Epigenetically stable hypomethylated plants to exploit epigenetic diversity

表观遗传学研究不依赖于DNA序列变化的生物性状。在植物中，许多表观遗传变化是稳定的，并且非常有效地从亲本传递给后代。因此，表观遗传变异是生物变异的一个重要来源，包括可能能够改善作物和发展可持续农业的性状。然而，在农业中使用表观遗传性状的主要限制是我们无法在不干扰关键发育途径的情况下诱导植物中足够的表观遗传多样性。我的工作假设是，这些表观遗传对植物发育的负面影响可能与一个名为IBM1的基因的表观遗传改变有关。在模式植物拟南芥（Arabidopsis thaliana）中，如果IBM1序列在位于其内含子之一的关键区域中失去DNA甲基化（一种强表观遗传标记），则会产生较短的非功能性转录本。由于功能性IBM1对于维持许多基因的正确表观遗传调控至关重要，因此IBM1功能的缺乏允许表观遗传缺陷的积累并降低植物跨代的适应性。在具有相同基因组序列但DNA甲基化降低程度不同的稳定拟南芥植物系中，我观察到IBM1基因总是以其甲基化的形式遗传，这表明该位点DNA甲基化的去除对植物适应性有负面影响。为了验证这一假设，我将调查植物表观遗传稳定性，健身减少，和不同的IBM1基因的表观遗传调控之间的关系。我还将测试人工产生对DNA甲基化不敏感的IBM1等位基因是否是一种合适的方法，以避免与表观遗传变异产生相关的负面影响。显然，在植物中产生新的表观遗传变异而不影响其适应性的可能性将产生更大的影响，如果直接探索到作物中，新性状可以被利用到育种计划中。在这个方向上，我的初步研究表明，IBM1的表观遗传调控是保守的小麦。因此，在这个项目中，我还将用一个对表观遗传调控不敏感的IBM1等位基因转化小麦，我将测试经过修饰的植物是否是产生新的稳定表观遗传性状的合适遗传材料。随着全基因组基因组学方法的使用，我将能够量化和比较IBM1对小麦表观遗传改变诱导的表型的贡献。由于小麦是单子叶植物的模式作物和集约育种的目标，本项目的实现将允许将IBM1表观遗传功能扩展到单子叶植物，并直接测试其表观遗传互补，作为促进将表观遗传变异引入作物的方法。小麦是世界上种植面积最大的作物，也是密集育种计划的目标，它被用作超过25亿人的关键粮食资源，对英国经济具有重要的战略意义。因此，该项目中产生的遗传物质将与育种者直接相关，从而可以调查和筛选与新小麦品种产生相关的表观遗传性状。简而言之，在这个项目中，我想描述IBM1在植物表型的表观遗传稳定性中的作用，并开发一种策略来增加具有诱导表观遗传变异的植物的适应性。在项目目标实现后，将有可能在不影响植物发育的情况下产生表观遗传变异性，从而大大促进表观遗传性状在作物育种计划中的使用。

Epigenetics studies biological traits which are not dependent on changes in DNA sequence. In plants, many of these epigenetic changes are stable and are transmitted very efficiently from parent to offspring. Therefore, epigenetic variability represents an important source of biological variation, including traits potentially able to improve crop plants and develop sustainable agriculture. However, the main limitation of using epigenetic traits in agriculture is our inability to induce sufficient epigenetic diversity in plants without interfering with critical developmental pathways. My working hypothesis is that these epigenetic negative effects on plant development could be associated with the epigenetic alteration of a single gene called IBM1. In the model plant Arabidopsis thaliana, if the IBM1 sequence loses DNA methylation (a strong epigenetic mark) in a crucial region located in one of its introns, a shorter non-functional transcript is produced. Since a functional IBM1 is essential to maintain correct epigenetic regulation at many genes, the lack of IBM1 function allows the accumulation of epigenetic defects and reduces plant fitness across generations. In stable Arabidopsis plant lines with identical genome sequence but different degrees of reduction in DNA methylation, I observed that IBM1 gene was always inherited in its methylated version, suggesting that the removal of DNA methylation at this locus has a negative impact on plant fitness. To test this hypothesis I will investigate the relationship between plant epigenetic stability, decrease of fitness, and different epigenetic regulation of the IBM1 gene. I will also test if the artificial generation of an IBM1 allele insensitive to DNA methylation can be a suitable approach to avoid the negative effects associated to the generation of epigenetic variability.Obviously, the possibility to generate new epigenetic variation in plants without affecting their fitness will generate a larger impact if directly explored into crops, where new traits could be exploited into breeding programs. In this direction my preliminary investigation suggests that the epigenetic regulation of IBM1 is conserved in wheat. Therefore, in this project I will also transform wheat with an IBM1 allele insensitive to epigenetic regulation, and I will test if the modified plants will be a suitable genetic material for the generation of new stable epigenetic traits. With the use of genome wide genomics approaches, I will be able to quantify and compare the IBM1 contribution to phenotypes induced by epigenetic alteration in wheat. As wheat is a model crop for monocots and target of intensive breeding, the achievement of this project will allow both to extend IBM1 epigenetic function into monocots, and to test directly its epigenetic complementation as method to facilitate the introduction of epigenetic variation into crops. Wheat is the most extensive cultivated crop worldwide and a target of intense breeding programs, it is used as critical food resource for more than 2.5 billion people, and it is strategically important for the UK economy. Therefore, the genetic material produced in this project will have direct relevance to breeders, allowing the investigation and screening of epigenetic traits relevant to the generation of new wheat varieties. In short, with the proposed project I want to characterize IBM1's role in the epigenetic stability of plant phenotypes, and to develop a strategy to increase fitness of plants with induced epigenetic variation. Following the achievement of the project objectives, it will become possible to generate epigenetic variability without affecting plant development, strongly facilitating the use of epigenetic traits in crop breeding programs.