Functional Genomics of Plant Polyploids

Pi：Luca Comai，华盛顿大学合伙：James A.Birchler，密苏里大学合伙：Z.Jeffrey Chen，德克萨斯农工大学合伙：R.W.Doerge，普渡大学合伙：Robert A.Martin enssen，密苏里大学冷泉港实验室合伙：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分校高级人员：安德烈亚斯·马德隆，普吉特大学声音多倍体，在包括开花植物在内的真核生物的进化史和多样性中可以发现。几种最重要的农作物是多倍体的，如小麦和油菜，许多作物的祖先中有可识别的多倍体，如玉米。全基因组复制通过将两个或多个不同的基因组组合起来，使单个基因组或异源多倍体倍增，从而产生同源多倍体。同源多倍体和异源多倍体表现出重复基因的功能差异，增加了变异，并导致了新的遗传交互作用，导致了更大的表型变异性和杂交优势。在这个项目中，我们将在三个互补的植物系统：拟南芥、油菜和玉米中验证几个关于剂量依赖和非加性基因调控机制的假说。近交衰退、异源多倍体不育和杂种优势的遗传基础将被确定。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被确定。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。通过比较新的多倍体种群的基因表达变化，以确定影响多倍体新的表型变异和杂交活力的基因座。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。本研究的结果不仅有助于阐明我们对多倍体的理解和非加性基因作用的遗传机制，而且可能为农作物的改良提供理论依据。将利用基因组信息学和统计方法简化微阵列数据的分析和管理。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(普吉特湾大学和加州理工州立大学圣路易斯·奥比斯波大学)的高级人员将把当代多倍体和基因组学模块纳入传统的遗传学和生物学课程。PIS将与当地高中和中学合作，通过在研究实验室组织暑期实习和研讨会，积极参与为未被充分代表的学生提供研究和教学职业机会。访问项目结果项目数据将在http://www.polyploidy.org/.上获得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/)和基因表达总览(geo：http://www.ncbi.nlm.nih.gov/Genbank/GenbankOverview.html).)中的微阵列数据中

PI: Luca Comai, University of WashingtonCo-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).