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

通过小麦-短柄草-水稻比较分析深入了解基因组的组织和进化

• 批准号: 0638558
• 负责人: Katrien Devos
• 金额: --
• 依托单位: University of Georgia Research Foundation Inc
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2006
• 资助国家: 美国
• 起止时间: 2006-10-01 至 2010-09-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0638558&HistoricalAwards=false
• 关键词: Gaining; Insight; into; Organization; Evolution

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.

PI: Katrien M. Devos（佐治亚大学）合作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）草科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也正在生成。然而，对小麦基因组进行测序仍然是一个挑战，因为它的规模很大。为了促进这一努力，需要更好地理解小麦基因组的组织和进化，而这反过来又可以通过研究一个合适的模型来促进。一个模式种应该与小麦密切相关，具有较小的基因组大小，是二倍体，有简单的生长需求，并且易于遗传操作。水稻是禾本科植物的一个很好的模型，但与小麦只有很远的亲缘关系。对温带禾草的另一种模式的研究导致了短柄草（Brachypodium distachyon）的鉴定。双歧杆菌的基因组测序预计将于2007年初完成。它的基因组序列将为禾本科植物基因组结构的比较分析提供一个框架。总体目标是开发双歧杆菌作为温带牧草的模型，并评估其在小麦基因组学中的应用。双歧杆菌染色体的物理图谱对双歧杆菌基因组序列的组装具有重要的指导意义。物理图谱是克隆在细菌人工染色体载体上的基因组片段的有序序列。物理图谱的构建需要在指纹共享的基础上将BAC克隆组装成连续的序列（称为contigs），并将这些contigs固定在染色体的遗传图谱上。本项目将完成双歧杆菌遗传图谱和物理图谱的绘制。该遗传图谱将利用约1000个与水稻和小麦基因组图谱具有高度同源性的双歧杆菌基因组序列构建。这些图谱和序列数据将用于与小麦的直系祖先陶氏小麦（Aegilops tauschii）的基因组比较研究。Ae的选择。小麦的可得性决定了小麦的可得性，而不是小麦本身。tauschii的长度为1 ~ 2 Mb，这是小麦中尚未发现的资源，并且与伊蚊的高度同源性是合理的。陶氏体和小麦基因组。十二个Ae。选择重组率不同、总碱基对达2200万Mb的陶什区与双歧杆菌和水稻进行比较分析。对于两个地区，研究结果的外推将通过使用美国和国际合作者生成的数据扩展到小麦的A和B基因组的比较来验证。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，对于两个区域也是多倍体，重复内容，基因密度，序列分歧，以及染色体结构的其他方面。获取项目成果所有序列数据将通过GenBank （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。