EAGER: Documenting Epigenetic Influence on Plant Quantitative Phenotypic Variation

美国和全世界农业稳定面临的一个主要挑战是天气条件的变化无常，加上可用水的减少。这些挑战要求开发更强的植物弹性，在农业背景下，可以扩大规模以满足美国的需求，并可以在多种作物上实施。常规育种通过选择能够承受各种环境压力(如干旱)的增强遗传学来提高植物产量。类似的收益也可能受到表观遗传学(DNA修饰)的影响。然而，使用表观遗传学来提高植物的抗逆性需要正式的示范和开发适当灵敏的计算技术来监测整个植物基因组的表观遗传学变化。这个项目测试了利用表观遗传学通过一种导致植物表观遗传学变化的新基因突变来增强植物。一些具有这种突变的植物表现出增强的生长和韧性，这种生长和弹性在突变被移除后保持不变，该项目将产生新的计算工具来分析这些长期(多代)影响。由于这项技术有可能转移到作物物种上，这项技术将对植物研究和作物改良产生广泛的影响。加速植物对环境变化的适应需要以一种最终可遗传给后代的方式调整基因表达，但对跨代表观遗传行为的机制知之甚少。该项目通过利用拟南芥中的MSH1系统来解决这一差距，以获得可诱导的跨代记忆和表型可塑性。一种用于全基因组甲基化分析的新的甲基IT程序将用于比较具有和不具有诱导表观遗传记忆效应的全同胞后代的DNA甲基化模式，以测试胞嘧啶甲基化行为与表型出现之间的直接关系。来自野生型接穗/msh1砧木的嫁接后代将通过在砧木基因型中引入sRNA产生的突变并分析后代在sRNA、甲基组和表型变化方面的比对来测试表观遗传效应。这项研究的结果将允许通过直接测试来评估表观基因组-表型关系。突破这一障碍有可能极大地改变该领域目前的想法，设计实验方法来检测微妙的、与基因相关的胞嘧啶甲基化变异将影响植物和动物系统中的表观基因组研究。该奖项反映了NSF的法定使命，并通过使用基金会的智力优势和更广泛的影响审查标准进行评估，被认为值得支持。

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.