Charlotte Ngo MSc Student, Yakimowski Lab Investigating the evolutionary origin(s) of EPSPS copy number variation in Amaranthus palmeri Agricultural use of herbicides has led to the repeated evolution of herbicide resistance in numerous agricultural weeds, posing significant challenges for food production and agriculture sustainability worldwide. The development of herbicide resistance over contemporary timescales has provided us with a unique opportunity to investigate the origins of this adaptation - has herbicide resistance arisen from de novo mutations or from standing genetic variation? Amaranthus palmeri (A. palmeri), a major agricultural weed originating from southwestern United States and Mexico, has been expanding northward, recently was detected in Canada. Many A. palmeri populations exhibit resistance to glyphosate, a common herbicide, primarily through EPSPS gene copy number variation. Yet it remains unclear whether such variation predated the commercialization of glyphosate in 1974. This project aims to answer an important evolutionary question concerning glyphosate resistance in A. palmeri - did the copy number variation of EPSPS exist as standing genetic variation, or did it evolve rapidly in response to glyphosate selection pressure? To investigate the origins of glyphosate resistance, I collected historic samples from the United States and Mexico from herbaria across the United States, spanning three different time periods (pre-1974, between 1974 and 1995, and post-1995), representing a broad geographic distribution. I extracted leaf tissue samples using a modified CTAB protocol, followed by quantification of EPSPS gene copy number using digital drop PCR (ddPCR). The project unveiled intriguing evolutionary patterns that can be explored further through genomic analyses of whole genomes. Given the expanding range of A. palmeri across North America, understanding the evolutionary mechanisms of herbicide resistance is imperative for unraveling the spread of not only A. palmeri but also other weed species. Moreover, the utilization of historical samples in this research serves as an exemplar for studying rapid adaptation to human-induced environmental changes.
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