Homogeneity among glyphosate-resistant Amaranthus palmeri in geographically distant locations

Authors: Molin, William; PATTERSON, ERIC - Michigan State University; SASKI, CHRISTOPHER - Clemson University

Submitted to: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/10/2020
Publication Date: 9/9/2020
Citation: Molin, W.T., Saski, C.A., Patterson, E.L. 2020. Homogeneity among glyphosate-resistant Amaranthus palmeri in geographically distant locations. PLoS ONE. 15(9):e0233813. https://doi.org/10.1371/journal.pone.0233813.
DOI: https://doi.org/10.1371/journal.pone.0233813

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 and Clemson University, 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: BACKGROUND: Glyphosate resistance in Amaranthus palmeri is a result of amplification of the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene and increased expression of the target site of glyphosate, EPSP synthase (EPSPS). The amplified unit, a 399-kb extrachromosomal DNA, the EPSPS cassette, was unique to glyphosate-resistant plants and contained 1 copy of the 10-kb EPSPS gene. Since the discovery of glyphosate-resistant A. palmeri, resistant plants have been reported in more than 25 states in 12 years. It is not known whether the resistance developed once and spread across the country or developed independently in several locations. RESULTS: Whole genome shotgun sequencing (WGS) and mapping of reads from both glyphosate-resistant and sensitive (R and S) plants to the reference cassette was performed to compare genomic representation and variation across the EPSPS cassette. Sampling of R and S biotypes from multiple states revealed complete assembly and deep representation with sequences from R plants, but lack of contiguity and breaks in coverage were observed with reads from S plants. Furthermore, very few polymorphisms were identified among the resistant individuals suggesting allelic imbalance. CONCLUSIONS: High sequence conservation of the EPSPS cassette from R populations widely separated across the USA indicated that glyphosate resistance most likely originated from a single population. The lack of homogeneity between the EPSPS cassette in resistant biotypes and the genome of sensitive plants may have resulted from non-homologous end joining and genome reshuffling events to induce new genetic variation. The evolutionary events leading to assembly of the EPSPS cassette are unknown.