Transposable Elements in Rice: A Whole Genome Approach

从植物基因组计划中输出的DNA序列的很大一部分将来自转座因子（TE）。 据估计，30%的水稻（Oryza sativa cv.日本晴，438 Mb），这是下一个主要的植物基因组计划的重点，是来自TE。 与TE不同，基因的功能可以部分地通过敲除突变体的表型、蛋白质或mRNA的定位以及微阵列的分析来推断。 这种功能基因组学方法在理解TE对基因组进化和功能的贡献方面价值不大。 除了别的以外，将TE与生物体的基因互补区分开来的是转座和扩增的能力。 TE动摇了原本保守的基因组，以这种方式，既威胁又增强了基因组的潜力。 该项目使用功能基因组学方法来辨别水稻TE的贡献，包括三个组成部分：（1）所有TE家族的鉴定和表征，（2）在密切相关的水稻栽培品种、亚种和相关物种中TE介导的多样性的定量和（3）TE多样性对表型变异产生的贡献的评估。 为此，将采用跨学科的全基因组方法，具体目标有五个。(i)通过计算鉴定水稻的转基因植株，并对转基因植株的家系进行遗传学分析。 一个主要的重点将是一种新的自动重复元件识别算法的测试。(ii)通过使用快速转座子显示屏幕来分析一组宽种杂交和各种胁迫环境，以评估选择的TE家族的活性。(iii)确定1000个TE插入位点的染色体分布，这些位点在两个不同的作图群体中具有多态性，并将这些位点的子集开发成锚标记。(iv)以作图群体和锚标记为基础，将基于TE的遗传变异与所选植物性状的表型变异相关联。(v)将该项目的所有数据整合到RiceGenes数据库中，从而以注释的形式将TE与QTL、突变表型、遗传标记和种质多样性联系起来，从而增加信息的价值。转座因子可能解释了禾本科进化枝中重要的农艺学成员（包括水稻、高粱、玉米和小麦）在大小上的巨大差异。 该联盟将作为如何在这些更复杂的基因组中研究TE的模型。

A large fraction of the DNA sequence output from plant genome projects will be derived from transposable elements (TEs). It is estimated that 30% of the small genome of rice (Oryza sativa cv. Nipponbare, 438 Mb), which is the focus of the next major plant genome project, is derived from TEs. Unlike a TE, the function of a gene can be deduced, in part, through the phenoytpe of a knockout mutant, the localization of protein or mRNA and the analysis of microarrays. Such functional genomics approaches are of little value in understanding the contribution of TEs to genome evolution and function. What distinguishes TEs from the genic complement of an organism, among other things, is an ability to transpose and amplify. TEs shake up an otherwise conservative genome and, in this way, both threaten and enhance genomic potential. This project uses a functional genomics approach to discern the contribution of the TEs of rice that includes three components: (1) the identification and characterization of all TE families, (2) the quantification of TE-mediated diversity in closely related Oryza sativa cultivars, subspecies and related species and (3) an assessment of the contribution of TE- diversity to the creation of phenotypic variation. To this an interdisciplinary, whole genome approach will be used with five specific objectives.(i) To computationally identify rice TEs and phylogenetically characterize TE families. A major focus will be the testing of a novel automated repeat element identification algorithm.(ii) To assess the activity of select TE families by using a rapid transposon display screen to assay a panel of wide-species crosses and a variety of stress environments.(iii) To determine the chromosomal distribution of 1000 TE insertion sites that are polymorphic in two different mapping populations and to develop a subset of these into anchor markers.(iv) To use the mapping populations and the anchor markers as the basis for correlating TE-based genetic variation with phenotypic variation for selected plant traits.(v) To integrate all data from this project into the RiceGenes database thus adding value to the infomation in the form of annotation linking TEs to QTLs, mutant phenoytpes, genetic markers and germplasm diversity. Transposable elements probably account for the huge difference in size among the agronomically important members of the grass clade including rice, sorghum, maize and wheat. This consortium will serve as a model for how TEs should be studied in these more complex genomes.