Genome-wide mapping of recombination hotspots in Arabidopsis

通过育种和基因重组控制自然遗传变异是作物改良的基石。在驯化过程中，作物会经历遗传瓶颈，这意味着野生祖先物种含有丰富的变异，对重新引入很有用。育种的一个限制是染色体的重组率是高度可变的。例如，尽管含有有用的遗传变异，但小麦、大麦和玉米染色体的大部分区域没有重组。我们正在研究重组控制的机理基础，目的是合理操纵这一过程，以加快作物育种。由于核心重组过程在植物间高度保守，我们的工作重点是具有广泛遗传和基因组资源的模式物种拟南芥。利用一种称为花粉分型的新实验技术，我们最近发现拟南蝽染色体具有狭窄的热点区域，重组的机会很高。这些热点位于基因启动子中，在那里开放的染色质包装允许进入DNA，我们假设这也允许进入重组机制。其他物种的热点是由染色质结构和初级DNA序列的组合控制的，我们将在拟南螺旋体中研究这些关系。首先，我们将使用群体遗传学方法，利用拟南芥群体之间的自然遗传多态性模式，生成全基因组热点图。由于重组打破了连锁遗传变异的区块，这种效应可以用来测量重组率和识别热点位置。拟南芥基因组用染色质图很好地注释了，这将使我们能够确定染色体组织的哪些方面与热点位置相关。此外，我们将测试热点是否与特定的DNA序列相关，以解决植物热点是遗传还是表观遗传决定的程度。利用花粉分型，我们将实验验证拟南芥基因组中最活跃热点的子集。为了直接测试染色质对热点活性的作用，我们将在表观遗传组织改变的突变背景下重复花粉分型。我们已经观察到的热点位于基因启动子中，我们将使用启动子染色质改变的突变体来测试对重组的影响。我们还将直接针对与基因沉默相关的染色质修饰热点，并研究这是否足以抑制重组。热点控制的知识将为操纵作物基因组重组提供新的见解。我们的战略目标是调节作物的热点活动，例如通过增加、抑制或重新安置它们，从而促进高产品种的培育。

Harnessing natural genetic variation through breeding and genetic recombination is a cornerstone of crop improvement. During domestication crops pass through genetic bottlenecks, meaning that wild progenitor species contain abundant variation that is useful to reintroduce. One limitation to breeding is that recombination rate is highly variable along chromosomes. For example, large regions of wheat, barley and maize chromosomes are non-recombining, despite containing useful genetic variation. We are investigating the mechanistic basis of recombination control, with the aim of rationally manipulating this process to accelerate crop breeding. As the core recombination process is highly conserved between plants, our work focuses on the model species Arabidopsis thaliana, which has extensive genetic and genomic resources. Using a novel experimental technique termed pollen-typing we have recently discovered that A.thaliana chromosomes have narrow hotspot regions with a highly elevated chance of recombination. These hotspots are located in gene promoters, where open chromatin packaging allows access to the DNA, and we hypothesize that this also allows access to the recombination machinery. Hotspots in other species are controlled by a combination of chromatin structure and primary DNA sequence, and we will investigate these relationships in A.thaliana. First we will use population genetics methods to generate a genome-wide hotspot map using patterns of natural genetic polymorphism between A.thaliana populations. As recombination breaks up blocks of linked genetic variation, this effect can be used to measure recombination rate and identify hotspot locations. The A.thaliana genome is well annotated with chromatin maps and this will allow us to determine which aspects of chromosome organisation correlate with hotspot locations. In addition we will test whether hotspots associate with specific DNA sequences, to resolve the extent to which plant hotspots are genetically versus epigenetically determined. Using pollen-typing we will then experimentally validate a subset of the most active hotspots in the A.thaliana genome. To directly test the role of chromatin on hotspot activity we will repeat pollen-typing in mutant backgrounds with altered epigenetic organization. The hotspots we have already observed are located in gene promoters and we will use mutants with altered promoter chromatin to test for effects on recombination. We will also directly target chromatin modifications associated with gene silencing to hotspots and investigate whether this is sufficient to suppress recombination. Knowledge of hotspot control will provide novel insight into manipulating recombination in crop genomes. Our strategic goal is to modulate hotspot activity in crops, for example by boosting, suppressing or relocating them, and thereby facilitating breeding of high-yielding strains.