Investigating Triticeae Epigenomes for Domestication

新杂交种的产生是改良作物的一种重要方式，因为它们在杂交种形成后直接表现出在祖父母中没有的新特性。越来越多的证据表明，这些新兴的表型可能的表观遗传起源。我们最近的玉米全基因组甲基化图谱（Regulski et al 2013）揭示了广泛的胞嘧啶甲基化变异，这些变异可以改变基因功能，并以副突变的方式稳定遗传。因此，需要测量表观遗传修饰的规模和遗传力，与基因和染色体功能的潜在变化（例如重组）相关，然后在育种中将其作为育种中的变异来源加以考虑。在这里，我们的目标是建立在我们在植物表观遗传学和基因组学的集体经验，绘制面包小麦的表观基因组，它与玉米和水稻一起提供了大多数人类营养。该项目的结果将是直接价值的育种家了解的程度和贡献的表观等位基因变异的性状，并在选择亲本表观等位基因变异，使新的杂交种。该项目还将利用小麦的实验优势，了解表观遗传标记在新小麦杂交种形成过程中如何重新编程，以及它们独立维持的基因组在新六倍体基因组稳定过程中如何相互影响。我们已经为绘制和理解小麦表观基因组建立了四个关键基础：小麦的第一个基因组序列组装（Brenchley et al 2012）;用于多个小麦基因组的基因空间的成本有效的测序和用于确定全基因组DNA甲基化模式的有效方法（加德纳等人提交）;对表观遗传机制的进一步理解（Calarco等人2012）;以及小麦杂交种中基因表达改变的证据（Pfeifer等人2014）。该项目汇集了世界领先的作物基因组测序、生物信息学和基因组分析方面的专业知识，在四个全面的相关研究项目中开展工作：确定小麦的完整表观基因组，包括重复区域;调查8个不同的优良小麦品系的表观基因组;确定表观遗传标记在新的小麦杂交种形成过程中是如何重置和稳定的，以及这些标记如何影响基因表达;以及确定环境条件是否会影响表观遗传标记的稳定性。该项目将产生关于表观等位基因如何形成和维持、多倍体小麦基因组如何相互影响以及它们如何影响基因功能的新知识。通过确定小麦品系表观遗传变异的程度及其对基因组功能和预测表型的影响，将对小麦育种产生根本性的重要影响。这些信息可以指导选择杂交形成的父母，并解释缺失的遗传力方面。

The production of new hybrids is a centrally important way of improving crops as they exhibit novel traits directly after hybrid formation, which are not found in progenitor parents. Growing evidence points to possible epigenetic origins for these emergent phenotypes. Our recent genome-wide map of methylation in maize (Regulski et al 2013) revealed extensive cytosine methylation variation that can alter gene functions and be stably inherited in ways reminiscent of paramutation. The scale and heritability of epigenetic modifications therefore needs to be measured, related to potential changes in gene and chromosome function (for example recombination), and then taken into account in breeding as a source of variation in breeding. Here we aim to build on our collective experience in plant epigenetics and genomics to map the epigenome of bread wheat, which, together with maize and rice, provides most human nutrition. Outputs of this project will be of immediate value for breeders for understanding the extent and contribution of epi-allelic variation to traits and in the choice of parental epi-allelic variation in making new hybrids. The project will also exploit experimental advantages of wheat to understand how epigenetic marks are re-programmed during the formation of new wheat hybrids, and how their independently maintained genomes influence each other during stabilization of the new hexaploid genomes. We have established four key foundations for mapping and understanding the wheat epigenome: the first genome sequence assembly of wheat (Brenchley et al 2012); an efficient method for the cost-effective sequencing of the gene space of multiple wheat genomes and for determining genome- wide DNA methylation patterns (Gardiner et al submitted); an improved understanding of the mechanisms of epigenetic inheritance (Calarco et al 2012); and evidence of altered gene expression in wheat hybrids (Pfeifer et al 2014). The project brings together world- leading expertise in crop genome sequencing, bioinformatics and genome analysis to work in four comprehensive linked research projects: defining the complete epigenome of the wheat including repetitive regions; surveying the epigenomes of 8 diverse elite wheat lines; identifying how epigenetic marks are re-set and stabilized during the formation of new wheat hybrids and how these marks influence gene expression; and determining if environmental conditions can influence the stabilization of epigenetic marks.This project will generate new knowledge of how epi-alleles are formed and maintained, how the genomes of polyploid wheat influence each other, and how they influence gene function. It will have a fundamentally important impact on wheat breeding by establishing the extent of epigenetic variation in wheat lines and its consequences on genome function and predicted phenotypes. Such information can guide the choice of parents for hybrid formation and explain aspects of missing heritability.