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，这对于创造和维持生物多样性非常重要；然而，人们对生物体如何在基因水平上响应这种空间变化的选择知之甚少。该项目研究植物适应土壤变化的遗传基础。 蛇纹石土壤对植物来说是特别具有挑战性的环境吗？它们缺乏多种必需的植物营养素，尤其是钙 (Ca)，并且含有有毒水平的镁 (Mg) 和重金属。然而，一些物种，例如Mimulus guttatus，能够在这些恶劣的土壤上和土壤下生长。这项研究将描述与分布在从不列颠哥伦比亚省到南加州的蛇纹石土壤内外的M. guttatus种群的蛇纹石适应相关的土壤、气候和适应性特征，并调查这些广泛分布的种群中的蛇纹石耐受性是否是通过相同或不同的遗传和生理机制进化而来的。建立植物适应的遗传基础以及广泛种群的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，以生产新作物和植物群落，对环境中出现的变化（包括盐度和矿物质营养胁迫）具有更强的适应能力。含酸浆的蛇纹石耐受性提供了植物适应的综合且易于理解的例子，因此除了对博士后、研究生和本科生以及代表性不足的少数族裔高中生进行指导外，研究人员还将开发和测试这项工作生成的数据的有效性，以向本科生展示生物学的核心概念。该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学校高中教师，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。将在 M. guttatus 中研究适应蛇纹土的分子遗传学基础，M. guttatus 是一种生态基因组模型物种，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成熟的稳定转化方法。蛇纹石土壤通常是致命的，但在北美西部，从不列颠哥伦比亚省到南加州，数百个不同地理和地质的地区的M. guttatus 已经多次适应了这些土壤。该项目的四个目标将导致最完整和详细的研究之一，研究植物物种如何进化以响应空间变化的选择，并阐明平行适应背后的生理、细胞和分子遗传机制。 在目标 1 中，将对来自五个地理和地质不同区域的 20 对相邻蛇纹石和非蛇纹石 M. guttatus 种群进行相互移植实验、离子组分析和详细土壤分析。 目标 2 将利用来自 40 个种群中每个种群的汇总种群基因组序列数据来识别平行蛇纹石适应的候选基因和 SNP，并评估单个候选基因和分子途径是否在广泛的蛇纹石区域中共享，或者是否针对特定的蛇纹石位点而进化。在目标 3 中，新的、高效且具有成本效益的 QTL 作图方法与生理学、离子组学和土壤移植实验相结合，将用于确定八个蛇纹石地区中对蛇纹石土壤局部适应最重要的基因座，确定 QTL 是否是独特的或跨区域共享的，并为每个主要 QTL 评估与耐受性相关的可能的生理机制。 目标 4 涉及使用精细遗传图谱、定位克隆和转基因实验方法，结合生理和生化功能测试来识别参与局部适应蛇纹土的最重要基因，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.