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

21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往往不可预测的环境。环境异质性导致不同的选择压力，这对创造和维持生物多样性很重要；然而，人们对生物如何在遗传水平上对这种空间变化的选择作出反应知之甚少。本项目研究植物适应土壤变化的遗传基础。蛇形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，尤其是钙（Ca），并且含有有毒的镁（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。本研究将从不列颠哥伦比亚省到南加州分布在蛇形土壤上和在蛇形土壤外分布的M. guttatus群体中，对蛇形适应相关的土壤、气候和适应性特征进行表征，并研究这些广泛分布的群体对蛇形的耐受性是否通过相同或不同的遗传和生理机制进化而来。建立植物适应广泛种群的遗传基础和平行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，以生产对环境新变化（包括盐度和矿物质营养胁迫）具有更大弹性的新作物和植物群落。Mimulus的蛇形植物耐受性提供了植物适应的综合和可访问的例子，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，以向本科生展示生物学的核心概念。这一资源将部分通过杜克大学的一门新的顶点本科课程来开发。调查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。作为一种具有快速世代、高质量基因组序列、丰富基因组资源和成熟稳定转化方法的生态基因组模式物种，本文将对古麻适应蛇形土壤的分子遗传学基础进行研究。蛇形土壤通常是致命的，但从不列颠哥伦比亚到南加州，在北美西部地理和地质上截然不同的地区，数百个种群已经反复适应了这些土壤。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1中，将对来自5个地理和地质多样性地区的20对相邻蛇形和非蛇形M. guttatus种群进行相互移植实验、基因组分析和详细的土壤分析。目标2将利用来自40个种群的基因组序列数据来确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共享，或者是否针对特定的蛇形位点进化。在aims 3中，将采用新的、高效和经济的QTL定位方法，结合生理、基因组学和土壤移植实验，确定8个蛇形土壤区域中对蛇形土壤局部适应最重要的位点，确定QTL是独特的还是跨区域共享的，并对每个主要QTL评估与耐受性相关的可能生理机制。目标4涉及使用精细遗传作图、定位克隆和转基因实验方法，结合生理和生化功能测试，确定参与蛇形土壤局部适应的最重要基因，并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.