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

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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.