Population Genomics of Glyphosate-Resistant Palmer Amaranth (Amaranthus palmeri) Using Genotyping-by-Sequencing (GBS)

Throughout the southeastern and southwestern United States, populations of Palmer amaranth (Amaranthus palmeri) have been identified with evolved resistance to the herbicide glyphosate. This project aims to determine the degree of genetic relatedness among a set of glyphosate-resistant and –susceptible lines by analyzing patterns of phylogeography and diversity on an intraspecific level. Seven different lines of Palmer amaranth from different geographic regions were tested against a glyphosate-resistant line from an Arizona locality for glyphosate resistance. The goal is to ascertain whether resistance evolved independently in the Arizona locality, or whether resistance spread from outside to the location. For example, the transportation of resistant seeds in harvesting equipment could be a source of gene flow via seed migration. The accumulation of shikimic acid via the shikimate assay and EPSPS copy number and were tested to confirm resistance. The susceptible lines showed an average of 41 mg/ml shikimic acid while the resistant lines showed an average of 0.1 mg/ml shikimic acid accumulation after exposure to a 500µm solution of glyphosate. Individuals from the Arizona glyphosate-resistant locality had increased copies of EPSPS in the range of 20 – 290-fold. This is the same mechanism previously identified in the Palmer amaranth lines from the southeastern US, therefore it is possible that resistance was introduced from elsewhere. DNA samples were collected for genotyping by sequencing (GBS) to perform single nucleotide polymorphism (SNP) calling, which will be used to determine the genetic structure of the different lines. Currently, neighbor joining trees and principle component analysis are being performed. This information about the evolution and migration of glyphosate resistance will be useful to design better strategies for herbicide resistance management.