Collaborative Research: RESEARCH PGR: The epigenomic selfing syndrome: revealing the impact of breeding system on epigenomes

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The evolution of mating system – whether a plant primarily self-fertilizes (inbreeds) or outcrosses (is pollinated by a different individual) – is one of the most frequent changes during plant evolution. Self-fertilization is associated with a common set of changes in floral development, together known as the selfing syndrome. For example, flowers of self-fertilizing species tend to be smaller and unscented because they do not need to attract pollinators. We know less about how the transition to self-fertilization impacts the genome and epigenome – the pattern of chemical modifications that control the way genes function. Using multiple plant species in two genera (Capsella and Mimulus), this research will investigate how genomes and epigenomes differ between self-fertilizing and outcrossing species. This work will help us understand hybridization barriers, which limit our ability to make inter-species crosses for breeding improved crops. This research will also increase our fundamental understanding of seed development, a critical aspect of agricultural productivity, and generate a wealth of sequence-based resources that will enable the plant genomics community to answer further questions. Research from this project will be incorporated into undergraduate and graduate courses taught by the PIs. Finally, this research will help maintain ongoing collaborations with local K-12 teachers to develop hands-on plant biology activities for use in their classrooms.Selfing fundamentally alters the nature of genomic conflicts and is predicted to affect several epigenetic phenomena, including genomic imprinting, effective ploidy, and host defense against transposons. RNA-directed DNA methylation (RdDM) plays a key role in epigenomic regulation and has been linked to genomic conflicts, suggesting that the nature or function of RdDM might be altered following the evolution of selfing. This project will test the hypothesis that there is a common pattern of epigenomic change following the transition to inbreeding and that these changes are mediated by RdDM. Because the selfing syndrome is only apparent when multiple transitions to selfing are compared, the relationship between mating system and the epigenome will be investigated using six inbreeder/outbreeder comparisons in two genera (Capsella and Mimulus). Specific areas of research include 1) determining how selfing impacts RdDM’s role in transposon defense and collateral gene silencing, 2) establishing the molecular cause of divergence in effective ploidy and determine whether these changes are common during the transition to selfing, 3) assessing the differential function of RdDM following the evolution of selfing, and 4) determining whether there is a reduced role for RdDM in selfing species.This award was co-funded by the Plant Genome Research Program in the Division of Integrative Organismal Systems and the Genetic Mechanisms Cluster in the Division of Molecular and Cellular Biosciences.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.