Connecting variation in genome structure and chromatin composition in Zea mays

University of Minnesota Ph.D. dissertation. February 2021. Major: Plant Biological Sciences. Advisor: Nathan Springer. 1 computer file (PDF); vi, 187 pages.In many crop species there is tremendous intraspecific variation for genome structure due to highly variable transposon insertions. The goal of my thesis research is to provide insight on genetic and epigenetic dynamics and their relationship with functional variation which has the potential to influence variation in regulation and gene expression. ‘Epigenetics’ describes heritable information not solely due to the DNA sequence, whereas ‘genetics’ is heritable information directly related to the DNA sequence. The central question of the chapters presented is to ask, what are the relative contributions of genetic (transposable element insertions) and epigenetic (localized chromatin changes) factors to variation in DNA methylation and gene expression? In order to address this topic, I first present background information on both DNA methylation and epigenetic influence in maize. It is pertinent to understand the many roles and mechanisms of DNA methylation in plant species in order to decipher the contributions to variation. While this DNA methylation has previously been assessed, the ability to tease apart epigenetics from genetics through polymorphism detection on a genome-wide scale is possible only with new technology. These advancements have helped us to understand information found within the maize epigenome which may not be captured by genetic variation and therefore provide additional data for predicting traits and improving the efficiency of plant improvement strategies. I have conducted several research studies to address the question of epigenetic stability in maize. To first address the dynamic between DNA methylation and transposable elements across the genome, I sought to characterize epigenetic patterns associated with TE families and the cause or effect of TE insertion on DNA methylation architecture.Chapter III presents the assessment of natural variation of transposon insertions and the impact on epiallele state. After identifying how these TEs interact with their flanking sequence I further questioned the genomic influence of the TE body in chapter IV. Accessible chromatin data has allowed identification of putative regulatory regions genome-wide and I pursued the question of how novel TE sequence can contribute to the regulatory dynamics of an organism. Through polymorphic TE insertions we were able to assess the influence of these enhancers on nearby gene expression. The final chapter of my thesis seeks to question the stability of the maize methylome. Now focusing on the shared and nonshared sequence between maize genotypes, I was able to analyze epigenetic variation in the presence or absence of sequence variation. A pan-genome study allows for identification of both core (present across all genotypes) and dispensable (variable between genotypes) epigenetic regions. Presence of variable methylation state is indicative of epigenetic patterns not predictable by sequence. The work presented below describes these broad inquiries in further detail working to answer essential questions regarding genetic and epigenetic contributions to maize phenotype