Determination of the mechanisms of MCPA resistance in Amaranthus powellii

Resistance to synthetic auxin herbicides was recently confirmed in a population of Amaranthus powellii. Following field studies, an RNA-seq experiment was devised to determine the mechanism of resistance to MCPA (a synthetic auxin herbicide) by comparing the level of gene expression of genes in the auxin pathway between the resistant and a susceptible population of Amaranthus powellii. The results identified several differentially expressed genes (DEGs) in the auxin pathway that were significantly downregulated in the resistant samples indicating that the resistance mechanism may be linked to a target site modification. Young leave tissue samples from four treaments were used for RNA extraction. The four treatments were as follows: resistant treated (501T), resistant untreated (501U), susceptible treated (511T), and susceptible untreated (511U). Treated samples were sprayed with 1225 g a.e./ha of MCPA (a synthetic auxin herbicide). At six hours after application, leaf tissue samples from both treated and untreated plants were sampled for RNA extraction. Samples were aligned to both a reference genome (Amaranthus hybridus) and an assembled de novo transcriptome (Amaranthus powellii) and gene count data was compared between all treatments to identify differentially expressed genes DEGs.