Identification, characterization, and dynamics of transposable elements in iris and brassica
Kentner, Edward Keoki
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Transposable elements (TEs) are ubiquitous components of plant genomes, yet their dynamics and the genetic variability due to their activities within populations has not been adequately investigated. This dissertation contains two studies designed to investigate the impact of transposable elements on plant genome evolution. In the first study, TY3/gypsy-like retrotransposons were characterized from Iris fulva and I. brevicaulis and used to develop molecular markers which can be used to study the insertion site polymorphism of the elements. The copy number of these IRRE elements (for IRis RetroElement), is ~1 × 105, accounting for ~6-10% of the ~10,000 Mb haploid Louisiana Iris genome. IRRE elements are transcriptionally active in Iris brevicaulis and I. fulva and their F1 and backcross hybrids, but evidence for increased transcription in hybrid plants was not found. The Iris genome contains many subfamilies of these elements which can be used to generate molecular markers in diverse Iris species. The second study investigates the insertion polymorphism of the CACTA-like DNA transposon Boc-1 in Brassica nigra. The insertion polymorphism of Boc-1 elements was assayed by transposon display in four populations from southern California, and compared to the polymorphism of presumably neutral control markers. The neutrality of the TE insertions was tested using an approach based on the analysis of fixation indices, and using existing TE population genetic theory that has been applied to elements from Drosophila. Based on comparisons among fixation indices, most Boc-1 insertions appear to be neutral, but there was evidence of forces preventing individual insertions from reaching high population frequencies. Some explanations for these apparently conflicting results based on the biology of the elements are discussed.