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

Robert Scott

Second Committee Member

Nathan Slaton

Third Committee Member

Andronikos Mauromoustakos

Fourth Committee Member

Amy Lawton-Rauh

Fifth Committee Member

Franck Dayan


ALS-inhibiting Herbicides, Amaranthus Palmeri, Glufosinate, Herbicide Resistance In Weed Species, Non-target-site Herbicide Resistance, PPO-inhibiting Herbicides


Palmer amaranth, one of the most aggressive and damaging broadleaf weeds in the USA, has evolved resistance to multiple herbicide modes of action. The overall objective of this research was to elucidate the mechanisms by which Palmer amaranth adapt to herbicide selection stress. This research aimed (1) to evaluate the efficacy of fomesafen, glufosinate, glyphosate and trifloxysulfuron to Amaranthus populations; (2) identify candidate genes for endowing tolerance to glufosinate; (3) investigate the involvement of non-target-site resistance (NTSR) mechanism in an ALS-resistant population; and (4) to examine the molecular basis of resistance to PPO inhibitors in Palmer amaranth populations from Arkansas. For objective 1, a total of 124 populations were collected in Arkansas between 2008 and 2015. Overall, 33%, 81%, and 100% of the populations were resistant to fomesafen, glyphosate, and trifloxysulfuron, respectively. Thirty percent of the populations were multiple resistant to fomesafen, glyphosate, and trifloxysulfuron. All populations were controlled >88% by glufosinate. For objective 2, the transcriptomes of glufosinate-tolerant and –sensitive biotypes were assembled using RNA-Seq. Thirteen candidate non-target genes were highly expressed in glufosinate-tolerant biotypes, including glutathione S-transferase (GST), two cytochrome P450, and nine additional genes related to stress signaling and detoxification. Validation of differential gene expression by quantitative real-time PCR revealed increased expression CYP72A219 and GST in glufosinate-treated tolerant biotypes, indicating their involvement in glufosinate tolerance. For objective 3, a population with cross resistance to multiple ALS-inhibiting herbicides was investigated. Two of the nine resistant plants harbored Ser653Asn mutation in the ALS gene. Resistant plants that lacked ALS mutations had elevated levels of CYP81B and GSTF10 genes. This Palmer amaranth population from Arkansas exhibit both target-site (TS) and NTSR to ALS inhibitors. For objective 4, resistance to PPO inhibitors was first detected in a population collected in 2011 with resistance attributed to PPO Gly210 deletion. Several PPO-resistant populations were confirmed in 2014 and 2015; the majority (55%) of the resistant biotypes carried the same mutation. An alternative target-site mutation Arg128Gly was also identified in at least one population. Overall, this research showed that Palmer amaranth has multiple genetic adaptation traits to counteract the lethal effects of herbicides.