Transposable elements (TEs) account for the majority of genome sequence in maize and other crops. Locus-specific and cytogenetic studies suggest that TEs can be highly variable within plant species and account for agronomically important QTL. However, we lack knowledge of the role of TEs in contributing to genomic, epigenomic, transcriptomic and phenotypic diversity in crop plants, in part due to the highly repetitive nature of these sequences, which has, to date, made them recalcitrant to available technologies. In this project we are developing annotation and diversity resources to enable the study of TEs in maize. Within this project these resources will be utilized to study the role of TEs in contributing to phenotypic variation through the use of quantitative genetics and population genetics approaches. These efforts will elucidate the potential to utilize knowledge of TE variation to understand genotype by environment interactions and to improve genotype-phenotype predictions in crop species. The project will monitor how TEs contribute to a dynamic maize genome and identify TEs that are moving in modern maize varieties. The proposed research will monitor the mechanisms through which TE variation can influence phenotype through the analysis of TE influences on chromatin and gene expression. These experiments will shed light upon the role of TE polymorphisms in contributing to variation in the maize epigenome, transcriptome and phenome. This project will provide foundational knowledge of the role of TEs that can be used to enhance maize improvement and responses to abiotic stress.
Collaborators: Jeff Ross-Ibarra, Emily Josephs, Shawn Kaeppler
Funding Agency: NSF
Project Timeline: 2019-2025
