HEI10: a master switch for recombination in plants

为了满足不断增长的全球人口的需求，社会正面临着提高作物产量和质量的重大挑战。解决这一挑战的方法之一是培育和进一步改进作物种质。例如，野生种群的抗病和抗逆性特征可能有利于引入优良品种。在这种情况下，有益的性状必须在许多代中逐渐渗入，以达到改良的品系。这一作物育种过程很大程度上依赖于后代在繁殖过程中自然发生的性状重配。具体来说，多样性是在称为减数分裂的特殊细胞分裂过程中产生的，减数分裂导致配子（性细胞）的产生。在减数分裂过程中产生遗传多样性的一种机制被称为交叉。在这里，同源染色体物理配对并交换互惠区域，从而产生新的遗传变异组合。然而，在许多最重要的作物物种中，染色体的交叉模式是高度扭曲的，包括小麦、玉米、大麦和番茄。因此，基因组的一些区域是无法进行育种的，尽管它们含有对农艺性状有影响的重要基因。当在植物、动物和真菌之间进行比较时，交叉水平通常较低，大多数物种在每次减数分裂中每条染色体只有1-2次交叉。然而，物种内部和物种之间的交叉水平也有相当大的差异。为了探索这一现象，我们之前使用拟南芥来确定交叉水平的自然变异。这些实验确定了一种名为he10的主要基因，该基因在拟南芥种群之间发生变化，并控制交叉水平。我们还发现，HEI10对剂量非常敏感。我们发现通过增加he10基因拷贝数和表达水平可以有效地提高总交叉水平。在育种方面，这将允许育种者使用更少的个体产生更多样化的种群。这将在时间和费用方面提供相当大的优势。因此，在本文中，我们描述了一个基础和应用实验相结合的方案，旨在完善HEI10作为重组主开关的使用，并将其部署在一个重要的作物物种（番茄）中。这个项目有三个主要目标。首先，我们将使用模式植物拟南芥来详细研究如何利用HEI10基因来增加重组。我们将进一步增加he10的剂量，以测试何时发生重组反应的饱和。我们将进一步改变减数分裂期间HEI10表达的时间。额外的基因修饰将与HEI10结合起来，以使杂交模式偏向于有利于育种的方式。其次，为了了解HEI10如何在分子水平上控制重组，我们将使用一种专门的技术来绘制沿染色体的HEI10结合位点。这将提供he10结合的高分辨率地图，我们将与现有的重组热点地图进行比较。利用一种新的技术，我们还将绘制he10在减数分裂不同阶段的结合图谱，以研究其与基因组结合的动力学。这一点很重要，因为在减数分裂过程中，he10病灶与染色体动态结合。第三，我们将用额外的he10基因拷贝转化番茄，并测试交叉是否增加。这一点很重要，因为重组限制了番茄的育种和性状改进，例如，当野生亲缘基因渗入时。由于减数分裂和he10基因高度保守，本研究结果将很容易应用于多种作物物种。本研究将为进一步深入了解植物有性生殖过程中性状重配的机制提供依据，并为开发新的育种工具奠定基础。

Society is facing a major challenge to improve crop yield and quality, in order to meet the needs of the growing global population. One means to address this challenge is to breed and further improve crop germ plasm. For example, disease and stress resistance traits from wild populations can be beneficial to introduce into elite varieties. In this case beneficial traits must then be introgressed over many generations to achieve an improved strain. This process of crop breeding largely relies on the trait re-assortment in offspring that occurs naturally during reproduction. Specifically, diversity is generated during a specialised cell division called meiosis, which results in production of gametes (sex cells). One mechanism that creates genetic diversity during meiosis is called crossover. Here homologous chromosomes physically pair and exchange reciprocal regions, which generates new combinations of genetic variation. However, crossover patterns along chromosomes are highly skewed in many of the most important crop species, including wheat, maize, barley and tomato. As a consequence, some regions of the genome are inaccessible for breeding, despite containing important genes with effects on agronomically important traits. When compared across plants, animals and fungi, crossover levels are typically low, with most species showing ~1-2 crossovers per chromosome per meiosis. However, there is also considerable variation in crossover levels within and between species. To explore this phenomenon we previously used Arabidopsis to identify natural variation in crossover levels. These experiments identified a major gene called HEI10 that varies between Arabidopsis populations and controls crossover levels. We also discovered that HEI10 is highly dosage sensitive. We found that by increasing the HEI10 gene copy number and expression levels we could efficiently increase total crossover levels. In the context of breeding this would allow breeders to generate more diverse populations using smaller numbers of individuals. This would provide considerable advantages in terms of time and expense. Therefore, in the proposed work we describe a combined program of basic and applied experiments designed to refine the use of HEI10 as a master-switch for recombination, and deploy it in an important crop species (tomato). This project has three major objectives. First, we will use the model plant Arabidopsis to investigate in detail how the HEI10 gene can be used to increase recombination. We will further increase HEI10 dosage to test when saturation of the recombination response occurs. We will further vary the timing of HEI10 expression during meiosis. Additional genetic modifications will be combined with HEI10 in order to bias the pattern of crossovers in ways that would be beneficial for breeding. Second, to understand how HEI10 controls recombination at the molecular level, we will use a specialised technique to map HEI10 binding sites along the chromosomes. This will provide a high-resolution map of where HEI10 binds, which we will compare to our existing maps of recombination hotspots. Using a novel technique we will also map HEI10 binding at different stages during meiosis, in order to investigate the dynamics of its binding to the genome. This is important as HEI10 foci shows dynamic binding to chromosomes during meiosis. Third, we will transform tomato with additional HEI10 gene copies and test whether crossover increases. This is important as recombination limits tomato breeding and trait improvement, for example when introgressions are made from wild relatives.As meiosis and HEI10 are highly conserved, the outcomes of the proposed research will be readily applicable to diverse crop species. The proposed research will provide a more detailed understanding of the mechanisms of trait re-assortment during plant sexual reproduction and will lay a foundation to develop novel tools to accelerate crop breeding.