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Dissertation/Thesis Abstract

From genes to ecosystems: The genetic basis of Populus angustifolia resistance to a galling herbivore, Pemphigus betae
by Zinkgraf, Matthew S., Ph.D., Northern Arizona University, 2012, 134; 3548562
Abstract (Summary)

A major focus in ecology is to put communities and ecosystems into an evolutionary framework by identifying heritable variation in foundation species that contributes to community organization and ecosystem processes. This concept, referred to as "Genes-to-Ecosystems", provides a conceptual framework for studying the genetically-based interactions within species and across hybrid complexes, and how they influence ecosystem processes. Populus provides a model system to span the continuum from genes to ecosystems because it is the first tree genus with a complete genome sequence. The genomics revolution provides unprecedented opportunities for exploring these questions in the foundation species, Populus angustifolia.

Using association-mapping techniques, I used a two-tiered approach to identify P. angustifolia genes that were associated with tree resistance to an important galling insect, Pemphigus betae. First, using mapped genetic markers in an admixed population of P. angustifolia from the Weber River (UT), two major finding emerged. First, three unlinked quantitative trait loci (QTL) for resistance were identified while controlling for population structure. Each QTL explained approximately 7-8% of the variation in tree resistance to P. betae. Second, linking these QTL to the Populus genome resulted in the discovery of 27 candidate genes (genes believed to be associated with resistance) for sink-source relations that collocated within the QTL regions.

Using candidate gene mapping in a "pure" population of P. angustifolia, I tested if genetic variation in specific sink-source relation genes were associated with tree resistance to P. betae. Using three genes from a previously identified QTL, genetic variation in these genes was surveyed and tested for associations with tree resistance. From this study two major findings emerged. First, a plant neutral invertase (NIN1 ) was associated with tree resistance based on both the gene haplotypes and individual SNP analyses. Second, gene haplotypes from an inhibitor of invertase (c/vif1) were independently associated with tree resistance. Genetic variation in each of the two sink-source relation genes explains approximately 6-8% of variation in tree resistance along the Weber River, Utah.

Lastly, gene introgression in the context of a whole genome duplication event was surveyed in a hybrid zone formed between P. fremontii and P. angustifolia. Using a maximum likelihood method, I identified 14 (10.2%) markers that occurred more than expected and 7 (5.1%) that occurred less than expected under neutral expectations. Linking these genetic markers to the Populus genome reveal that the Salicoid whole genome duplication significantly influences the rate of gene introgression (p < 0.002) in Populus. These patterns of introgression are driven by an increase in positively introgressing markers located in two paralogous segments located on linkage groups II/V and VIII/X that resulted from the Salicoid duplication event. In addition, three of four paralogous marker pairs from the introgressing regions were significantly correlated (p < 0.05), suggesting that epistatic interactions among paralogous regions may facilitate co-introgression of both paralogous segments.

Indexing (document details)
Advisor: Allan, Gerard J.
Commitee: DiFazio, Stephen P., Service, Philip M., Whitham, Thomas G.
School: Northern Arizona University
Department: Biological Sciences
School Location: United States -- Arizona
Source: DAI-B 74/05(E), Dissertation Abstracts International
Subjects: Plant biology, Ecology, Genetics
Keywords: Admixtures, Candidate gene mapping, Community genetics, Genome duplication, Invertase, Populus angustifolia
Publication Number: 3548562
ISBN: 978-1-267-84102-5
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