The evolution of herbicide resistance

当代的快速进化是研究进化对环境压力反应的动力学的机会。基因拷贝数变异是一种常见但研究较少的遗传变异形式，已成为一种在适应环境胁迫中发挥作用的机制，包括植物对除草剂抗性的进化。拷贝数变异的起源(S)及其与抗性表型的关系，以及拷贝数的上限(S)在植物中还不是很清楚。此外，基因拷贝数变异和基因组背景之间的潜在相互作用是公认的，但很少被研究，特别是在一个地理范围内。因此，为了提高对基因拷贝数进化的理解，我提出了一种数量遗传学方法。我将以植物对除草剂草甘膦的抗性进化为模型，探索基因拷贝数的进化极限(S)。帕尔梅里抗病基因EPSPS(5-烯醇丙酮基-莽草酸-3-磷酸合成酶)的拷贝数在1-100之间。这种作物杂草正在扩大其以前的限制范围--美国西南部和墨西哥--现在发生在美国各地，并向加拿大边境蔓延。 我的长期研究目标将促进对拷贝数变异在进化中的作用的理解：抗逆性状的遗传机制、进化起源(S)和进化极限(S)是什么？基因拷贝数变异有多常见，它参与环境适应的频率有多高？这里提出的短期研究调查了EPSPS拷贝数变异是否解释了整个地理范围内草甘膦抗性的大部分变异，以及其他基因组变异是否起到了作用。历史植物样本为研究EPSPS拷贝数变异是否早于草甘膦的开发和普遍使用提供了机会。为了预测EPSPS拷贝数变异的未来轨迹，我们将通过人工选择寻找基因拷贝数上限(S)来扩展EPSPS拷贝数变异。这个项目是一个难得的机会，可以结合对一种性状的历史、当代和未来演变的研究，以应对环境变化。 拟议中的进化生物学和农业交叉研究计划为3名博士、4名硕士和10名理科硕士HQP提供了培训机会。为了发展可持续的农业实践，关键是要了解除草剂在农业杂草种群进化中的作用，以及抗性进化是否有可能加剧，或者已经达到稳定的极限。该项目将对HQP进行现场生物学、实验设计、数量遗传学、统计学、基因组学和生物信息学方面的培训，以及为学术、工业和/或政府研究准备HQP的口头和书面交流。

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.