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。环境的异质性导致了不同的选择压力，这对创造和维持生物多样性很重要；然而，关于生物如何在遗传水平上对这种空间变化的选择做出反应，人们知之甚少。本项目研究植物适应土壤变异的遗传基础。蛇纹岩土壤对植物来说是特别具有挑战性的环境？它们缺乏几种基本的植物营养，特别是钙(Ca)，并含有有毒的镁(Mg)和重金属。然而，一些物种，如点滴鹦鹉，能够在这些严酷的土壤上和离开这些土壤生长。这项研究将对分布在不列颠哥伦比亚省到南加州的蛇纹土壤上和蛇纹土壤外分布的滴虫种群与蛇纹适应相关的土壤、气候和适合性特征进行表征，并调查这些广泛分布的种群是否通过相同或不同的遗传和生理机制进化出对蛇纹的耐受性。建立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，这将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，对环境中新出现的变化，包括盐分和矿质营养胁迫具有更强的适应能力。Mimulus中的蛇行耐受性提供了一个综合和可获得的植物适应例子，因此，除了指导博士后、研究生和本科生，以及未被充分代表的少数族裔高中生外，研究人员还将开发和测试这项工作产生的数据的有效性，为本科生演示生物学的核心概念。这一资源将部分通过杜克大学开设的一门新的顶石本科课程来开发。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。将研究适应蛇纹岩土壤的分子遗传学基础。古特塔斯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成熟的稳定转化方法。蛇纹石土壤通常是致命的，但从不列颠哥伦比亚省到加利福尼亚州南部，北美西部从不列颠哥伦比亚省到南加州的不同地理和地理区域，数以百计的古塔斯分枝杆菌种群一再适应这些土壤。该项目的四个目标将导致对植物物种如何对空间变化的选择做出反应的最完整和最详细的研究之一，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理不同地区的20对相邻的蛇形和非蛇形滴虫种群进行相互移植实验、离子剖面法和详细的土壤分析。目标2将利用来自40个种群中每个种群的集合基因组序列数据来确定潜在的平行蛇形适应的候选基因和SNPs，并评估单个候选基因和分子通路是否在广泛的蛇形区域共享，或者是否已经对特定的蛇形区域做出了进化。在目标3中，结合生理、离子和土壤移植实验，将使用新的、高效和经济的QTL定位方法，以确定对八个蛇纹岩地区的蛇纹岩土壤的局部适应最重要的基因座，确定QTL是唯一的还是跨地区共享的，并对每个主要QTL评估与耐性有关的可能的生理机制。目的4利用精细的遗传作图、定位克隆和转基因实验方法，结合生理生化功能的测试，确定与蛇纹岩土壤局部适应有关的最重要的基因，并对其细胞和分子机制进行表征。

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.