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Title:Understanding the genetic basis of dioecy in waterhemp (Amaranthus tuberculatus) and palmer amaranth (Amaranthus palmeri)
Author(s):Montgomery, Jacob Samuel
Advisor(s):Tranel, Patrick
Contributor(s):Hind, Sarah; Catchen, Julian
Department / Program:Crop Sciences
Discipline:Crop Sciences
Degree Granting Institution:University of Illinois at Urbana-Champaign
Degree:M.S.
Genre:Thesis
Subject(s):Amaranthus Sex-determination
Abstract:Amaranthus tuberculatus and Amaranthus palmeri are two of the most agronomically important weeds in the American Midwest. The over-dependence upon chemical control of these weeds has led to the evolution of resistance to many commonly used herbicides across multiple modes of action, including herbicides that target protoporphyrinogen oxidase (PPO). The rapid evolution of these resistance mechanisms necessitates investigation of novel weed control strategies to supplement chemical control methods. One such method for dioecious weeds may include a genetic control strategy, where manipulation of sex-ratios artificially increases the proportion of males within a population to the point of collapse due to lack of seed producers. Chapter 1 includes a literature review of the biology of A. tuberculatus and A. palmeri, PPO-inhibitor resistance, dioecy in plants, and a brief summary of gene-drive technology which could be used to implement such a genetic control strategy. Chapter 2 focuses on the isolation of the recently discovered G399A PPO2 substitution, which confers resistance to PPO-inhibiting herbicides in A. palmeri. Our results allow future studies to examine G399A in planta without the influence of any secondary mechanisms of resistance. Chapter 3 begins our investigation of dioecy within A. tuberculatus and A. palmeri. Here, we identify genomic sequences associated with maleness through a genome-wide association study approach in both species. Results confirm males to be the heterogametic sex, allow for predictions of the size of the male-specific Y (MSY) region, and identify markers to be used in future mapping studies to identify this MSY region in each species. Chapter 4 reports whole-genome assemblies of A. tuberculatus, A. palmeri, and Amaranthus hybridus. Pac-Bio and chromatin conformation capture sequence allowed for the assembly and ordering of contigs to form a near-chromosomal-level of the A. palmeri genome. For the two remaining species, we adapted a trio binning technique, which entailed the sequencing of an interspecific cross and the subsequent separation of haplotypes. These haplotypes were assembled independently to produce two genomes for the price of one. Chapter 5 is aimed at using the previously developed markers for maleness and reference genomes to identify candidate MSY regions in A. tuberculatus and A. palmeri. We identify one contiguous region believed to be the A. palmeri MSY region and several contigs that are hypothesized to be contained within the A. tuberculatus MSY region. The sixth and final chapter includes concluding remarks and future research objectives. These findings lay the groundwork for future studies to understand the mechanism of sex-determination in these species and may allow for the development of a novel genetic weed control strategy.
Issue Date:2020-05-14
Type:Thesis
URI:http://hdl.handle.net/2142/108200
Rights Information:Copyright 2020 Jacob Montgomery
Date Available in IDEALS:2020-08-26
Date Deposited:2020-05


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