Functional Genomics of Plant Polyploids

PI：Luca Comai，加州大学戴维斯分校PI：James A. Birchler，密苏里大学Co-PI：Z。Jeffrey Chen，德克萨斯农工大学合作研究者：R。W.普渡大学，Dobson，联合PI：Robert A. Martienssen，冷泉港实验室合作研究者：J. Chris Pires，密苏里大学高级人员：Edward Himelblau，加州理工州立大学圣路易斯奥比斯波高级人员：Andreas Madlung，普吉特海湾大学多倍体可以在真核生物的进化历史和多样性中找到，包括开花植物。几种最重要的农作物是多倍体，如小麦和芸苔属，许多作物在其祖先中具有可识别的多倍体，如玉米。全基因组复制通过使单个基因组倍增而产生同源多倍体，或通过组合两个或更多个相异基因组而产生异源多倍体。同源多倍体和异源多倍体表现出重复基因的功能分歧，增加变异，并导致新的遗传相互作用，导致更大的表型变异和杂种优势（杂种优势）。本项目将在拟南芥、芸苔属和玉米这三个互补植物系统中对剂量依赖性和非加性基因调控机制的几个假说进行检验。确定近交衰退、异源多倍体不育和杂种优势的遗传基础。将确定使用转基因报告基因和内源基因的多倍体基因调控的分子基础模型。将测试染色质结构和RNA干扰在非加性基因调控中的作用。新的多倍体群体中的基因表达变化将被比较，以确定影响多倍体中从头表型变异和杂种优势的基因座。在后测序时代，多倍体是植物生物学中最具挑战性的领域之一。这项研究的结果不仅将阐明我们对多倍体和非加性基因作用的遗传机制的理解，而且还可能使农作物的改良成为可能。微阵列数据分析和管理将使用基因组信息学和统计方法学进行简化。 研究和培训活动将在项目网站上每月更新。来自两所主要教学学院（普吉特海湾大学和加州理工州立大学圣路易斯奥比斯波）的高级人员将把当代多倍性和基因组学单元纳入传统的遗传学和生物学课程。项目研究员将与当地高中和中学合作，在研究实验室组织暑期实习和研讨会，积极参与使代表性不足的学生获得研究和教学职业机会。http://www.polyploidy.org/ 种子将保存在拟南芥生物资源中心（ABRC：http：//www.biosci.ohio-state.edu/plantbio/Facilities/abrc/abrchome.htm）和玉米遗传合作储备中心（http：//w3.ag.uiuc.edu/maize-coop/）。 DNA序列将保存在GenBank（http：//www.ncbi.nlm.nih.gov/Genbank/）中，微阵列数据保存在Gene Expression Omnibus（GEO：http：//www.ncbi.nlm.nih.gov/Genbank/Genbank Overview.html）中。

PI: Luca Comai, University of California, DavisCo-PI: James A. Birchler, University of MissouriCo-PI: Z. Jeffrey Chen, Texas A&M UniversityCo-PI: R. W. Doerge, Purdue UniversityCo-PI: Robert A. Martienssen, Cold Spring Harbor LaboratoryCo-PI: J. Chris Pires, University of MissouriSenior Personnel: Edward Himelblau, California Polytechnic State University San Luis ObispoSenior Personnel: Andreas Madlung, University of Puget SoundPolyploidy can be found throughout the evolutionary history and diversity of eukaryotes, including flowering plants. Several of the most important agricultural crops are polyploid, such as wheat and Brassica, and many have identifiable polyploidy in their ancestry, such as maize. Whole genome duplication creates an autopolyploid by multiplying a single genome or an allopolyploid by combining two or more divergent genomes. Auto- and allopolyploids exhibit functional divergence of duplicate genes, increased variation and result in novel genetic interactions leading to greater phenotypic variability and hybrid vigor (heterosis). In this project, several hypotheses will be tested concerning the mechanisms of dosage-dependent and non-additive gene regulation in three complementary plant systems: Arabidopsis, Brassica and corn. The genetic basis of inbreeding depression, allopolyploid sterility, and hybrid vigor will be determined. Models for the molecular basis of gene regulation in polyploids using transgenic reporters and endogenous genes will be determined. The roles of chromatin structure and RNA interference in non-additive gene regulation will be tested. Gene expression changes in new polyploidy populations will be compared to identify loci affecting de novo phenotypic variation and hybrid vigor in polyploids.In the post-sequencing era, polyploidy is one of the most challenging fields in plant biology. Results from this research will not only illuminate our understanding of polyploidy and the genetic mechanisms of non-additive gene action, but may also enable the improvement of agricultural crops. Microarray data analysis and management will be streamlined using genome informatics and statistical methodologies. Research and training activities will be updated monthly at the project website. The senior personnel from two primarily teaching colleges (University of Puget Sound and California Polytechnic State University San Luis Obispo) will implement contemporary polyploidy and genomics modules into traditional genetics and biology curricula. The PIs will actively participate in exposing underrepresented students to research and teaching career opportunities by organizing summer internships and workshops in research laboratories in collaboration with local high and middle schools.Access to project outcomesProject data will be available at http://www.polyploidy.org/. Seeds will be deposited in the Arabidopsis Biological Resource Center (ABRC: http://www.biosci.ohio-state.edu/~plantbio/Facilities/abrc/abrchome.htm) and the Maize Genetics Cooperation Stock Center (http://w3.ag.uiuc.edu/maize-coop/). DNA sequences will be deposited in GenBank (http://www.ncbi.nlm.nih.gov/Genbank/) and microarray data in the Gene Expression Omnibus (GEO: http://www.ncbi.nlm.nih.gov/Genbank/GenbankOverview.html).