Survey of the genomic landscape surrounding the EPSPS gene in glyphosate resistant Amaranthus palmeri from geographically distant populations in the United States

Authors: Molin, William; Wright, Alice; VANGESSEL, MARK - University Of Delaware; MCCLOSKEY, WILLIAM - University Of Arizona; JUGULAM, MITHILA - Kansas State University; Hoagland, Robert

Submitted to: Pest Management Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/7/2017
Publication Date: 3/1/2018
Citation: Molin, W.T., Wright, A.A., Vangessel, M.J., McCloskey, W.B., Jugulam, M., Hoagland, R.E. 2018. Survey of the genomic landscape surrounding the EPSPS gene in glyphosate resistant Amaranthus palmeri from geographically distant populations in the United States. Pest Management Science. 74:1109-1117.

Interpretive Summary: Palmer pigweed (Amaranthus palmeri) with resistance to the herbicide glyphosate has been found across the United States and in each case the resistance was due to amplification of the target site. Scientists in the USDA-ARS Crop Production Systems Research Unit, Stoneville, MS conducted research to determine whether the basis for resistance was the same for populations from geographically distant locations. The results showed that the amplified unit conferring resistance from each location were identical indicating that resistance developed once and then rapidly spread across the country. These results are important to farmers because it shows increased diligence is needed to prevent the spread of herbicide resistant weeds.

Technical Abstract: Glyphosate-resistance in Amaranthus palmeri, one of the most prevalent herbicide-resistant weeds in the United States, is due to amplification and increased expression of the gene encoding the target site of glyphosate, 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS). The EPSPS gene and the surrounding 287 kilobases (kb) of amplified sequence is unique to glyphosate-resistant plants and termed the EPSPS cassette. It has only been sequenced from one A. palmeri population from Mississippi. This research compares EPSPS cassettes from several resistant and sensitive populations from geographically distant locations within the United States including Mississippi, Arizona, Kansas, Maryland, Delaware and Georgia. PCR products from forty primer pairs specific to the cassette were similar in size and sequence in resistant populations. Several primer pairs failed to generate PCR products from sensitive populations. Regions of the cassette sequenced in the resistant populations were found to be nearly identical to that from Mississippi. Gene expression analysis showed that both EPSPS and another gene in the cassette, a reverse transcriptase, were elevated in all resistant populations tested relative to the sensitive populations. EPSPS cassettes from distant resistant populations were nearly homologous. Considering the complexity of the cassette, and the degree of similarity among some cassette sequences, glyphosate resistance most likely evolved once and then rapidly spread across the United States.