Deciphering metabolic resistance to multiple herbicides in Amaranthus palmeri via transcriptome analysis

BACKGROUND: Multiple herbicide resistance in Palmer amaranth (Amaranthus palmeri S. Watson) poses a serious threat to US crop production. A Palmer amaranth population (KCTR) from Kansas was found resistant to herbicides across six sites-of-action, including ALS-, PS II-, EPSPS-, PPO-, HPPD-inhibitors and synthetic auxins. Previous physiological and metabolic studies suggested that resistance in this population is predominantly associated with enhanced herbicide metabolism, possibly mediated by cytochrome P450 (P450) and/or glutathione S-transferase (GST) enzyme activity. The aim of this study was to identify candidate genes potentially associated with multiple herbicide resistance in KCTR Palmer amaranth population. RESULTS: Differential gene expression analysis revealed 414, 129, 529, 152 and 688 genes differentially expressed in resistant plants as compared to susceptible, following chlorsulfuron, 2,4-D, atrazine, mesotrione and lactofen treatments, respectively. CYP72A219 paralogs, CYP704B1-like and GST-ct genes were constitutively up-regulated in resistant plants as compared to susceptible. Validated by qRT-PCR, CYP72A219 and CYP704B1-like were 3.4- to 6.6-fold and 5.9- to 12.4-fold up-regulated in resistant plants as compared to susceptible without any treatment. CONCLUSIONS: Identifying genes associated with multiple herbicide metabolism is critical for understanding cross-resistance and evaluating new herbicides for resistance risk. These candidate resistance-associated genes serve as targets for functional validation studies in future to help develop molecular markers for screening broad-spectrum herbicide resistance. © 2026 Society of Chemical Industry.