Transposable Elements in Rice: A Whole Genome Approach

植物基因组计划输出的DNA序列的很大一部分将来自转座元件(TES)。据估计，水稻小基因组的30%。日本晴，438Mb)，这是下一个主要植物基因组计划的重点，是从TES衍生而来的。与TE不同，基因的功能可以部分地通过基因敲除突变体的表型、蛋白质或信使核糖核酸的定位和微阵列的分析来推断。这种功能基因组学方法在理解TES对基因组进化和功能的贡献方面价值不大。与生物体的基因互补不同的是，除了其他事情外，还有转座和扩增的能力。TES撼动了原本保守的基因组，以这种方式既威胁又增强了基因组潜力。该项目使用功能基因组学方法来识别水稻TES的贡献，它包括三个部分：(1)所有TE家族的鉴定和特征；(2)在紧密相关的水稻品种、亚种和相关物种中TE介导的多样性的量化；(3)TE多样性对创造表型变异的贡献的评估。为此，将使用跨学科的全基因组方法，有五个具体目标：(I)通过计算机识别水稻TE并确定TE家族的系统发育特征。主要的重点将是测试一种新的自动重复元件识别算法。(Ii)通过使用快速转座子显示屏来分析一组广泛物种杂交和各种胁迫环境来评估选择的TE家族的活性。(Iii)确定在两个不同的作图群体中具有多态的1000个TE插入位点的染色体分布，并将这些插入位点的子集开发成锚标记。(Iv)使用作图群体和锚标记作为将基于TE的遗传变异与所选植物性状的表型变异相关联的基础。(V)整合来自该项目被引入到RiceGenes数据库中，从而以将TES链接到QTL的注释的形式增加了信息的价值，突变表型、遗传标记和种质多样性。转座因子可能解释了包括水稻、高粱、玉米和小麦在内的草类支系中在农学上重要的成员之间大小的巨大差异。该联盟将作为如何在这些更复杂的基因组中研究TES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.