Functional Genomics of Plant Polyploids

多倍体在植物进化中起着重要的作用。超过70%的开花植物在其谱系中至少有一个多倍体事件，或者是通过单个基因组加倍（自多倍体），或者是更常见的，通过结合两个或更多不同但相关的基因组（异源多倍体）。许多重要的农作物，如紫花苜蓿、油菜、棉花、马铃薯和小麦，都是明显的多倍体，而其他作物，如玉米、大豆和卷心菜，则保留了古代多倍体事件的痕迹。虽然多倍体的重要性已被广泛认识，但其成功的原因尚不完全清楚。基因组冗余可能提供一些选择优势，通过组合基因组的相互作用导致新的基因表达模式，通过基因组变化导致重复基因的功能分化。因此，多倍体不仅会导致来自祖先的所有性状的可加性，而且经常产生在亲本中不存在或超过亲本范围的新表型。这种现象类似于杂种优势，在杂种优势中，杂交基因型通常具有超过其近亲亲本的表型。模式植物和重要作物基因组学研究的快速发展促使该联盟的成立，以研究植物多倍体的功能基因组学。该联盟旨在揭示植物多倍体进化成功的分子机制和植物杂交种的农业利用。本研究旨在研究拟南芥、芸苔和玉米再合成和天然自多倍体和/或异源多倍体基因表达和基因组结构的变化。基因表达变化将通过mRNA显示和EST芯片进行检测。在异色区鉴定的基因的新的微阵列将被开发和用于基因表达测定在拟南芥和芸苔。甲基化状态、转座子活性、染色质状态和染色体排列的变化将使用分子、生化和细胞学技术的组合来确定。将比较每个植物系统的二倍体、自多倍体和异源多倍体，以确定多倍体对基因表达和基因组结构的影响。将比较不同倍性水平的自交系玉米和杂交种玉米，以确定倍性和杂合性对基因表达的相对影响。将比较早期和晚期的芸苔多倍体，以测试多倍体形成后世代变化的稳定性，以及这些变化是否协调一致并模仿天然多倍体。这些研究将提供伴随多倍体形成和进化的基因表达和基因组变化的全面调查。最重要的是，它们应该揭示导致这些变化的一些主要机制，并阐明我们对多倍体为什么在自然界和农业中如此成功的总体理解。参与者：Thomas C. Osborn， PI, University of wisconsin; james A. Birchler, University of missouri。杰弗里·陈，副主任，德克萨斯A & M大学，卢卡·科迈，副主任，华盛顿大学，罗伯特·A·马田森，副主任，冷泉港实验室，丽贝卡·多奇，副主任，普渡大学

Polyploidy has played a prominent role in plant evolution. More than 70% of flowering plants have had at least one polyploid event in their lineage, either by doubling of a single genome (autopolyploidy) or, more commonly, by combining two or more distinct but related genomes (allopolyploidy). Many important crop plants, such as alfalfa, canola, cotton, potato and wheat, are obvious polyploids, and others, such as maize, soybean, and cabbage, retain the vestiges of ancient polyploid events. Although the importance of polyploidy has been widely recognized, the reasons for its success are not fully understood. Genome redundancy may provide some selective advantage, both through interactions of the combined genomes causing novel patterns of gene expression and through genome changes causing functional divergence of duplicated genes. Thus, polyploidy does not merely result in additivity for all traits from the progenitors, but often produces novel phenotypes that are not present in the parents or exceed the range of the parents. This phenomenon is analogous to heterosis, in which hybrid genotypes often have phenotypes that exceed those of their inbred parents.Rapid progress in genomic research of model plants and important crops has prompted the assembly of this consortium to study functional genomics of plant polyploids. The consortium is aimed at uncovering molecular mechanisms responsible for the evolutionary success of plant polyploids and agricultural utilization of plant hybrids. The theme of the proposed research is to investigate changes in gene expression and genome structure in resynthesized and natural autopolyploids and/or allopolyploids of Arabidopsis, Brassica and maize. Gene expression changes will be assayed using mRNA display and EST microarrays. New microarrays of the genes identified in heterochromatic regions will be developed and used for gene expression assays in Arabidopsis and Brassica. Changes in methylation state, transposon activity, chromatin status, and chromosomal arrangements will be determined using a combination of molecular, biochemical, and cytological techniques. The diploids, autopolyploids, and allopolyploids of each plant system will be compared to determine the effects of polyploidy on gene expression and genome structure. Inbred and hybrid maize at different ploidy levels will be compared to determine the relative effects of ploidy and heterozygosity on gene expression. Early and advanced generation polyploids of Brassica will be compared to test for stabilization of changes in the generations after polyploid formation and whether these changes are concerted and mimic natural polyploids. These studies will provide a comprehensive survey of the gene expression and genome changes accompanying polyploid formation and evolution. Most importantly, they should reveal some of the major mechanisms giving rise to these changes, and illuminate our overall understanding of why polyploids have been so successful in nature and agriculture.Participants:Thomas C. Osborn, PI, University of WisconsinJames A. Birchler, Co-PI, University of MissouriZ. Jeffery Chen, Co-PI, Texas A & M UniversityLuca Comai, Co-PI, University of WashingtonRobert A. Martienssen, Co-PI, Cold Spring Harbor LaboratoryRebecca Doerge, Co-PI, Purdue University