The evolution of herbicide resistance

快速的当代进化是一个机会来研究进化的动态，以应对环境压力。基因拷贝数变异是一种常见的但尚未得到充分研究的遗传变异形式，它已成为一种机制，可以在适应环境胁迫中发挥作用，包括植物抗除草剂的进化。拷贝数变异的起源、与抗性表型的关系以及拷贝数的上限在植物中尚不清楚。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，但很少研究，特别是在地理范围内。因此，为了促进对基因拷贝数进化的理解，我提出了一种定量遗传方法。我将以苋菜（Amaranthus palmeri）对普遍存在的除草剂草甘膦（glyphosate）的抗性进化为模型，探索基因拷贝数的进化极限。耐药基因EPSPS（5烯醇丙酮酰-莽草酸-3-磷酸合成酶）拷贝数在1 ~ 100之间。这种作物杂草正在扩大其以前受限制的范围-美国西南部和墨西哥-现在出现在美国各地并向加拿大边境移动。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：抗逆性性状的遗传机制、进化起源和进化极限是什么？基因拷贝数变异有多普遍？它在适应环境的过程中有多频繁？本文提出的短期研究探讨了EPSPS拷贝数变异是否解释了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了作用。历史上的植物样本提供了机会来调查EPSPS拷贝数的变化是否早于草甘膦的发展和普遍使用。为了预测EPSPS拷贝数变异的未来轨迹，我们将通过人工选择扩展EPSPS拷贝数变异，寻找基因拷贝数的上限(s)。这个项目是一个难得的机会，结合了对一种特征的历史、当代和未来演变的调查，以应对环境变化。在进化生物学和农业交叉的拟议研究项目为3名博士，4名硕士和10名HQP理学士提供培训机会。对于可持续农业实践的发展，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，还是已经达到稳定的极限是至关重要的。该项目将训练HQP在野外生物学、实验设计、定量遗传学、统计学、基因组学和生物信息学，以及口头和书面交流方面的能力，为HQP的学术、工业和/或政府研究做准备。

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.