Development of multi-parent advanced intercoss populations for fine mapping QTL in wheat

鉴定含有控制性状基因的染色体小片段可以提高植物育种的速度、效率和效果。识别这些片段的一种方法是寻找DNA标记和特征之间的相关性。通常，标记是染色体上已知位置的一小段DNA。标记和性状之间的强相关性表明一个基因对接近标记的性状有影响。这一过程通常是通过寻找两个近亲杂交的后代之间的相关性来进行的。在这种受控杂交中，其他影响种群基因构成的因素，如移民，都被消除了。这最大限度地减少了标记和性状之间虚假相关性的发生。这种方法有两个局限性。首先，双亲本群体中的标记性状关联在育种者使用的品系中并不一定重要。其次，当标记和基因相距相当远时，相关性就会出现，而这些相关性几乎没有实际用途。理想情况下，相关性的存在应该表明该标记与该基因接近。植物育种者可以选择是否存在标记，而不是选择性状。这样可以更快更便宜。已经开发出克服这些限制的方法。一种是在相关标记和特征之前，在连续的几代中反复杂交个体。这些额外的杂交导致来自父母双方的基因彻底洗牌，从而提高了只有在标记与基因非常接近时才能检测到标记-性状关联的机会。这样的种群被称为“高级交叉”。高级交叉不要求只有两个父母。多亲本可以使种群更能代表育种者所使用的品系。多亲本高级杂交（MAIC）群体的建立需要时间，并且需要比通常更多的标记。然而，DNA标记的成本正在稳步下降。因此，重要的是现在建立MAIC人口，以便利用更便宜的标记系统。本提案所述的工作旨在建立冬小麦的这一资源。我们将建立两个MAIC种群，一个以当前的精英种群为基础，一个以具有历史意义的旧种群为基础。在可用的时间内，我们还将从每一种群的第一代推导出一组近交系。这些将提供给所有感兴趣的利益攸关方。这些种群在精细制图中的使用是有限的，但它们仍然可以比现有的替代方法更精确地定位基因。我们还确定了两个预先存在的高度异交冬小麦种群。这些没有在控制条件下保持，但仍然可能作为MAIC人口使用。我们将从每个种群中生成1000行，以创建可立即用于非常精细映射的资源。尽管人们了解使用MAIC人口的理论，但我们需要确认它在实践中是否有效。为此，我们将使用一种称为DArT（数字阵列技术）的廉价遗传标记系统对个体和自交系的样本进行基因分型（遗传指纹）。使用这些数据，我们可以检查洗牌过程是否如预期的那样发生，并且预先存在的种群确实可以被视为MAIC种群。最后，我们将使用DArT数据寻找与雄性不育相关的基因，这些基因存在于已建立的异交群体中。这些基因的位置大致已知，但我们将对其进行改进，以提供MAIC力量的实际演示。更精确地定位这种基因也将有助于未来基因实验的设计和执行。

The identification of small segments of chromosomes containing genes that control traits can improve the speed, efficiency and effectiveness of plant breeding. One method of identifying such segments is to look for correlations between DNA markers and traits. Typically, a marker is a short length of DNA with a known location on a chromosome. A strong correlation between marker and trait is an indication of a gene with an effect on the trait close to the marker. This process is typically carried out by searching for correlations among the progeny of a cross between two inbred parents. In such controlled crosses other factors affecting the genetic make-up of a population, such as migration, are eliminated. This minimises the occurrence of spurious correlations between markers and traits. This approach has two limitations. Firstly, marker-trait associations in bi-parental populations are not guaranteed to be important among the lines used by breeders. Secondly, correlations occur when marker and gene are quite a distance apart and these have little practical use. Ideally, the presence of a correlation should indicate that the marker is close to the gene. Plant breeders can then select for presence or absence of the marker, rather than selecting for the trait. This can be quicker and cheaper. Methods have been developed to overcome these limitations. One is to repeatedly cross individuals over successive generations before correlating markers and traits. These extra crosses cause thorough shuffling of genes coming from each of the parents, thereby improving the chance that marker-trait associations are only detected if the marker is very close to the gene. Such populations are called 'Advanced Intercrosses'. There is no requirement for an Advanced Intercross to have only two parents. Multiple parents can make the population more representative of the lines used by breeders. Multiparent Advanced Intercross (MAIC) populations take time to set up and more markers are required than usual. However, the cost of DNA markers is falling steadily. It is therefore important that MAIC populations are established now, to exploit cheaper marker systems as they become available. The work described in this proposal sets out to establish this resource for winter wheat. We shall set up two MAIC populations, one based on current elite lines and one based on older lines of historic importance. Within the time available, we shall also derive a set of inbred lines from the first generation of each population. These will be made available to all interested stakeholders. The use of these populations in very fine mapping is limited, but they will still allow location of genes with greater precision than possible with available alternatives. We have also identified two pre-existing highly outcrossed winter wheat populations. These have not been maintained under controlled conditions but are still likely to be of use as MAIC populations. We will generate 1000 lines from each of these populations to create a resource available immediately for very fine mapping. Although the theory behind the use of MAIC populations is understood, we need to confirm that it works in practice. For this purpose, we will use a system of cheap genetic markers called DArT (Digital Array Technology) to genotype (genetically fingerprint) samples of individuals and inbred lines. Using these data, we can check that the shuffling process occurs as expected and that the pre-existing populations can indeed be treated as if they were MAIC populations. Finally, we will use the DArT data to hunt for associations with the genes responsible for male sterility, present in the established outcrossing populations. The location of these genes in roughly known, but we shall refine it to provide a practical demonstration of the power of the MAIC. Locating this gene with greater precision will also help in the design and execution of future genetic experiments.