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

Population structure and genome-wide linkagedisequilibrium (LD) were investigated in 192 Hordeumvulgare accessions providing a comprehensive coverage ofpast and present barley breeding in the Mediterraneanbasin, using 50 nuclear microsatellite and 1,130 DArTmarkers. Both clustering and principal coordinate analysesclearly sub-divided the sample into five distinct groupscentred on key ancestors and regions of origin of thegermplasm. For given genetic distances, large variation inLD values was observed, ranging from closely linked markers completely at equilibrium to marker pairs at50 cM separation still showing significant LD. Mean LDvalues across the whole population sample decayed belowr2 of 0.15 after 3.2 cM. By assaying 1,130 genome-wideDArT markers, we demonstrated that, after accounting forpopulation substructure, current genome coverage of 1marker per 1.5 cM except for chromosome 4H with 1marker per 3.62 cM is sufficient for whole genome associationscans. We show, by identifying associations withpowdery mildew that map in genomic regions known tohave resistance loci, that associations can be detected instrongly stratified samples provided population structure iseffectively controlled in the analysis. The population wedescribe is, therefore, shown to be a valuable resource,which can be used in basic and applied research in barley.