Low levels of linkage disequilibrium in wild barley (Hordeum vulgare ssp spontaneum) despite high rates of self-fertilization

High levels of inbreeding cause populations to become composed of homozygous, inbred lines. High levels of homozygosity limit the effectiveness of recombination, and therefore, retard the rate of decay of linkage (gametic phase) disequilibrium (LD) among mutations. Inbreeding and recombination interact to shape the expected pattern of LD. The actual extent of nucleotide sequence level LD within inbreeding species has only been studied in Arabidopsis, a weedy species whose global range has recently expanded. In the present study, we examine the levels of LD within and between 18 nuclear genes in 25 accessions from across the geographic range of wild barley, a species with a selfing rate of approximate to 98%. In addition to examination of intralocus LD, we employ a resampling method to determine whether interlocus LID exceeds expectations. We demonstrate that, for the majority of wild barley loci, intralocus LID decays rapidly, i.e., at a rate similar to that observed in the outcrossing species, Zea mays (maize). Excess interlocus LID is observed at 15% of two-locus combinations; almost all interlocus LID involves loci with significant geographic structuring of mutational variation.