RNAseq Analysis of Herbicide Response in Imazamox Resistant and Susceptible Echinochloa colona Populations

Weeds with resistance to multiple herbicides are increasing in incidence and are of growing concern to farmers.  MS1, a field population of Echinohcloa colona with resistance to imazamox, fenoxaprop, quinclorac, and propanil, was reported in Sunflower County, MS.  Treatment of MS1 with cytochrome P450 inhibitors in the presence of imazamox reduced the level of resistance, indicating involvement of herbicide metabolism in the resistance mechanism.  Due to the complexity of the mechanism and the lack of sequence data for this species, a RNA-seq approach was taken to explore the mechanism.  RNA was isolated from untreated and imazamox treated plants for MS1 and a susceptible population, Bond2.  MiSeq SE165 and HiSeq PE100 runs were performed.  Differential expression analysis of treated and untreated samples for preliminary assemblies of each population revealed an increase in expression of several genes associated with stress response, including genes involved in calcium signaling, ubiquitination, defense responses, cell wall modifications, and metabolism.  Of particular interest was a cytochrome P450 734A6 homolog.  In subsequent qPCR studies, this transcript showed a two fold increase in expression in MS1 compared to Bond2 four hours after imazamox treatment.  Additional research will be needed to determine the role (if any) of this enzyme in herbicide resistance.  Future work includes generating final transcriptomes for each population and analysis of expression differences to identify potential genes that may account for resistance.  A list of candidate genes associated with increased imazamox resistance will facilitate additional studies needed to elucidate the mechanism of resistance in this population.