Association of Mobile Genetic Elements with EPSPS Gene Duplication

Weed populations can have high genetic plasticity and rapid responses to environmental selection pressures.  For example, 100-fold duplication of the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene evolved in the weed species Amaranthus palmeri to confer resistance to glyphosate, the world’s most important herbicide.  However, the gene duplication mechanism is unknown.  We sequenced the EPSPS gene and genomic regions flanking EPSPS loci in A. palmeri, and searched for mobile genetic elements or repetitive sequences.  The EPSPS gene was 10,229 bp, containing 8 exons and 7 introns.  The gene duplication likely proceeded through a DNA-mediated mechanism, as introns exist in the duplicated gene copies and the entire duplicated sequence is at least 30 kb in length.  Our data support the presence of two EPSPS loci in susceptible (S) A. palmeri, and that only one locus was duplicated in glyphosate-resistant (R) A. palmeri.  The EPSPS gene duplication event likely occurred recently, as no sequence polymorphisms were found within introns of duplicated EPSPS copies from R individuals.  Sequences with homology to miniature inverted-repeat transposable elements (MITEs) were identified next to EPSPS gene copies only in R individuals.  Additionally, a putative Activator (Ac) transposase and a repetitive sequence region were associated with duplicated EPSPS genes.  The mechanism controlling this DNA-mediated duplication remains unknown.  Further investigation is necessary to determine if the gene duplication may have proceeded via DNA transposon-mediated replication, and/or unequal recombination between different genomic regions resulting in replication of the EPSPS gene.