Date of Graduation


Document Type


Degree Name

Doctor of Philosophy in Crop, Soil & Environmental Sciences (PhD)

Degree Level



Crop, Soil & Environmental Sciences


Nilda Burgos

Committee Member

Edward Gbur

Second Committee Member

Jarrod Hardke

Third Committee Member

Amy Lawton-Rauh

Fourth Committee Member

Nathan Slaton

Fifth Committee Member

Robert Scott


Echinochloa Colona, Herbicide, Multiple Resistance, Quinclorac, RNA-sequencing, Weed Physiology


Echinochloa species are highly adaptive weeds that have the potential to impact crops in a variety of environments. This has positioned them as the most problematic weeds in a number of USA cropping systems with some species having the distinction of the 'worst herbicide-resistant weeds' in the world. Recent evidence has positioned Echinochloa colona (junglerice) as the most dominant in Arkansas and throughout the Mid-South, USA, especially in rice (Oryza sativa L.) and soybean (Glycine max L.) production fields. A history of extensive herbicide-use for management and a lack of integrated or diverse approaches to management have led to rampant herbicide resistance within production fields. The goal of this research is to assess herbicide-resistant E. colona from the field to the genomic level. Five objectives are the focus of this research: (1) characterize the current status of herbicide-resistant Echinochloa in Arkansas rice and assess the distribution of resistance patterns with time, (2) evaluate the underlying mechanisms driving multiple resistance in E. colona (3) assemble a de novo transcriptome of E. colona and assess the mechanisms of resistance to quinclorac, (4) use the transcriptome to characterize the response to propanil in multiple-resistant and susceptible E. colona and identify the basis for resistance to propanil, and (5) use the transcriptome analysis in response to multiple herbicides to identify the biological functions of susceptible and resistant E. colona following herbicide treatment. This research used a population that is highly resistant to propanil and quinclorac, and with elevated tolerance to cyhalofop and glufosinate. This E. colona accession has non-target site resistance via independent mechanisms involving cytochrome P450 enzymes and glycosyltransferase enzymes for propanil and quinclorac, respectively. Herbicide resistance co-evolved with abiotic stress tolerance potentially through the enhancement of the trehalose biosynthetic pathway. This research had generated the first assembled transcriptome of E. colona and description of the transcriptomic responses to the common rice herbicides cyhalofop, propanil, and quinclorac, as well as the non-selective herbicide glufosinate. This research generated the first global transcriptome comparison across multiple herbicides, characterizing the patterns of gene expression following herbicide treatment with diverse herbicide modes of action.