Homogeneity among glyphosate-resistant Amaranthus palmeri in geographically distant locations

Since the initial report of glyphosate-resistant (GR) Amaranthus palmeri (S) Wats. in 2006, resistant populations have been reported in more than 28 states. It is not known whether the resistance evolved once and spread across the country or evolved independently in several locations. Glyphosate resistance in A. palmeri is due to amplification of the 5-enolpyruvylshikimate-3-phosphate synthase ( EPSPS ) gene and the concomitant increased expression of EPSP synthase, the target enzyme of glyphosate. The amplified unit, a 399-kb extrachromosomal circular DNA, called the EPSPS replicon, is unique to glyphosate-resistant plants and contains one copy of the 10-kb EPSPS gene. To compare genomic representation and variation across the EPSPS replicon , whole genome shotgun sequencing (WGS) and mapping of sequences from both GR and susceptible (GS) biotypes to the replicon consensus sequence was performed. A single leaf from each of two plants from each population were combined as a sample. Sampling of GR biotypes from AZ, KS, GA, MD and DE and GS biotypes from AZ, KS and GA revealed complete contiguity and deep representation with sequences from GR plants, but lack of homogeneity and contiguity with breaks in coverage were observed with sequences from GS biotypes. Very few polymorphisms were identified among GR individuals indicating high sequence conservation among the EPSPS replicons from GR populations widely separated across the USA. These results support the hypothesis that glyphosate resistance most likely originated from a single location or population and rapidly spread across the USA. We show that the replicon has spread across the country to different populations with similar levels of amplification with little to no sequence variation.