Collaborative Research: Effects of Genetic Diversity, Epigenetic Change, and Root-associated Fungal Colonization on Trait Variation in the Foundation plant Spartina alterniflora

从诊断人类健康问题到理解生物体对环境的反应，各种各样的问题都依赖于破译DNA序列如何转化为重要特征。该项目侧重于盐沼，盐沼是重要的沿海栖息地，通过支持主要渔业和提供抵御大型海洋风暴的保护，使人类受益。它利用新的DNA测序方法来研究一种关键的盐沼植物的不同菌株如何对压力环境变化做出反应，以及如何通过与一种未被充分研究的耐压真菌的相互作用来促进对压力的反应。除了使盐沼受益外，这种类型的理解对于预测对环境变化的反应、管理生物多样性、开发可持续作物以及改进疾病治疗方法至关重要。该项目将支持各级学生的教育和培训，包括来自不同和服务不足人群的本科生。此外，该项目将由三名女性研究人员领导，她们将成为科学界女性的榜样。本研究将探讨互花米草的遗传和表观遗传多样性、根相关真菌、植物结构和生理性状变异（形态、营养含量、耐盐性）之间的关系。具体而言，该项目将基因组学方法与温室和田间调查和实验相结合，以解决以下问题：(1)植物遗传和表观遗传变异、根相关真菌、植物结构和生理性状如何在潮间带梯度上相互关联？(2)根相关真菌的存在和菌株是否影响植物对非生物变量的结构和生理性状响应，这种影响是否通过表观遗传变化介导？(3)候选基因或基因网络如何参与对生物和非生物环境的结构和生理反应，以及它们是否受到表观遗传调控？这项工作利用了一种新的减少代表性的DNA测序epiGBS方案与亚硫酸处理的DNA来测量互花草的遗传和表观遗传多样性。此外，真菌分离物的下一代测序将允许记录暗隔内生菌在这一关键基础物种对其动态盐沼栖息地的反应中的作用。

Issues as diverse as diagnosing human health problems and understanding organismal response to the environment rely on deciphering how DNA sequences are translated into important traits. This project focuses on salt marshes, important coastal habitats that benefit humans by supporting key fisheries and providing protection from large oceanic storms. It takes advantage of novel DNA sequencing approaches to examine how different strains of a critical salt marsh plant react to stressful environmental variation, and how responses to stress may be facilitated by interactions with an understudied stress-tolerant fungus. In addition to benefiting salt marshes, this type of understanding is critical for predicting response to changing environments, managing biodiversity, developing sustainable crops, and improving treatments for disease. The project will support the education and training of students at multiple levels, including undergraduate students from diverse and under-served populations. Additionally, the project will be led by three female investigators, serving as role models for women in science.This research will examine the relationships among plant genetic and epigenetic diversity, root-associated fungi, and plant structural and physiological trait variation (morphology, nutrient content, salt tolerance) across an inundation gradient in the intertidal foundation plant species Spartina alterniflora. Specifically, the project combines genomic approaches with field surveys and experiments in the greenhouse and the field to address the following questions: (1) How are plant genetic and epigenetic variation, root-associated fungi, and plant structural and physiological traits related across an intertidal gradient?; (2) Does the presence and strain of root-associated fungi affect plant structural and physiological trait response to abiotic variables, and is this effect mediated by epigenetic change?; and (3) How are candidate genes or gene networks involved in the structural and physiological response to the biotic and abiotic environment, and are they epigenetically regulated? The work takes advantage of a novel reduced representation DNA sequencing epiGBS protocol with bisulphite treated DNA to measure genetic and epigenetic diversity in S. alterniflora. Additionally, next generation sequencing of fungal isolates will allow for documentation of the role of dark septate endophytes in the response of this critical foundation species to its dynamic salt marsh habitat.