The evolution of herbicide resistance

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Rapid contemporary evolution is an opportunity to investigate the dynamics of evolution in response to environmental stress. Gene copy number variation, a common but understudied form of genetic variation, has emerged as a mechanism that can play a role in adaptation to environmental stress, including the evolution of herbicide resistance in plants. The origin(s) of copy number variation, its relationship to resistance phenotype, and the upper limit(s) to copy number are not well understood in plants. Moreover, the potential interaction between a gene copy number variant and genomic background is acknowledged but rarely investigated, especially across a geographic range. Therefore, to advance understanding of gene copy number evolution I propose a quantitative genetic approach. I will use the evolution of resistance to the ubiquitous herbicide, glyphosate, in Amaranthus palmeri as a model to explore the evolutionary limit(s) of gene copy number. Copy number of resistance gene EPSPS (5enolpyruvyl- shikimate-3-phosphate synthase) ranges from 1 to >100 in A. palmeri. This crop weed is expanding its previously restricted range - southwest US and Mexico - now occurring across the US and moving toward the Canadian border. My long-term research goals will advance understanding of the role of copy number variation in evolution: What are the genetic mechanisms, evolutionary origin(s) and evolutionary limit(s) of stress resistance traits? How common is gene copy number variation, and how often is it involved in adaptation to the environment? The short-term research proposed here investigates whether EPSPS copy number variation explains the majority of variation in glyphosate resistance across the geographic range, and whether other genomic variation contributes. Historical plant samples provide opportunity to investigate whether EPSPS copy number variation pre-dated the development and ubiquitous use of glyphosate. To forecast the future trajectory of EPSPS copy number variation, we will extend EPSPS copy number variation through artificial selection in search of the upper limit(s) of gene copy number. This program is a rare opportunity to combine investigation of the historical, contemporary and future evolution of a trait in response to environmental change. The proposed research program at the intersection of evolutionary biology and agriculture provides training opportunities for 3 PhD, 4 MSc and 10 BSc HQP. For development of sustainable agriculture practices it is critical to understand the role herbicides play(ed) in the evolution of agricultural weed populations, and whether resistance evolution has potential to intensify, or has reached a stable limit. This program will train HQP in field biology, experimental design, quantitative genetics, statistics, genomics and bioinformatics, as well as both oral and written communication - preparing HQP for academic, industrial and/or government research.