| dc.description.abstract | Herbicide resistance is currently the largest threat facing the field of weed science. With evolved resistance represented by 21 out of 31 herbicide modes of action, and no new active ingredients to alleviate resistance pressure, it is crucial for scientists to approach weed management from a new perspective. Molecular genetics is a growing field that, until recently, has been underutilized by weed scientists. Genomics, functional gene annotation, and differential gene expression analysis are tools now being applied to weed science that allow us to better understand weed species and how herbicide resistance evolves, particularly in polyploid species.
This dissertation begins with a literature review to discuss the framework of and provide background on the research, particularly into the chosen species, Poa annua (annual bluegrass) and Digitaria ischaemum (smooth crabgrass). The second chapter details an extensive survey of herbicide resistant populations of P. annua across the United States to identify potential target-site mutations across four common modes of action and six herbicides. Due to the polyploid nature of P. annua, new sequencing methods were utilized outside of the standard methodology, as the conflicting subgenomes were introducing noise during Sanger sequencing. Ultimately, 1,349 P. annua populations were collected for resistance screening and 389 populations were identified as resistant to at least one mode of action.
In the third chapter a potential quinclorac-resistant biotype of D. ischaemum (AL_R1) was identified in the field. The evolution of quinclorac-resistant biotypes of D. ischaemum is detrimental to the turfgrass industry, as it removes one of the only postemergence herbicides, as well as the only grass selective herbicide available for controlling crabgrass. A greenhouse dose-response study was conducted in order to confirm the resistance status compared to a known quinclorac-susceptible population of D. ischaemum (AL_S1). All replicates of AL_S1 were controlled at or below the standard rate, while none of the AL_R1 replicates were controlled at more than 55% of the highest rate use, validating its status as a resistant population. AL_S1 was then selected as the reference biotype for assembling the D. ischaemum genome, as detailed in chapter 4. Previous research indicated D. ischaemum is a polyploid species, and investigations were made into analyzing the subgenomes to confirm this. D. ischaemum was successfully assembled into an allotetraploid configuration, with subgenomes C and D to account for the existing genome of D. exilis, a tetraploid with subgenomes A and B. The assembled genome showed evidence of segmental allopolyploidy in D. ischaemum, given large sections of subgenome C were identified in subgenome D. Comparative analyses were also performed with existing genomes of D. exilis and D. insularis to determine if either species was a progenitor or shared a common ancestor with D. ischaemum, but no similar parentage was established between the species.
The final chapter utilized AL_R1 and AL_S1 to perform a differential gene expression analysis of inherently expressed genes to elucidate potential target-site genes for quinclorac. The mechanism of resistance to quinclorac is currently unknown, and this study sought to uncover genes with potential mutations and genes that were differentially expressed between the resistant and susceptible without being treated with quinclorac. Ultimately, no target-site mutations were identified from known mutations to other synthetic auxins, and while the differential expression study indicated clear differences between AL_R1 and AL_S1, no genes stood out as potential targets. The mechanism of action of quinclorac is a complex process that likely involves proteins still unknown, which highlights the need for further research to fully comprehend the molecular pathways induced. | en_US |
