Degree Type

Dissertation

Date of Award

2017

Degree Name

Doctor of Philosophy

Department

Ecology, Evolution, and Organismal Biology

Major

Genetics and Genomics

First Advisor

Jonathan F. Wendel

Abstract

Polyploidy is an evolutionary phenomenon resulting in the duplication of the whole genome. The merger of two diverged genomes, in the case of allopolyploidy, had multiple effects on the evolution of genes, gene expression, and the structure of the newly doubled genome. Gene pathways and gene co-expression networks are also duplicated as a whole and must be reconciled in the nascent polyploid. A considerable body of work addresses how pathways and gene co-expression networks evolve in diploids. Here I extend this approach to address how duplicated pathways and networks evolve in polyploids.

The effects of polyploidy on gene pathways and gene co-expression network duplication are investigated in the natural cotton allopolyploids Gossypium hirsutum and G. barbadense. I used targeted sequence capture to look at evolutionary rates in the genes of the anthocyanin biosynthesis pathway across in over 40 different polyploid accessions. The evolutionary rates of these genes do not correlate with position or branching as would be expected. I further investigated the expression of the genes in the anthocyanin biosynthesis pathway, and of the whole genome, by generating RNA-seq libraries across several tissues in the polyploid cotton species and their diploid progenitors. Evolutionary rates were correlated with expression levels, module assignment, and connectivity. More generally, the gene co-expression network as a whole generally is preserved between diploids and polyploids, but certain modules exhibit specific homoeolog biases and non-additive expression.

I also studied expression in fibers from wild and domesticated G. hirsutum, adding a layer of complexity, in the form of the strong selective pressure of domestication, to the gene coexpression analyses. While I still find general preservation of the gene co-expression network, some modules show extreme homoeolog bias in the fiber as well. Comparisons between the wild and domesticated fiber co-expression networks show that there are drastic alterations in topology of the network due to strong, human-mediated selection. In addition, gene co-expression relationships have been strongly rewired as a consequence of the process of domestication.

Copyright Owner

Joseph Patrick Gallagher

Language

en

File Format

application/pdf

File Size

198 pages

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