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

交配系统的进化是植物进化中最频繁的变化之一，无论是植物主要是自交(近交系)还是异交(由不同的个体授粉)。自花受精与花发育的一系列常见变化有关，统称为自花综合征。例如，自花授粉物种的花往往更小，也更无味，因为它们不需要吸引传粉者。我们对向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。利用两个属的多种植物(山葵和水芹)，这项研究将研究自交和异交物种之间的基因组和表观基因组的差异。这项工作将帮助我们了解杂交障碍，这些障碍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，种子发育是农业生产力的关键方面，并产生丰富的基于序列的资源，使植物基因组学社区能够回答进一步的问题。这个项目的研究将被纳入私人投资促进机构教授的本科生和研究生课程。最后，这项研究将有助于保持与当地K-12教师的持续合作，以开发在他们的课堂上使用的动手植物生物学活动。自交从根本上改变了基因组冲突的性质，并被预测会影响几种表观遗传现象，包括基因组印记、有效倍性和宿主对转座子的防御。RNA引导的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的性质或功能可能会随着自交的进化而改变。这个项目将检验这样一个假设，即在向近亲交配过渡之后，存在一种共同的表观基因组变化模式，并且这些变化是由RdDM介导的。由于自交综合征只有在比较到自交的多次转换时才明显，因此将通过两个属(Capsella和Mimulus)的六个自交者/外交者的比较来研究交配系统和表观基因组之间的关系。具体的研究领域包括：1)确定自交如何影响RdDM在转座子防御和伴随基因沉默中的作用；2)确定有效倍性分化的分子原因并确定这些变化在向自交的转变过程中是否常见；3)评估RdDM在自交进化后的不同功能，以及4)确定RdDM在自交物种中的作用是否降低。该奖项由整合组织系统部门的植物基因组研究计划和分子和细胞生物科学部门的遗传机制集群共同资助。该奖项反映了NSF的法定使命，并通过使用基金会的智力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.