Mapping Complex Agronomic Traits in Autotetraploid Potato

绘制同源四倍体马铃薯的复杂农艺性状

• 批准号: BB/N008952/1
• 负责人: Zewei Luo
• 金额: $ 50.48万
• 依托单位: University of Birmingham
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2016
• 资助国家: 英国
• 起止时间: 2016 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FN008952%2F1
• 关键词: Mapping; Complex; Agronomic; Traits; Autotetraploid

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.

世界正面临着前所未有的挑战，以提供可持续的粮食供应，造成人口迅速增加和土地萎缩，种植传统的粮食作物，如小麦，水稻等，主要是由于城市化和气候变化。联合国粮农组织将马铃薯列为世界第三大粮食作物，因为与许多作物相比，马铃薯产量高，营养价值高，对灌溉和耕地的要求不那么严格。然而，迫切需要开发新品种，其具有遗传改良的农艺性能，特别是对恶劣栽培环境的适应性，例如低降雨量和温度，抗病性以及高块茎产量和质量。马铃薯基因组的多倍性构成了一个重大挑战。多倍体生物的每个细胞有多套染色体。当多倍体细胞分裂时，与具有两组染色体的二倍体细胞相比，它们表现出更复杂的染色体配对行为，从而产生更广泛的重组（基因改组）和基因分离（分配）结果。多倍体在植物和动物的进化中起着关键作用，特别是开花植物，其中许多目前是多倍体，而其余的在其进化历史中经历了多倍体。马铃薯是同源四倍体，具有相同基因组的四个拷贝，并显示四体遗传，这是许多其他重要作物，包括韭菜，甘蔗，苜蓿和一些经济上重要的水产养殖物种，包括大西洋鲑鱼和鳟鱼所共有的特征。为了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，如产量和抗病性，以及人类和其他动物中与健康和疾病相关的大多数性状。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依据。在大多数物种基因组中发现的大量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定位提供了控制数量性状的基因组位置、数量和效应的估计。QTL定位的理论和方法已经很好地建立，并且QTL定位在二倍体物种中是常规的。然而，同类型的研究远远落后于同源四倍体物种，主要是由于缺乏适当的方法进行这些分析。由于同源四倍体的遗传与二倍体的遗传明显不同，因此不适合使用为二倍体开发的方法对同源四倍体进行相同的分析。该项目将为同源四倍体物种的QTL的DNA标记辅助定位和其他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。我们将进行实验，对栽培马铃薯的远交分离群体进行测序，以获得马铃薯基因组中均匀分布的DNA序列变体。将序列数据与来自相同群体的几个农艺学上重要的数量性状的表型数据整合，以使得能够使用待开发的分析方法对这些性状进行QTL作图。这将提供严格的四体基础上的QTL作图实践的第一个例子。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，并促进优良同源四倍体作物品种和水产养殖动物品种的遗传育种。

项目成果

Amn1 governs post-mitotic cell separation in Saccharomyces cerevisiae.

Amn1 控制酿酒酵母有丝分裂后细胞分离

• DOI: 10.1371/journal.pgen.1007691
• 发表时间: 2018-10
• 期刊: PLoS genetics
• 影响因子: 4.5
• 作者: Fang O;Hu X;Wang L;Jiang N;Yang J;Li B;Luo Z
• 通讯作者: Luo Z

Genome Duplication Increases Meiotic Recombination Frequency: A Saccharomyces cerevisiae Model.

基因组复制增加减数分裂重组频率：酿酒酵母模型

• DOI: 10.1093/molbev/msaa219
• 发表时间: 2021-03-09
• 期刊: Molecular biology and evolution
• 影响因子: 10.7
• 作者: Fang O;Wang L;Zhang Y;Yang J;Tao Q;Zhang F;Luo Z
• 通讯作者: Luo Z

A highly robust and optimized sequence-based approach for genetic polymorphism discovery and genotyping in large plant populations.

• DOI: 10.1007/s00122-016-2736-9
• 发表时间: 2016-09
• 期刊: TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik
• 作者: Jiang N;Zhang F;Wu J;Chen Y;Hu X;Fang O;Leach LJ;Wang D;Luo Z
• 通讯作者: Luo Z

Orthogonal contrast based models for quantitative genetic analysis in autotetraploid species

基于正交对比的同源四倍体物种定量遗传分析模型

• DOI: 10.1111/nph.15284
• 发表时间: 2018-10-01
• 期刊: NEW PHYTOLOGIST
• 影响因子: 9.4
• 作者: Chen, Jing;Zhang, Fengjun;Luo, Zewei
• 通讯作者: Luo, Zewei

Sampling Variation of RAD-Seq Data from Diploid and Tetraploid Potato (Solanum tuberosum L.).

二倍体和四倍体马铃薯 (Solanum tuberosumL.) 的 RAD-Seq 数据的采样变异

• DOI: 10.3390/plants10020319
• 发表时间: 2021-02-07
• 期刊: Plants (Basel, Switzerland)
• 作者: Dang Z;Yang J;Wang L;Tao Q;Zhang F;Zhang Y;Luo Z
• 通讯作者: Luo Z