Genome-wide association studies depend upon the extent of linkage disequilibrium (LD), the number and distribution of markers and the underlying structure in populations under study. Outbreeding species generally exhibit limited LD and consequently a very large number of markers are required for effective whole genome association genetic scans. In contrast, several of the world?s major food crops are self-fertilizing inbreeding species with narrow genetic bases and theoretically extensive LD. Together these are predicted to result in a combination of low resolution and a high frequency of spurious associations in LD-based studies. However, inbred elite plant varieties represent a unique human-induced pseudo-outbreeding population that has been subjected to strong selection for advantageous alleles. By assaying 1524 genome-wide SNPs in a collection of European barley cultivars we demonstrate that, after accounting for population sub-structure, the level of LD exhibited in elite north west European barley, a typical inbred cereal crop, can be effectively exploited to map traits using whole genome association scans with several hundred to thousands of bi-allelic SNPs.