EAGER: Documenting Epigenetic Influence on Plant Quantitative Phenotypic Variation

Project: Research project

Project Details


A major challenge to the stability of US and worldwide agricultural is the increasing variability of weather conditions coupled with diminishing water availability. These challenges require the development of greater plant resiliency that, in an agricultural context, can be scaled to meet US needs and can be implemented in multiple crops. Conventional breeding enhances plant yield by selecting for enhanced genetics that can withstand various environmental stresses (e.g., drought). Similar gains might also be influenced by epigenetics (modifications to DNA). However, using epigenetics to enhance plant resilience requires formal demonstration and the development of appropriately sensitive computational technologies to monitor epigenetic changes across the plant genome. This project tests using epigenetics to enhance plant by using a new genetic mutation that leads to epigenetic changes in plants. Some plants with this mutation show enhanced growth and resilience that is maintained after the mutation is removed and this project will generate new computational tools to analyze these long-lasting (multi-generational) effects. Due to the potential for transferring this technology to crop species, this technique will have broad impacts on plant research and crop improvement.

Accelerated plant adaptation to environmental change requires adjustment of gene expression in a manner that is ultimately heritable to offspring, yet little is known of the mechanism of transgenerational epigenetic behavior. This project addresses this gap by exploiting the MSH1 system in Arabidopsis for inducible transgenerational memory and phenotypic plasticity. A novel Methyl-IT program for genome-wide methylation analysis will be used to contrast DNA methylation patterns in full sib progeny with and without induced epigenetic memory effects to test for a direct relationship between cytosine methylation behavior and phenotype emergence. Graft progeny out-comes from wild type scion/msh1 rootstock will be tested for epigenetic effects by introducing mutations for sRNA production to the rootstock genotype and assaying progeny for alignment in sRNA, methylome and phenotype changes. Outcomes from this study will permit assessment of epigenome-phenotype relationship by direct testing. Breaking through this barrier has the potential to dramatically alter current thinking in the field, and designing experimental methods for the detection of subtle, gene-associated cytosine methylation variation would impact epigenomic re-search in both plant and animal systems.

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.

Effective start/end date11/15/1810/31/21


  • National Science Foundation: $300,000.00


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