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，PI: Z. Jeffrey Chen，德克萨斯a&m大学，co -PI: R. W. Doerge，普渡大学，co -PI: Robert A. Martienssen，冷泉港实验室，co -PI: J. Chris Pires，密苏里大学，高级人员：Edward Himelblau，加州州立理工大学圣路易斯分校，高级人员：多倍体可以在真核生物的进化史和多样性中找到，包括开花植物。一些最重要的农作物是多倍体，如小麦和芸苔，许多在其祖先中具有可识别的多倍体，如玉米。全基因组复制通过单个基因组复制产生自多倍体，或通过组合两个或多个不同的基因组产生异源多倍体。自多倍体和异源多倍体表现出重复基因的功能分化，变异增加，并导致新的遗传相互作用，从而导致更大的表型变异性和杂种优势。在本项目中，将对拟南芥、芸苔和玉米这三个互补植物系统中剂量依赖性和非加性基因调控机制的几个假设进行测试。确定近交抑制、异源多倍体不育和杂种活力的遗传基础。利用转基因报告基因和内源基因来确定多倍体基因调控的分子基础模型。染色质结构和RNA干扰在非加性基因调控中的作用将被测试。将比较多倍体新群体的基因表达变化，以确定影响多倍体新生表型变异和杂交活力的位点。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。本研究结果不仅有助于我们对多倍体和非加性基因作用的遗传机制的认识，而且对农业作物的改良具有指导意义。微阵列数据分析和管理将使用基因组信息学和统计方法进行精简。研究和培训活动将每月在项目网站上更新。来自两所主要教学学院（普吉特海湾大学和加州州立理工大学圣路易斯奥比斯波分校）的高级人员将把当代多倍体和基因组学模块应用到传统的遗传学和生物学课程中。pi将积极参与，与当地高中和中学合作，在研究实验室组织暑期实习和讲习班，使代表性不足的学生有机会从事研究和教学工作。访问项目成果项目数据可访问http://www.polyploidy.org/。种子将存放在拟南芥生物资源中心（ABRC: http://www.biosci.ohio-state.edu/~plantbio/Facilities/abrc/abrchome.htm）和玉米遗传合作库存中心（http://w3.ag.uiuc.edu/maize-coop/）。DNA序列将存储在GenBank （http://www.ncbi.nlm.nih.gov/Genbank/）中，微阵列数据将存储在Gene Expression Omnibus （GEO: http://www.ncbi.nlm.nih.gov/Genbank/GenbankOverview.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).