Use of SSR Marker Data to Study Linkage Disequilibrium and Population Structure in Hordeum vulgare: Prospects for Association Mapping in Barley

Abstract

Random samples of lines developed for genetic mapping are in extreme linkage disequilibrium and have no population structure. In contrast, non-random sets of existing cultivars, breeding lines or accessions have unknown linkage disequilibrium and may have complex structure. We examined simple-sequence repeat (SSR) marker information for several such germplasm sets. Disequilibrium was high among cultivars and lines of cultivated barley (H. vulgare ssp. vulgare) and low among accessions of H. vulgare ssp. spontaneum. Within diverse sets of barley germplasm, there was frequent disequilibrium among non-linked loci, suggesting that association mapping without consideration of population structure would have a high rage of Type-I error. Among subsets representing known germplasm groups, disequilibrium between non-linked loci was greatly reduced while disequilibrium among closely linked loci was largely maintained. Similar effects were obtained using subsets identified by model-based analysis of population structure. With sufficient marker density and control of population structure, patterns of disequilibrium among loci in barley may be appropriate for association mapping of trait loci.