Collaborative Proposal: The ecological genomic basis of parallel serpentine adaptation in Mimulus

21世纪世纪生物学的一个主要挑战是了解生物体如何适应复杂且通常不可预测的环境。环境的异质性导致不同的选择压力，这是重要的创造和维持生物多样性，但是，很少有人知道生物如何在遗传水平上对这种空间变化的选择。本项目研究植物适应土壤变化的遗传基础。 肥沃的土壤对植物来说是特别具有挑战性的环境？它们缺乏几种必需的植物营养素，特别是钙（Ca），并含有有毒水平的镁（Mg）和重金属。然而，一些物种，如Mimulus guttatus，能够在这些恶劣的土壤上生长。这项研究将描述土壤，气候和健身性状相关的蛇纹岩适应人口的M。guttatus分布在和关闭蛇纹石土壤从不列颠哥伦比亚省到南部加州，并调查是否在这些广泛的人口蛇纹石耐受性已经通过相同或不同的遗传和生理机制。确定植物适应广泛种群的遗传基础和平行程度，将有助于更广泛地了解植物生理学、生态学和进化，从而提高保护和随后利用遗传多样性的能力，以生产新的作物和植物群落，使其更能适应环境中新出现的变化，包括盐度和矿物质营养压力。Mimulus中的serritol耐受性提供了植物适应的综合性和可访问的例子，因此除了指导博士后，研究生和本科生以及代表性不足的少数民族高中生之外，研究人员还将开发和测试这项工作产生的数据的有效性，以证明本科生生物学的核心概念。这一资源将部分通过杜克大学新的顶点本科课程开发。研究人员还将培训一名公立高中教师，并协助开发、教学、评估和修改入门和AP生物学课程的教学模块。guttatus是一种生态基因组模式物种，具有快速的世代时间、高质量的注释基因组序列、广泛的基因组资源和良好的稳定转化方法。土壤中的腐殖酸通常是致命的，但数百个种群的M。在北美西部从不列颠哥伦比亚省到南加州的地理和地质上不同的地区，点滴虫反复适应这些土壤。该项目的四个目标将导致对植物物种如何响应空间变化的选择而进化的最完整和详细的研究之一，并阐明平行适应的生理，细胞和分子遗传机制。 在目标一中，将对20对相邻的蛇纹岩和非蛇纹岩进行相互移植实验、离子动力学分析和详细的土壤分析。来自五个地理和地质不同地区的guttatus种群。 目标2将利用来自40个群体中的每一个群体的合并群体基因组序列数据来鉴定平行蛇形适应的候选基因和SNP，并评估单个候选基因和分子途径是否在广泛的蛇形区域中共享或响应于特定的蛇形位点而进化。在目标3中，新的，高效和成本效益的QTL定位方法结合生理，离子和土壤移植实验，将被用来确定的位点，是最重要的地方适应蛇纹石土壤在每个8个蛇纹石地区，确定QTL是唯一的或跨区域共享，并为每个主要QTL评估可能的生理机制参与耐受性。 目的4涉及使用精细的遗传作图，定位克隆，转基因实验方法结合生理和生化功能的测试，以确定最重要的基因参与当地适应蛇纹石土壤和表征其细胞和分子机制。

A major challenge in 21st century biology is to understand how organisms adapt to complex and often unpredictable environments. Environmental heterogeneity results in divergent selective pressures that are important for creating and maintaining biological diversity; however, little is known about how organisms respond to such spatially varying selection at the genetic level. This project investigates the genetic basis of plant adaption to variation in soils. Serpentine soils present particularly challenging environments for plants ? they are deficient in several essential plant nutrients, notably calcium (Ca), and contain toxic levels of magnesium (Mg) and heavy metals. However some species, such as Mimulus guttatus, are able to grow both on and off of these harsh soils. This research will characterize soil, climatic, and fitness traits related to serpentine adaptation from populations of M. guttatus distributed on and off serpentine soils from British Columbia to southern California, and investigate whether serpentine tolerance in these widespread populations has evolved via the same or different genetic and physiological mechanisms. Establishing the genetic basis of plant adaptation to and the degree of parallelism across widespread populations will contribute to a broader understanding of plant physiology, ecology and evolution that will advance the ability to conserve and subsequently to exploit genetic diversity to produce new crops and plant communities with greater resilience to emerging changes in the environment, including salinity and mineral nutrient stress. Serpentine tolerance in Mimulus provides an integrative and accessible example of plant adaptation, so in addition to mentoring of postdocs, graduate and undergraduate students, and underrepresented minority high school students, the investigators will develop and test the effectiveness of data generated by this work to demonstrate core concepts in biology for undergraduates. This resource would be developed in part through a new capstone undergraduate course at Duke University. The investigators will also train a public school high school teacher and assist in the development, teaching, assessment, and modification of teaching modules for introductory and AP biology classes.The molecular genetic basis of adaptation to serpentine soil will be investigated in M. guttatus , an ecological genomic model species with a rapid generation time, high quality annotated genome sequence, extensive genomic resources, and well developed methods for stable transformation. Serpentine soils are usually lethal, but hundreds of populations of M. guttatus have repeatedly adapted to these soils across geographically and geologically distinct regions in western North America, from British Columbia to southern California. The four aims in the project will result in one of the most complete and detailed studies of how plant species evolve in response to spatially varying selection and elucidate the physiological, cellular, and molecular genetic mechanisms underlying parallel adaptation. In Aim 1, reciprocal transplant experiments, ionomic profiling, and detailed soil analysis will be conducted for 20 pairs of adjacent serpentine and non-serpentine M. guttatus populations from five geographically and geologically diverse regions. Aim 2 will utilize pooled population genomic sequence data from each of the 40 populations to identify candidate genes and SNPs underlying parallel serpentine adaptation, and evaluate whether individual candidate genes and molecular pathways are shared across widespread serpentine regions or have evolved in response to particular serpentine sites. In Aim 3, new, highly efficient and cost-effective methods for QTL mapping combined with physiological, ionomic, and soil transplant experiments, will be used to identify the loci that are most important for local adaptation to serpentine soils at each of the eight serpentine regions, determine whether QTLs are unique or shared across regions, and for each major QTL evaluate the likely physiological mechanisms involved in tolerance. Aim 4 involves using fine-scale genetic mapping, positional cloning, and transgenic experimental approaches combined with tests of physiological and biochemical function to identify the most important genes involved in local adaptation to serpentine soils and characterize their cellular and molecular mechanisms.