UMD Theses and Dissertations
Permanent URI for this collectionhttp://hdl.handle.net/1903/3
New submissions to the thesis/dissertation collections are added automatically as they are received from the Graduate School. Currently, the Graduate School deposits all theses and dissertations from a given semester after the official graduation date. This means that there may be up to a 4 month delay in the appearance of a given thesis/dissertation in DRUM.
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Item Population Declines and Genetic Variation: Effects of Serial Bottlenecks(2015) Callicrate, Taylor Eilers; Song, Jiuzhou; Fleischer, Robert C; Animal Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Islands foster unique biodiversity, yet also present biogeographic limitations that impose increased risk for population extinction through demographic and genetic constraints and decreased probability of surviving a catastrophe. Of particular interest, especially with regard to endangered species, is the genetic response of insular species to severe population declines or translocations. Both types of events, considered population bottlenecks, are expected to reduce genetic variation, and correspondingly, adaptive potential. For these reasons, it is important to understand how bottlenecks interact with insular population dynamics to affect genetic diversity. I used a combination of a laboratory model experiment and population genetics study of an in situ bottleneck in an endangered species to investigate how quantitative and molecular genetic variation are affected during bottlenecks. I used a laboratory animal model (red flour beetle, Tribolium castaneum) to compare how quantitative genetic variation is affected if a serial bottleneck occurs in a novel versus familiar environment. The experiment was designed to model a founder event or translocation to a new island with a novel environment. I found that phenotypic and additive variance for a quantitative trait were larger following a bottleneck occurring in the novel environment, suggesting that the novel environment could improve adaptive potential in bottlenecked populations. Next, I used molecular genetic markers to assess variation and signatures of selection in the Laysan finch (Telespiza cantans), a Hawaiian honeycreeper endemic to a small Northwestern Hawaiian island. Laysan finches experienced a major bottleneck on Laysan in the early 20th century, followed by a translocation and series of founder events as populations were established on the islets of Pearl and Hermes Reef (PHR) in the 1960s – 70s. I found that, contrary to expectation, bottlenecked Laysan finch populations did not show declines in genetic variation and were not differentiated as a result of genetic drift. These results are potentially caused by insular demographic dynamics. I identified loci with extreme differentiation between modern populations, potentially indicating genomic signals of selection. These regions could be important for adaptation to the novel environment on PHR and are candidates for future study.Item Identification of a single nucleotide polymorphism associated with adiposity following transcriptional profiling of gene expression in the anterior pituitary gland(2006-07-23) muchow, michael; Porter, Tom E; Molecular and Cell Biology; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Although the anterior pituitary secretes three hormones that affect metabolism and body fat stores, a comprehensive analysis of pituitary gene expression associated with body fat has not been performed. This research used cDNA microarrays to investigate pituitary gene expression in two chicken lines that were selected for low and high body fat (Lean and Fat). RNA was extracted from pituitaries at 1, 3, 5, and 7 weeks of age. 386 genes that showed significant differences in expression levels by line or in the line-by-age interaction were analyzed further. Differentially expressed genes between lines are potential candidates as genetic markers for high and low potential for body fat accumulation. One such candidate, the lysophosphatidic acid (LPA) receptor-1 (LPAR1), was identified as a potential marker, being differentially expressed between the 2 lines at the early ages. Genomic DNA from the Fat and Lean F0 generation was sequenced upstream of the LPAR1 coding region. A SNP consisting of a T to C transversion that introduces a GATA-1 transcription factor binding site was identified in the Lean line (Fisher's Exact Test, p ≤ 0.001). The fattest and leanest animals of both sexes in the back-crossed F2 generation (n=48 each) were genotyped by allele-specific PCR, and an association was present between the genotype and phenotype (generalized linear model, p ≤ 0.05). Expression of GATA transcription factors in mice inhibits differentiation of preadipocytes into mature adipocytes. LPAR1 also inhibits differentiation of preadipocytes in mice, and LPAR1 knock-out mice become significantly fatter than wild-type mice. A SNP that introduces a GATA site in the promoter of LPAR1 could up-regulate its expression in the Lean line, and increased LPA signaling could then inhibit preadipocyte differentiation. Conversely, loss of the GATA binding site could explain decreased levels of LPAR1 expression and attenuated inhibition of adipocyte maturation in the Fat line.Item GENETIC DIVERSITY AND LINKAGE DISEQUILIBRIUM IN WILD SOYBEAN, LANDRACES, ANCESTRAL, AND ELITE SOYBEAN POPULATIONS(2005-04-20) Hyten, Jr., David Lee; Costa, Jose M.; Plant Science and Landscape Architecture (PSLA); Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Domestication, founder effects, and artificial selection can impact populations by reducing genome diversity and increasing the extent of linkage disequilibrium (LD). To understand the impact of these genetic bottlenecks and selection on sequence diversity and LD within soybean [Glycine max (L.) Merr.], 111 genes and three chromosomal regions located on linkage groups A2, G, and J were characterized in soybean. Four soybean populations were evaluated: 1) the wild ancestor of soybean (G. soja), 2) the population resulting from domestication (landraces), 3) Asian introductions from which North American cultivars were developed (ancestors), and 4) elite cultivars from the 1980's (elite). A total of 438 single nucleotide polymorphisms (SNPs) and 58 insertions-deletions were discovered within the 102 genes. Sequence diversity was lower than expected in G. soja with an overall theta equal to 0.00235, and was less than half that value (theta = 0.00115) in the landraces. Domestication eliminated most unique haplotypes with G. soja containing 240 unique haplotypes while the landraces only contained 42 unique haplotypes. The founder effect of the introduction of soybean to North America followed by intensive artificial selection, resulted in only a 30% decrease in nucleotide diversity. A total of 738 SNPs were discovered and genotyped in the four populations throughout three chromosomal regions. In G. soja LD did not extend past 100 kb while in the three cultivated soybean populations LD extended from 90 kb up to 600+ kb, most likely as a result of increased inbreeding and domestication. The three chromosomal regions varied in the extent of LD within the populations. G. soja is the greatest resource for unique alleles and may be best suited for fine mapping utilizing association analysis. The landraces do not contain much more variability than the elite cultivars but may have enough diversity to facilitate genetic improvement of elite cultivars. Finally, due to the extended levels of LD in the landraces and the elite cultivars, whole genome association analysis may be possible for the discovery of QTL.