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

交配系统的进化-无论植物主要是自花受精（近交）还是异交（由不同的个体授粉）-是植物进化过程中最常见的变化之一。自花受精与花发育中的一系列常见变化有关，统称为自交综合征。例如，自交物种的花朵往往较小且无味，因为它们不需要吸引传粉者。我们对自花受精的转变如何影响基因组和表观基因组-控制基因功能的化学修饰模式-知之甚少。本研究将利用两个属（荠菜属和Mimulus）的多个植物物种，研究自交和异交物种的基因组和表观基因组之间的差异。这项工作将帮助我们了解杂交障碍，这限制了我们进行物种间杂交以培育改良作物的能力。这项研究还将增加我们对种子发育的基本理解，这是农业生产力的一个重要方面，并产生丰富的基于序列的资源，使植物基因组学界能够回答进一步的问题。该项目的研究将纳入PI教授的本科和研究生课程。最后，这项研究将有助于保持与当地K-12教师正在进行的合作，开发动手植物生物学活动，用于他们的classical.Selfing从根本上改变了基因组冲突的性质，预计会影响几个表观遗传现象，包括基因组印记，有效倍性，和宿主防御转座子。RNA指导的DNA甲基化（RdDM）在表观基因组调控中起着关键作用，并与基因组冲突有关，这表明RdDM的性质或功能可能随着自交的进化而改变。本项目将检验以下假设：在向近亲繁殖过渡后，表观基因组变化存在一种常见模式，并且这些变化由RdDM介导。由于自交综合征是明显的，只有当多个过渡到自交进行比较，交配系统和表观基因组之间的关系进行了研究，使用6个近交/远交比较两个属（荠属和Mimulus）。具体的研究领域包括：1）确定自交如何影响RdDM在转座子防御和旁系基因沉默中的作用，2）确定有效倍性趋异的分子原因，并确定这些变化在向自交过渡期间是否常见，3）评估自交进化后RdDM的差异功能，以及4）确定RdDM在自交物种中的作用是否降低。由整合有机体系统部的植物基因组研究计划和分子与细胞生物科学部的遗传机制集群资助。该奖项反映了NSF的基金会的使命是履行其法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

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.