Structure of linkage disequilibrium in barley landrace populations and commercial varieties

Linkage disequilibrium (LD) is the nonrandom association of alleles at two (or more) loci. The extent of LD in natural and domesticated populations is mainly related to the effective recombination rate, the mating system and the population size. LD is promoted by drift, hitchhiking and epistatic selection, i t has become the matter of intensive studies in human genetics with the objective of identifying genes for genetic diseases and, more recently, in crop species such as Zea mays. Population subdivision and population admixture are also influencing the pattern of LD and should be carefully taken into account in data interpretation. In autogamous species few data are available and it is still not clear the extent to which this approach could be suitable. Indeed, the low effective recombination rate may cause high LD over too large portion of the genome making ineffective any study of association between neutral and selected loci. In our study we analysed the structure of LD in 10 barley landrace populations (30 individuals per population) and 60 commercial varieties using 10 mapped SSR and 20 ISSR loci. A very low LD was found in landrace populations in comparison whith what expected in strictly autogamous species suggesting that these material could be very useful for association genetics studies in barley.