Soleimani, Vahab D2013-11-082013-11-0820052005Source: Dissertation Abstracts International, Volume: 66-12, Section: B, page: 6401.http://hdl.handle.net/10393/29264http://dx.doi.org/10.20381/ruor-12856In the absence of whole genome sequencing, molecular markers are indispensable tools for the study of genome evolution, genetic diversity measurements, and genotype identification. We have used sequence-specific amplified polymorphism (S-SAP) markers that were derived from the BARE-1, an active retrotransposon of barley, to measure the contribution of this element to the evolution of barley genome among 103 cultivars that are commonly grown in Canada and the United States. The results were compared to the genome diversity measures obtained by the single nucleotide polymorphisms (SNP). The barley populations were divided into groups based on various agronomic traits such as end use, i.e., feed versus malting, and seed morphology, i.e., naked versus covered kernel. Analysis of the genetic structure in the population using analysis of molecular variance (AMOVA) for both S-SAP and SNP attributed the largest co-variance component (90%) to the genetic diversity among cultivars within groups. Co-variance component between groups was about 6% which indicated that there was no justification for population differentiation along the set based upon agronomic traits. Genetic relationships among cultivars was assessed by cluster analysis with UPGMA and found to vary substantially between S-SAP and SNP datasets. Quantitative analysis of BARE-1 retrotransposon with real-time PCR in a small group of cultivars showed significant differences in the copy number of the element among cultivars. Most of the BARE-1 elements were in the form of solo LTRs, indicating a high rate of homologous recombination between retrotransposon copies in the genome. Differences of up to 3000 BARE-1 copies per haploid genome were found among cultivars that have been developed and registered within the past three decades. Informative SNPs such as those with high polymorphic information content (PIC) values were used to generate identification keys to distinguish barley cultivars which were otherwise indistinguishable at the morphological and biochemical levels.257 p.enBiology, Botany.Biology, Genetics.Agriculture, Plant Culture.Thesis