The population dynamics of transposons in self- and cross-fertilizing plant populations are investigated both theoretically and empirically. Models were developed to evaluate the influence of host breeding system on transposon populations. Modeling results suggest that the selfing rate is likely to have important effects on the abundance and polymorphism patterns of transposable elements in plant genomes. A primary characterization of diversity and abundance of transposons in the self-pollinating species Arabidopsis thaliana was conducted using genomic sequencing data, providing strong evidence for recent element mobility. Utilizing this information, a PCR-based approach was implemented to examine transposon dynamics in populations of Arabidopsis thaliana and its outcrossing relative, Arabidopsis lyrata. The results provide evidence for the importance of purifying selection in controlling transposon abundance in outcrossing populations, but not in selfers. Differences observed between the species are consistent with the hypothesis that host breeding systems influence the selective pressure acting on transposons.

In sexually reproducing individuals, intraorganismal genetic heterogeneity (IGH) or mosaicism is thought to occur infrequently while genetic homogeneity is presumed the norm. In organisms that undergo modular development, such as long-lived plants, IGH has been substantially documented. In Arabidopsis thaliana we have shown that non-parental DNA that is inherited at low but detectable rates can also manifest on single plants as genotypically distinct somatic sectors suggesting that even short-lived annual plants show IGH. The underlying mechanism responsible for generating this type of IGH remains unknown. In order to better understand this phenomenon I have tested the hypothesis that among genome changes that occur in response to stress, these putative triggers also up-regulate IGH. Metabolic stress, cold stress, mechanical damage and ROS exposure were examined. To test for IGH, transgene markers and polymorphic molecular markers were used. Also, presented in this thesis is work investigating the effect of in vitro propagation through tissue culture on IGH frequencies. Regenerated plants as well as undifferentiated callus tissue were genotyped and assayed for sequence reversions. Molecular genotyping revealed an outcome contrary to that predicted by the initial hypothesis showing instead that a high frequency of restoration occurred in the progeny of un-treated control plants. With the exception of samples passed through tissue culture, molecular marker changes, including single and double reversions of alleles, were detected in every line at some low level Furthermore, many of the revertants were found to be genetic mosaics. DNA sequence analyses revealed that sequences flanking three molecular markers that had undergone reversion were near identical to the great-grandparent of the sequenced individual. These results suggest that stress is perhaps an inhibitor of restoration. Although there may be other explanations for the results described in this thesis, the evidence implicates genome restoration as a mechanism for generating IGH.

Thesis (Ph. D.)--University of Nevada, Reno, 2006. / "December 2006." Includes bibliographical references. Online version available on the World Wide Web. Library also has microfilm. Ann Arbor, Mich. : ProQuest Information and Learning Company, [2006]. 1 microfilm reel ; 35 mm.

Thesis (Ph. D.)--Worcester Polytechnic Institute. / Keywords: Zn; Heavy metal; ATPase. Includes bibliographical references (156-180 leaves ).

Diss. (sammanfattning). Uppsala : Sveriges lantbruksuniv., 2003. / Härtill 4 uppsatser.

Thesis (Ph.D.)--University of Missouri-Columbia, 2006. / The entire dissertation/thesis text is included in the research.pdf file; the official abstract appears in the short.pdf file (which also appears in the research.pdf); a non-technical general description, or public abstract, appears in the public.pdf file. Title from title screen of research.pdf file (viewed on April 27, 2009) Vita. Includes bibliographical references.

Thesis (Ph. D.)--Washington State University, December 2008. / Title from PDF title page (viewed on Jan. 15, 2008). "School of Biological Sciences." Includes bibliographical references.

Thesis (Ph. D.)--Auburn University, 2008. / Abstract. Vita. Includes bibliographical references.

Thesis (Ph. D.)--Michigan State University. Dept. of Biochemistry and Molecular Biology, 2008. / Title from PDF t.p. (viewed on July 10, 2009) Includes bibliographical references. Also issued in print.

Thesis (Ph. D.)--West Virginia University, 2009. / Title from document title page. Document formatted into pages; contains ix, 125 p. : ill. (some col.). Includes abstract. Includes bibliographical references (p. 98-125).