It is critical to continue developing varieties of crops that are highly productive while minimizing environmental impact. To accomplish this, plant breeding relies upon the genetic variation within a species to find new priorty traits. Most efforts are focused on characterizing the variations that occur as changes to a single nucleotide of the genome. However, there is evidence that transposable elements are a major source of variability among the genomes of different varieties of the same species. Transposable elements, originally called "jumping genes," are small pieces of DNA that can make additional copies and move to new genomic locations. Transposable elements, first discovered in corn (maize) by Barbara McClintock, account for approximately 85% of the corn genome. It is known that transposable elements can influence nearby DNA and cause phenotypes by changing when and how genes are expressed. An intriguing ongoing question is how this vast majority of the genome composed of transposable elements actually functions and contributes to traits. This project addresses this question by documenting the variation of transposable elements in different varieties of corn, and then examines how transposable elements create phenotypic variation in corn. The knowledge from this project can reveal all new breeding potential for corn and can help shape future crop improvement based on transposable elements. In the process, undergraduate and graduate students will be trained in computational and quantitative analysis of genomes through hands-on workshops and training. All resources will be available through public websites.
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, knowledge of the role of TEs in contributing to genomic, epigenomic, transcriptomic and phenotypic diversity in crop plants is lacking, in part due to the highly repetitive nature of these sequences, which has, to date, made them recalcitrant given available technologies. The activities will develop 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 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.
This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.
