Theoretical and Applied Genetics

, Volume 119, Issue 1, pp 175–187

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


    • Genetics ProgrammeScottish Crop Research Institute (SCRI)
  • W. T. B. Thomas
    • Genetics ProgrammeScottish Crop Research Institute (SCRI)
  • F. Á. van Eeuwijk
    • Biometrics Applied StatisticsWageningen University
  • S. Ceccarelli
    • International Center for Agricultural Research in the Dry Areas (ICARDA)
  • S. Grando
    • International Center for Agricultural Research in the Dry Areas (ICARDA)
  • A. M. Stanca
    • CRA, Genomic Research Centre
  • N. Pecchioni
    • Dipartimento di Scienze AgrarieUniversità di Modena e Reggio Emilia
  • T. Akar
    • Central Research for Field Crops
  • A. Al-Yassin
    • NCARTT
  • A. Benbelkacem
    • ITGC
  • H. Ouabbou
    • INRA Morocco, CRRA
  • J. Bort
    • Department de Biologia VegetalUniversitat de Barcelona
  • I. Romagosa
    • Centre UdL-IRTAUniversitat de Lleida
  • C. A. Hackett
    • BioSSSCRI
  • J. R. Russell
    • Genetics ProgrammeScottish Crop Research Institute (SCRI)
Original Paper

DOI: 10.1007/s00122-009-1027-0

Cite this article as:
Comadran, J., Thomas, W.T.B., van Eeuwijk, F.Á. et al. Theor Appl Genet (2009) 119: 175. doi:10.1007/s00122-009-1027-0


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 r2 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.

Supplementary material

122_2009_1027_MOESM1_ESM.doc (2.1 mb)
Supplementary material 1 (DOC 2,133 kb)

Copyright information

© Springer-Verlag 2009