Genomic Context of Amplified EPSPS Loci in Glyphosate-Resistant Palmer Amaranth

The herbicide glyphosate is widely used for weed control in the U.S. and other parts of the world in conjunction with transgenic glyphosate-resistant crops. For years, glyphosate and glyphosate-resistant crops comprised an effective weed management strategy. The resulting widespread application of glyphosate in cropping areas placed dramatic selection pressure on local weed populations. Subsequently, several weeds resistant to glyphosate have emerged. Glyphosate functions by inhibiting a plant enzyme critical for production of aromatic amino acids: 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS). We identified a mechanism for glyphosate resistance mediated by amplification of the EPSPS gene. Within the populations used for our study, glyphosate resistance correlates with increases in: EPSPS genomic copy number, EPSPS transcript expression, EPSPS protein level and EPSPS enzymatic activity. Thus, it appears amplification of the EPSPS gene leads to overproduction of EPSPS enzyme, so much so that – even in the presence of glyphosate – there is an abundant supply of uninhibited EPSPS. Our present work includes sequencing of the approximately 85 EPSPS loci in a glyphosate-resistant Amaranthus palmeri plant from Georgia to determine the molecular genetic basis of EPSPS gene amplification. Preliminary genome analyses focus on the EPSPS gene are designed to determine (a) the size of the amplified locus, (b) whether EPSPS amplification involves an RNA intermediate, (c) whether gene amplification was a recent event, and (d) whether amplification is mediated by a mobile genetic element.