Date Available


Year of Publication


Degree Name

Master of Science (MS)

Document Type

Master's Thesis


Agriculture, Food and Environment


Plant Pathology

First Advisor

Dr. Christopher L. Schardl


Seed-transmissible epichloid fungal endophytes are best known for their roles as defensive mutualists in cool-season grasses. Historically, the discovery of fungal endophytes was driven by investigations of plant toxicity to livestock, followed by extensive study of their alkaloids and protection against insects and nematodes. Epichloae can produce four classes of alkaloids: ergot alkaloids, lolines (saturated aminopyrrolizidines), indole–diterpenes, and peramine. It is increasingly evident that these hereditary symbionts have much more diverse chemical profiles both in individual populations and between them. To this end, differences in chemotypic profiles of these symbionts may translate to different evolutionary and environmental advantages across plant species, as well as influences on phenotypic measurements. In an ecological sense, the chemotypic diversity within the species may reflect frequency-dependent selection for the alkaloids, which can be metabolically expensive to produce. To date, there has yet to be extensive study on the alkaloid profiles of the fungal symbiont Epichloë brachyelytri in the cool-grass host Brachyelytrum erectum. This project aims to initiate the required genomic population analyses to comprehend endophyte frequency and chemotypic diversity among and between populations throughout the state of Kentucky.

In a previous survey of B. erectum in the Kentucky Palisades, 50% of the plants had fungal endophytes, with two endophyte genotypes that differed in alkaloid profiles. In the investigation, 21 populations of B. erectum were sampled and the genetic and chemotypic diversity analyzed by high-throughput tiller extraction and multiplex PCR. Biosynthesis genes for ergot alkaloids (e.g., chanoclavine and ergovaline), aminopyrrolizidines (e.g., lolines), and pyrrolopyrazines (e.g., peramine), as well as genes for mating type and phylogenetic barcodes, were interrogated to determine endophyte presence and diversity. Morphological measures for all samples were also assessed, and six populations were sampled for transcriptome analysis. The results of these studies will expand the understanding of how endophyte frequency distributions and genetic diversity can influence functional and phylogenetic diversity.

Digital Object Identifier (DOI)

Funding Information

This project was supported by the Dimensions in Biodiversity Grant from the National Science Foundation (NSF) (2021-current) and the Eller/Billings Award from the Appalachian Center at the University of Kentucky (2023).