The goal of this project is to assess the role of high levels of self-fertilization in enhancing the conditions for linkage disequilibrium within plant species. Linkage disequilibrium refers to a correlation in allelic state between two different genetic loci at the population or species level. The statistic used to measure this correlation provides an index of the non-random distribution of alleles at different loci or of different nucleotide sties within a locus. All other things being equal, sexually reproducing organisms are expected to reach a state of linkage equilibrium because recombination ultimately randomizes the genome at all scales of resolution (the correlation in allelic state approaches zero independent of genetic distance). However, the rate of approach to equilibrium may be slow because it depends on the breeding system and the extent of linkage between genes. A nonrandom distribution is important because selection on a gene will perturb the frequencies of all other genes in linkage disequilibrium with the selected gene. Such perturbations can reduce the efficiency of selection because selection at one locus may be contravened by selection at a second locus in linkage disequilibrium with the first. This situation is known as linkage drag. Self-fertilization and linkage interact to restrict recombination, because self-fertilization reduces heterozygosity and thereby reduces the effective rate of recombination between genes or between nucleotide sites within a gene.
It is obviously important to characterize the extent of linkage disequilibrium in inbreeding species to better understand how restricted recombination may affect adaptive potential. This project will investigate the extent of linkage disequilibrium within wild barley (Hordeum vulgare ssp. spontaneum), a species with a rate of self-fertilization greater than 98%. The project will sample nucleotide sequences from a number of loci and the accessions sequenced will be chosen to span the geographic range of wild barley. The genetic scale of the samples will permit a measure of linkage disequilibrium at different physical and genetic distances ranging from (a) physical distances up to approximately 5,000 base pairs; (b) moderately linked genes (recombination fraction < 0.01); and (c) loosely linked genes (recombination fraction > 0.1). This investigation will permit a direct empirical assessment of how the interaction between selection, linkage and recombination restricts adaptive potential in inbreeding species.
