RESEARCH-PGR: Impact of Transposable Element Bursts on the Rice Genome and Epigenome

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Mechanisms that diversify genomes, at both the sequence and epigenetic levels, underlie phenotypic variation. With accelerated climate change, it is essential that mechanisms diversifying crop genomes be understood and applied to feed future generations. Most plant and animal genomes are derived from transposable elements (TEs), mobile fragments of DNA that often increase in copy number as they transpose from one genomic locus to another. The ability of TEs to insert near genes and alter their regulation and to promote genomic rearrangements and epigenetic changes has recently been recognized as a significant contributor to adaptive evolution. Stated simply, TEs can shake up otherwise (structurally) conservative genomes. This project exploits long read DNA sequencing technology and single cell epigenetic analyses to reveal how the rapidly amplifying TE called mPing alters, in real time, the rice genome, while avoiding host (epigenetic) silencing and mutagenic insertions. With respect to broader impacts, this project also addresses a crisis in the agricultural workforce, which is the oldest and least diverse among the sciences, by introducing undergraduates at a Hispanic Serving Institution to the excitement of plant genomics through authentic research experiences for up to 2000 incoming students/year. The research goals of this project are two-fold. The first is to understand the totality of structural genomic variation generated in three recombinant inbred (RI) populations by the massive amplification of the rice TE family Ping/mPing. Based on prior results, it is anticipated that at least 50,000 additional mPing insertion sites [with ~15% in accessible chromatin regions (ACRs)] and numerous structural variants (SVs) including copy number and presence absence variants and inversions will be identified. The second goal is to determine the consequences of a subset of these lesions on epigenetic regulation and reproductive isolation by generating a rice single cell cis-regulatory atlas and assessing the impact of mPing inserts in targeted RI lines. While the vast majority of the ~50,000 de novo mPing insertions may be neutral or eliminated by selection over evolutionary time, in the short term they will provide an invaluable tool to evaluate the function of ACRs more quickly and for far less cost than any other method currently available. Results of this project will reveal the potential of rapid TE amplification to reshape the epigenome, lead to reproductive isolation, and, for SVs, to rapidly generate the genomic variation that underlies pangenomes. All data generated by this project will be made available through deposition at established long-term sequence repositories such as the NCBI Short Read Archive (SRA) and Gene Expression Omnibus (GEO).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.