The unique genomic landscape surrounding the EPSPS gene in glyphosate resistant Amaranthus palmeri: A repetitive path to resistance

Authors: Molin, William; Wright, Alice; LAWTON-RAUH, AMY - Clemson University; SASKI, CHRISTOPHER - Clemson University

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/23/2016
Publication Date: 1/17/2017
Citation: Molin, W.T., Wright, A.A., Lawton-Rauh, A., Saski, C.A. 2017. The unique genomic landscape surrounding the EPSPS gene in glyphosate resistant Amaranthus palmeri: A repetitive path to resistance. BMC Genomics. doi:10.1186/s12864-016-3336-4.

Interpretive Summary: Pigweed (Amaranthus palmeri) resistance to the herbicide glyphosate occurs as a result of the plant making multiple copies of the herbicide target site, a process called amplification. Scientists in the USDA-ARS Crop Production Systems Research Unit, Stoneville, MS and Clemson University conducted research to determine the sequence of the amplified gene and the genetic material surrounding the gene. The results showed that the resistant pigweeds have evolved a unique mechanism which allows them to circumvent the toxic effects of the herbicide. These results are important because they alert farmers and industrial representatives to the need to control pigweeds by alternative methods and restrict applications of the same herbicide year after year.

Technical Abstract: The expanding number and global distributions of herbicide resistant weedy species threaten food, feed, fiber and bioproduct sustainability and agroecosystem longevity. Amongst the most competitive weeds, Amaranthus palmeri S. Wats has rapidly evolved increased resistance to glyphosate primarily through massive amplification and apparently random insertion of the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene across the genome. Increased EPSPS gene copy numbers results in higher titers of the EPSPS enzyme, the target of glyphosate, and confers resistance to glyphosate treatment. To understand the genomic unit and mechanism of EPSPS gene copy number proliferation, we developed and used a bacterial artificial chromosome (BAC) library from a highly resistant biotype and sequenced the local genomic landscape flanking the EPSPS gene. By sequencing overlapping BACs, a 297 kb sequence was generated, hereafter referred to as the “EPSPS amplicon.” This region included several putative genes, dense clusters of tandem and inverted repeats, putative helitron sequences and regulatory elements. Whole genome shotgun sequencing (WGS) of two biotypes exhibiting high and no resistance to glyphosate was performed to compare genomic representation across the amplicon. Mapping of sequences for both biotypes to the reference EPSPS amplicon revealed significant differences in both repetitive units and coding content between these biotypes, which may have resulted from a compounded-building mechanism leading to copy number amplification and distribution. Agricultural practices have been transformed by the adoption of glyphosate resistant cropping systems in major crops such as corn, soybean, canola, and cotton. The complex array of repetitive elements and especially the putative helitron sequences within the EPSPS amplicon suggest adaptive structural genomic mechanisms that drive amplification and distribution around the genome.