This project will advance our understanding of epigenetic inheritance. Epigenetic inheritance refers to the transmission of environmental effects to offspring, distinctly and in addition to genetic inheritance. There is a critical need to study epigenetic transmission because this phenomenon has been implicated in both agricultural genetics and human disease. Epigenetic markers play a crucial role in the differentiation of stem cells during normal human development, the disruption of development, the propensity to develop obesity or cancer, and the virulence of microbes. In many cases, these markers are induced by environmental factors such as diet, temperature, chemical exposure, and maternal care. The objective of this project is to investigate the epigenetics of a model trait in a model species: trichome number in Mimulus guttatus (yellow monkeyflower). Trichomes are leaf hairs that help to defend the plant from natural enemies. They are easily scored and provide a repeatable response to environmental stimulus that is epigenetically transmitted to progeny. Extensive prior work makes this system well suited to the mechanistic study of epigenetic inheritance. In particular, the researchers will determine whether DNA methylation is responsible for epigenetic transmission of trichome patterning. This project represents integrative research that crosses the boundaries of ecology, evolution, development, genomics, and molecular biology. There is also a substantial educational component to the project with a particular focus on the recruitment of Native American students into scientific research
This project explored the molecular and genetic bases of transgenerational trichome induction in Mimulus. It is common that plant species respond to insect damage by developing defensive traits, such as growing thorns. Transgenerational induction is the remarkable phenomenon in which a plant that experiences damage can transmit a signal to its progeny to increase their defense, even though these offspring have never themselves experienced damage. This process must involve an epigenetic mechanism and the first aim of these studies was to investigate this mechanism. We were able to show that simulated insect damages induces extensive changes in the gene expression patterns of progeny. Some of these changes likely relate to the focal trait in our studies (trichomes are plant hairs that impede and deter some insect herbivores). However, the gene expression work suggests that other defenses may also be induced such as chemical compounds in the leaves. The work yielded a number of additional Intellectual products. These include a large catalog of gene expression profiles. We contributed these to the Joint Genome Institute (Department of Energy) which produced a greatly improved annotation of the Mimulus genome. Second, we generated the first Mimulus ‘methylome’ a genome-wide characterization of methylation types and frequencies. Third, we constructed an ultra-high density genetic map of Mimulus and whole-genome genotyped a large panel of Recombinant Inbred Lines (RILs). The map identifies several novel genomic features and also corrects several assembly errors in the current Mimulus genome sequence. The Mimulus genome sequence and annotation are used by researchers across the nation. We will make our Methylome similarly available when it is finalized. Finally, we have fine mapped and started to characterize a number of genetic loci that affect plant defense generally. The Broader Impacts of the work were not limited to the data sets described above. The work provided training in genetics and genomics to two graduate students at the University of Kansas and two more at Central Washington University. It also enabled a number of undergraduate research opportunities at both universities. Finally, we have begun to work with a teacher at a local high school (Olathe East High School, Olathe, KS) to integrate Mimulus experiments into the science curriculum. The RILs mentioned above are key to this exercise as it allows students to take plant measurements in the classroom and then immediately relate those to genomic data.
