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United States Department of Agriculture

Agricultural Research Service

Research Project: Characterization and Mitigation of Herbicide-Resistant and Recalcitrant Weeds

Location: Crop Production Systems Research Unit

Title: Identification of genetic elements associated with EPSPS gene amplification

Authors
item Gaines, Todd -
item WRIGHT, ALICE
item MOLIN, WILLIAM
item Lorentz, Lothar -
item Riggins, Chance -
item Tranel, Patrick -
item Beffa, Roland -
item Westra, Philip -
item Powles, Stephen -

Submitted to: PLoS One
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: April 28, 2013
Publication Date: June 10, 2013
Citation: Gaines, T.A., Wright, A.A., Molin, W.T., Lorentz, L., Riggins, C.W., Tranel, P.J., Beffa, R., Westra, P., Powles, S.B. 2013. Identification of genetic elements associated with EPSPS gene amplification. PLoS One. 8(6):1-10.

Interpretive Summary: Pigweed (Amaranthus palmeri) has become resistant to the herbicide glyphosate, the world’s most important herbicide, by making multiple copies of the target gene but the mechanism leading to resistance has not been described. Scientists in USDA-ARS Crop Production Systems Research Unit, Stoneville, MS conducted research to determine the structure of the gene and its flanking regions to identify genetic causes for the accumulation of multiple gene copies. No genetic mutations were found; however resistant plants contained miniature inverted-repeat transposable elements (MITEs) and a putative Activator (Ac) transposase which are genetic elements that can cause increases in gene copy number. These results show the pigweed has several adaptive mechanisms which allows it to overcome herbicide treatments. These results are instructive to farmers and industrial representatives by alerting them to the consequences of repetitive herbicide applications.

Technical Abstract: Weed populations can have high genetic plasticity and rapid responses to environmental selection pressures. For example, 100-fold amplification of the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene evolved to confer resistance to glyphosate, the world's most important herbicide, in the weed species Amaranthus palmeri. However, the gene amplification 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 amplification likely proceeded through a DNA-mediated mechanism, as introns exist in the amplified gene copies and the entire amplified 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 of these was amplified in glyphosate-resistant (R) A. palmeri. The EPSPS gene amplification event likely occurred recently, as no sequence polymorphisms were found within introns of amplified EPSPS copies from R individuals. Sequences with homology to miniature inverted-repeat transposable elements (MITEs) are present in the genomes of both S and R individuals, but are found within 500 bp from both ends of EPSPS gene copies only in R individuals. Additionally, a putative Activator (Ac) transposase and a repetitive sequence region are consistently located downstream of amplified EPSPS genes. We propose two potential mechanisms that may have contributed to the gene amplification: DNA transposon-mediated replication, and unequal recombination between different genomic regions resulting in replication of the EPSPS gene.

Last Modified: 8/19/2014