Gaining Insight into the Organization and Evolution of Genomes Through Wheat - Brachypodium - Rice Comparative Analysis

PI：Kailen M.Devos(佐治亚大学)共同PI：Olin D.Anderson，Jan Dvorak(加州大学戴维斯分校)，Pablo D.Rabinowicz(基因组研究所)，John Vogel(加州大学河滨分校)草本植物家族包含一些最重要的主要作物，如水稻、玉米和小麦。水稻的全基因组序列数据已经可用，玉米的全基因组序列数据正在生成中。然而，由于小麦基因组的大小，测序仍然是一个挑战。为了促进这一努力，需要更好地了解小麦基因组的组织和进化，而这反过来可以通过研究合适的模型来促进。模式物种应该与小麦密切相关，具有较小的基因组大小，是二倍体，具有简单的生长要求，并服从于基因操作。水稻一直是牧草的一个很好的模式，但与小麦只有遥远的亲缘关系。对温带牧草的另一种模式的探索导致了Brachypodium disachyon的鉴定。预计将在2007年初完成对分枝杆菌基因组的测序。它的基因组序列将为牧草基因组结构的比较分析提供一个框架。总的目标是发展B.disachyon作为温带牧草的模式，并评估其在小麦基因组学中的效用。利用染色体的物理图谱可以很大程度上帮助构建紫背天牛基因组序列。物理图谱是克隆在细菌人工染色体(BAC)载体中的基因组片段的有序序列。构建物理图谱需要根据它们的指纹共享将BAC克隆组装成连续的序列(称为重叠群)，并将重叠群锚定在染色体的遗传图谱上。该项目将完成稻瘟病菌遗传图谱和物理图谱的开发。遗传图谱将使用大约1000个B.disachyon基因组序列构建，这些序列与所绘制的水稻和小麦基因具有很高的同源性。这些图谱和序列数据将用于与小麦的直系祖先节节麦进行比较基因组研究。选择Ae.节节麦而不是小麦本身是由Ae的可获得性决定的。Tauschii的序列准备好的BAC重叠群1到2 Mb长，这是一种小麦中尚未获得的资源，并被Ae之间的高度同源性所证明。节节麦和小麦基因组。12Ae.将选择重组率不同且总计2200万个碱基对(Mb)的结节菌区域与稻曲霉和水稻进行比较分析。对于两个地区，通过使用美国和国际合作者产生的数据对小麦的A和B基因组进行比较，将研究结果外推到面包小麦将得到验证。测序区域内的重组率将被估计并用于探索区域沿染色体的位置和重组率的影响，以及两个区域的多倍体、重复内容、基因密度、序列分歧和染色体结构的其他方面的影响。获取项目成果所有序列数据将通过基因库(http://www.ncbi.nlm.nih.gov/).)发布遗传图谱和比较数据将通过GrainGenes(http://wheat.pw.usda.gov/GG2/index.shtml)和Gramene(http://www.gramene.org/).)提供项目网页(可通过http://www.cropsoil.uga.edu/faculty1/devoslab.htm)访问)将提供有关项目总体目标、里程碑和进展的信息。

PI: Katrien M. Devos (University of Georgia)Co-PIs: Olin D. Anderson, Jan Dvorak (University of California, Davis), Pablo D. Rabinowicz (The Institute for Genomic Research), John Vogel (University of California, Riverside)The grass family contains some of the most important staple crops such as rice, maize and wheat. Whole-genome sequence data is available for rice and is being generated for maize. Sequencing the wheat genome, however, remains a challenge due to its large size. To facilitate this endeavor, a better understanding of the organization and evolution of wheat genome is required, and this in turn, can be facilitated by studying a suitable model. A model species should be closely related to wheat, have a small genome size, be a diploid, have simple growth requirements, and be amenable to genetic manipulation. Rice has served as a good model for the grasses, but is only distantly related to wheat. A search for an alternative model for temperate grasses has led to the identification of Brachypodium distachyon. Sequencing of the B. distachyon genome is expected to be completed by early 2007. Its genomic sequence will provide a framework for comparative analyses of genome structure in grasses. The overall goal is to develop B. distachyon as a model for temperate grasses and assess its utility for wheat genomics. A physical map of B. distachyon chromosomes would greatly aid the assembly of B. distachyon genome sequence. A physical map is an ordered sequence of genomic fragments cloned in a bacterial artificial chromosome (BAC) vector. The construction of a physical map requires assembling BAC clones into contiguous sequences (called contigs) on the basis of their fingerprint sharing, and anchoring the contigs on a genetic map of the chromosome. The development of genetic and physical maps of B. distachyon will be accomplished in this project. The genetic map will be constructed using about 1000 B. distachyon genomic sequences that have high homology to mapped genes in rice and wheat. The maps and sequence data will be used for comparative genomic studies with Aegilops tauschii, an immediate ancestor of wheat. The choice of Ae. tauschii rather than wheat itself was governed by the availability in Ae. tauschii of sequence-ready BAC contigs 1 to 2 Mb long, a resource not yet available in wheat, and was justified by the high degree of homology between the Ae. tauschii and wheat genomes. Twelve Ae. tauschii regions that differ in recombination rate and totaling 22 million base pairs (Mb) will be selected for comparative analyses with B. distachyon and rice. For two regions, extrapolation of the research results to bread wheat will be validated by extending the comparisons to the A and B genomes of wheat using data generated by US and international collaborators. Recombination rates within the sequenced regions will be estimated and used to explore the effects of position of a region along the chromosome and recombination rate, and for two regions also polyploidy, of repeat content, gene density, sequence divergence, and other aspects of chromosome structure. Access to project outcomesAll sequence data will be released through GenBank (http://www.ncbi.nlm.nih.gov/). The genetic maps and comparative data will be made available through GrainGenes (http://wheat.pw.usda.gov/GG2/index.shtml) and Gramene (http://www.gramene.org/). A project webpage (accessible via http://www.cropsoil.uga.edu/faculty1/devoslab.htm) will provide information about the overall goals, milestones and progress of the project.