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Transcriptomic analysis of Ambrosia trifida response to glyphosate: Overlap of cell death pathways between herbicide resistance and pathogen defense?

Christopher Van Horn: USDA-ARS-PWA

<div>Giant ragweed (<em>Ambrosia trifida</em>) is an important weed in US corn and soybean production. The evolution of herbicide resistance and particularly the unique rapid response to glyphosate in this species, not only makes it difficult to manage in cropping systems, but is a highly interesting case of a potential plant response to abiotic stress by utilization of known biotic stress response pathways. The giant ragweed rapid response to glyphosate resembles a programmed cell death response to pathogens seen in other plant species. Due to a lack of genomic resources for giant ragweed, we sequenced the transcriptome of a glyphosate-resistant rapid response individual using Illumina MiSeq and conducted an RNA-seq time course study on three glyphosate-resistant and -susceptible individuals each, before and after glyphosate treatment using Illumina HiSeq technology. <em>De novo</em> assembly using Newbler returned 158,314 contigs, of which 65,623 contigs were greater than or equal to 500 bp. From a subset of 143 unique differentially expressed contigs related to plant response to biotic and abiotic stresses, we identified 15 potential candidates involved in the resistance and/or rapid response to glyphosate that could be used for further functional genomics research. This is the first coupled transcriptome sequence and RNA-sequencing experiment of giant ragweed. This transcriptome data may serve as a reference for further gene expression and functional genomics studies, and will provide a valuable molecular resource for future research of herbicide resistance mechanisms in this species as well as other weeds.</div>