 192 Hordeum vulgare accessions providing a comprehensive coverage of past and present barley breeding in the Mediterranean basin, using 50 nuclear microsatellite and 1,130 DArT® markers. Both clustering and principal coordinate analyses clearly sub-divided the sample into five distinct groups centred on key ancestors and regions of origin of the germplasm. For given genetic distances, large variation in LD values was observed, ranging from closely linked markers completely at equilibrium to marker pairs at 50 cM separation still showing significant LD. Mean LD values across the whole population sample decayed below r 2 of 0.15 after 3.2 cM. By assaying 1,130 genome-wide DArT® markers, we demonstrated that, after accounting for population substructure, current genome coverage of 1 marker per 1.5 cM except for chromosome 4H with 1 marker per 3.62 cM is sufficient for whole genome association scans. We show, by identifying associations with powdery mildew that map in genomic regions known to have resistance loci, that associations can be detected in strongly stratified samples provided population structure is effectively controlled in the analysis. The population we describe is, therefore, shown to be a valuable resource, which can be used in basic and applied research in barley.

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Acknowledgments

The above work was funded by the European Union-INCO-MED program (ICA3-CT2002-10026). SCRI received grant in aid from the Scottish Government Rural and Environment Research and Analysis Department.

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Authors and Affiliations

  1. Genetics Programme, Scottish Crop Research Institute (SCRI), Invergowrie, Dundee, DD2 5DA, Scotland, UK

    Jordi Comadran, W. T. B. Thomas & J. R. Russell

  2. Biometrics Applied Statistics, Wageningen University, Wageningen, The Netherlands

    F. Á. van Eeuwijk

  3. International Center for Agricultural Research in the Dry Areas (ICARDA), Aleppo, Syria

    S. Ceccarelli & S. Grando

  4. CRA, Genomic Research Centre, 29017, Fiorenzuola d’Arda (PC), Italy

    A. M. Stanca

  5. Dipartimento di Scienze Agrarie, Università di Modena e Reggio Emilia, Reggio Emilia, Italy

    N. Pecchioni

  6. Central Research for Field Crops, Ankara, Turkey

    T. Akar

  7. NCARTT, Amman, Jordan

    A. Al-Yassin

  8. ITGC, Constantine, Algeria

    A. Benbelkacem

  9. INRA Morocco, CRRA, Settat, Morocco

    H. Ouabbou

  10. Department de Biologia Vegetal, Universitat de Barcelona, Barcelona, Spain

    J. Bort

  11. Centre UdL-IRTA, Universitat de Lleida, Lleida, Spain

    I. Romagosa

  12. BioSS, SCRI, Invergowrie, Dundee, Scotland, UK

    C. A. Hackett

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  1. Jordi Comadran
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  3. F. Á. van Eeuwijk
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  9. A. Al-Yassin
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  14. C. A. Hackett
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  15. J. R. Russell
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Corresponding author

Correspondence to Jordi Comadran.

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Communicated by A. Kilian.

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Comadran, J., Thomas, W.T.B., van Eeuwijk, F.Á. et al. Patterns of genetic diversity and linkage disequilibrium in a highly structured Hordeum vulgare association-mapping population for the Mediterranean basin. Theor Appl Genet 119, 175–187 (2009). https://doi.org/10.1007/s00122-009-1027-0

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