Mapping Complex Agronomic Traits in Autotetraploid Potato

世界在提供可持续粮食供应方面面临着前所未有的挑战，这是由于人口的快速增长和小麦、水稻等传统粮食作物种植用地的减少，这主要是由于城市化和气候变化造成的。粮农组织将马铃薯列为世界第三大粮食作物，因为它产量高，营养价值高，与许多农作物相比，对灌溉和耕地的要求不那么严格。然而，迫切需要开发具有遗传改良农艺性能的新品种，特别是对低降雨和低温度、抗病、高块茎产量和品质等恶劣栽培环境的适应性。马铃薯基因组的多倍体特性构成了一个重大挑战。多倍体生物的每个细胞有多组染色体。当多倍体细胞分裂时，它们表现出比具有两组染色体的二倍体细胞复杂得多的染色体配对行为，创造了更广泛的重组(基因改组)和基因分离(分裂)的结果。多倍体在动植物，特别是开花植物的进化中发挥了关键作用，其中许多植物目前是多倍体的，而其他植物在进化史上经历了多倍体。马铃薯是一种同源四倍体，具有相同基因组的四个拷贝，并表现出四倍体遗传，这一特征在许多其他重要作物中都有，包括葱、甘蔗、紫花苜蓿和一些重要的经济水产养殖物种，包括大西洋鲑鱼和鲑鱼。要开发具有遗传改良性能的新马铃薯品种，需要了解影响目标性状的基因的数量和位置。自然界中大多数可观察到的性状都是数量或复杂的，包括关键的农艺性状，如产量和抗病能力，以及大多数与人类和其他动物的健康和疾病相关的性状。因此，了解数量性状的表型变异是如何受遗传控制的，为植物育种提供了必要和合理的基础。在大多数物种基因组中发现丰富的DNA序列变异，为定位数量性状表型的基因提供了信息来源，即所谓的数量性状基因座(QTL)定位。QTL定位提供了对基因组位置、控制数量性状的基因的数量和效应的估计。QTL定位的理论和方法已经很好地建立了，并且在二倍体物种中进行QTL定位是常规的。然而，同种类型的研究远远落后于同源四倍体物种，这主要是因为缺乏适当的方法来进行这些分析。由于同源四倍体的遗传与二倍体的遗传有很大的不同，用二倍体的方法对同源四倍体进行同样的分析是不合适的。该项目将为DNA标记辅助定位QTL和其他同源四倍体物种的定量遗传分析提供科学基础和新的分析工具。待开发的方法将适当考虑同源四倍体遗传的基本而复杂的特征。我们将开展实验，对栽培马铃薯的异种分离群体进行排序，以寻找均匀分布在马铃薯基因组中的DNA序列变体。这些序列数据将与来自同一群体的几个重要农艺数量性状的表型数据相结合，以便使用将要开发的分析方法来定位这些性状的QTL。这将提供第一个在严格的四体基础上进行QTL定位的例子。该项目的完成将为同源四倍体物种的基础遗传学和基因组学研究提供前所未有的机会，并促进同源四倍体作物品种和水产养殖动物品种的遗传育种。

The world is facing an unprecedented challenge to provide a sustainable food supply, caused by a rapid population increase and shrinkage of land for growing traditional food crops such as wheat, rice etc., largely due to urbanization and climate change. The FAO has ranked potato as the world's third most important food crop based on its high yield, nutritional value and less stringent requirements for irrigation and arable land to grow compared with many crops. However, there is an urgent need for the development of new varieties with genetically improved agronomic performance, particularly adaptability to harsh cultivation environments such as low rainfall and temperature, resistance to disease, and high tuber yield and quality. A major challenge is posed by the polyploid nature of the potato genome. Polyploid organisms have multiple sets of chromosomes per cell. When polyploid cells divide, they show much more complicated chromosome pairing behaviour compared to diploid cells with two sets of chromosomes, creating a wider range of outcomes for recombination (gene shuffling) and gene segregation (partitioning). Polyploidy has played a key role in the evolution of plants and animals, particularly flowering plants, many of which are currently polyploid, while the rest have experienced polyploidy in their evolutionary history. Potato is an autotetraploid with four copies of the same genome and shows tetrasomic inheritance, a characteristic shared by many other important crops including leek, sugarcane, alfalfa and some economically important aquaculture species, including Atlantic salmon and trout. To develop new potato varieties with genetically improved performance requires knowledge of the number and location of genes that affect the target traits. Most observable traits in nature are quantitative or complex, including key agronomic traits, such as yield and resistance to disease, as well as most traits relevant to health and disease, in humans and other animals. Therefore understanding how phenotypic variation in quantitative traits is genetically controlled provides an essential and rational basis for plant breeding. Discovery of abundant DNA sequence variants in the genome of most species provides a source of information for locating genes that underlie quantitative trait phenotypes, the so called mapping of Quantitative Trait Loci (QTL). QTL mapping provides estimates of genome locations, the number and effects of the genes controlling a quantitative trait. Theory and methods for QTL mapping have been well established and QTL mapping is routinely practiced in diploid species. However, the same type of study lags far behind in autotetraploid species, primarily due to the lack of appropriate methods for these analyses. Since inheritance in autotetraploids differs markedly from that in diploids, it is inappropriate to use the methods developed for diploids to conduct the same analysis in autotetraploids. This project will deliver the scientific basis and novel analytical tools for DNA-marker assisted mapping of QTL and other quantitative genetic analyses in autotetraploid species. The methods to be developed will take proper account of the essential yet complex features of autotetraploid inheritance. We will carry out experiments to sequence an outbred segregating population of cultivated potato for evenly distributed DNA sequence variants in the potato genome. The sequence data will be integrated with phenotype data of several agronomically important quantitative traits from the same population to enable mapping of QTL for these traits using the analytical methods to be developed. This will provide the first example of QTL mapping practice on a rigorous tetrasomic basis. Accomplishment of this project will open unprecedented opportunities for basic genetics and genomics research in autotetraploid species, and facilitate genetic breeding for elite autotetraploid crop cultivars and aquaculture animal varieties.