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Title:Recent advances using genetic analyses in waterhemp
Author(s):Murphy, Brent P
Director of Research:Tranel, Patrick J
Doctoral Committee Chair(s):Tranel, Patrick J
Doctoral Committee Member(s):Riggins, Chance; Clough, Steven; Jamann, Tiffany; Diers, Brian
Department / Program:Crop Sciences
Discipline:Crop Sciences
Degree Granting Institution:University of Illinois at Urbana-Champaign
Degree:Ph.D.
Genre:Dissertation
Subject(s):Amaranthus tuberculatus
herbicide resistance
waterhemp
QTL mapping
dioecy
comparative genomics
Amaranthus arenicola
Abstract:Amaranthus tuberculatus (Moq.) Sauer is a driver weed species within maize and soybean production systems in the Midwestern United States. The development of herbicide resistance is a contributing factor leading to management challenges in the species. Recently, non-target-site herbicide resistance has been increasingly associated with new evolutionary events, further limiting the potential for effective herbicide programs to control the weed, leading to a need for new management options. Understanding the genetic diversity present within the A. tuberculatus gene pool, including for key traits such as non-target-site herbicide resistance and dioecy, may contribute to the advancement of effective management strategies. Inheritance, segregation, and linkage mapping of non-target-site resistance was conducted in two A. tuberculatus populations, one from Illinois and the other from Nebraska, to the Group 27 herbicide, tembotrione. Resistance in the two populations appeared to be derived from different evolutionary events, as it displayed dominant inheritance and multigenic segregation in the Nebraska population whereas it displayed additive, single-gene inheritance in the Illinois population. Genetic mapping was only successful for the Nebraska population, in which two quantitative trait loci (QTL) were identified. Candidate gene models associated with the dioecy trait were identified using two properties: uniqueness to the male-specific region and the presence of purifying selection. Of the 147 gene models predicted to be contained within the male-specific region, three fulfilled both filtering criteria: 00g213060, 00g213110 and 00g277460. GO-term enrichment analysis of the 1-Kbp proximal promoter region suggested that 00g213060 may prove interesting due to enrichment of terms associated with floral initiation and floral organ development. Hybridization studies and gene-flow experiments were conducted between A. tuberculatus and its close phylogenetic neighbor, A. arenicola. Under directed crosses, hybridization fecundity was comparable to those of intraspecific crosses. Results from pollen-competition experiments suggested that gene flow from A. tuberculatus to A. arenicola will occur frequently even in the presence of an intraspecific pollen donor. The studies described within this dissertation have made significant contributions to the understanding of non-target-site herbicide resistance, and the total genetic diversity of A. tuberculatus, both in the context of target traits such as dioecy and to the gene pool as a whole. Two QTL associated with resistance to a Group 27 herbicide were identified from a Nebraska A. tuberculatus population, and an Illinois population was determined to have evolved the trait independently. A single candidate gene model with a high likelihood to play a role in the dioecy trait was identified within the male-specific region of A. tuberculatus. Finally, I present evidence that A. arenicola may be within the primary gene pool of A. tuberculatus and could contribute to weedy adaptation in the species.
Issue Date:2021-04-16
Type:Thesis
URI:http://hdl.handle.net/2142/110797
Rights Information:Copyright 2021 Brent Murphy
Date Available in IDEALS:2021-09-17
Date Deposited:2021-05


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