Physical Mapping of the Wheat D Genome

项目负责人：Jan Dvorak，加州大学戴维斯分校/美国农业部农业研究中心，奥尔巴尼分校，项目负责人：Olin D. Anderson，加州大学戴维斯分校，项目负责人：Bikram S. Gill，堪萨斯州立大学，项目负责人：罗明成，加州大学戴维斯分校，高级人员：李万龙，堪萨斯州立大学小麦遗传学和基因组学研究的进展对于提高产量潜力、抗病虫害和耐恶劣环境条件的小麦品种的持续发展至关重要。小麦的细胞核中含有大量的DNA。小麦也是多倍体；它起源于种间杂交，其细胞核包含三个不同的基因组，分别命名为A， B和D，每个基因组由不同的二倍体物种贡献。本项目的目标是开发小麦染色体物理定位的基因组资源，并将其应用于小麦D基因组染色体物理定位。染色体的物理图谱是基因的线性顺序和染色体上的其他标志的物理表示。为了构建物理地图，基因组DNA被分割，DNA片段被克隆，每个克隆都被“指纹”。指纹之间的重叠被用来识别来自染色体相邻区域的DNA片段。基因和其他标记在这些片段中的位置被确定，重叠DNA片段的序列与沿着染色体的标记的线性顺序对齐。物理图谱对于基因克隆、育种过程中标记基因的遗传标记的发展非常重要，并且通常是基因组测序的先决条件。小麦多倍体和大基因组要求在其染色体的物理定位中使用新的策略。与其试图构建全球小麦物理图谱，不如首先构建小麦D基因组的二倍体祖先Aegilops tauschii的染色体物理图谱。这些图谱将作为构建中国春小麦D基因组三条染色体物理图谱的模板。与捷克共和国实验植物学研究所（IEB）的国际合作将促进这一步骤，该研究所开发了一种通过染色体流分选分离小麦单个染色体的技术。该项目补充了正在进行的国家和国际小麦基因组测序工作，并为美国博士后研究人员和不同教育水平的学生提供了培训机会。三个CS染色体的序列准备物理图谱将使在该项目结束时启动小麦基因组测序在理论上成为可能。虽然在小麦基因组序列向研究界开放之前，还需要其他项目和未知的数年时间，但该项目生成的锚定物理图谱将为遗传和基因组项目以及多倍体基因组进化研究提供宝贵的资源。该项目计划的研究与其他几个国家和国际项目相平行，这些项目旨在获取知识或开发资源，以完成所有21条CS染色体的物理图谱。这些项目之间的协同作用将大大扩大其个别影响。为了进一步扩大该项目的影响，将组织以下具体活动：在加州大学戴维斯分校为研究生和博士后培训生开设了一个全国性的指纹和物理测绘研讨会，在IEB为美国研究生和博士后培训生开设了一个全国性的国际实习机会，通过流式分选获得植物染色体分离的技能，目前在美国还没有。以及其他植物分子细胞遗传学技术。最后，一些项目实验室将接待高中和大专学生，这些学生将在家庭机构中获得基因组学和生物技术暑期研究项目的支持。项目数据库（WheatDB）可以在http://wheatdb.ucdavis.edu:8080/wheatdb/index.jsp上访问。这个公共数据库将成为指纹、物理地图信息和该项目产生的所有其他可交付成果的初始存储库。它还提供了方便地访问、显示和分析生成数据的工具。该项目的数据也将被整合到GrainGenes （http://wheat.pw.usda.gov/GG2/index.shtml）和Gramene （http://www.gramene.org/）这两个公共网站中。GrainGenes提供小麦和其他谷物的分子和表型信息汇编。Gramene是一个开源的、用于比较禾本科基因组分析的数据资源。

PI: Jan Dvorak, University of California, DavisCo-PI: Olin D. Anderson, UC Davis/USDA-ARS, Albany, CACo-PI: Bikram S. Gill, Kansas State UniversityCo-PI: Mingcheng Luo, University of California, DavisSenior Personnel: Wanlong Li, Kansas State UniversityAdvances in wheat genetics and genomics are essential for the sustained development of wheat varieties with enhanced yield potential, resistance to pests and diseases, and tolerance of adverse environmental conditions. Wheat has an exceptionally large amount of DNA in its nucleus. Wheat is also polyploid; it originated by interspecific hybridization, and its nucleus contains three different genomes, designated A, B, and D, each contributed by a different diploid species. The goal of this project is to develop genomic resources for physical mapping of wheat chromosomes and to deploy them in physical mapping of chromosomes of the wheat D genome. A physical map of a chromosome is a physical representation of the linear order of genes and other landmarks along the chromosome. To construct a physical map, genomic DNA is fragmented, DNA fragments are cloned and each clone is ?fingerprinted?. Overlaps between fingerprints are used to identify DNA fragments from neighboring regions of a chromosome. The location of genes and other markers in these fragments is determined and the sequence of overlapping DNA fragments is aligned to the linear order of markers along a chromosome. Physical maps are important for gene cloning, the development of genetic markers for tagging genes during breeding, and often a prerequisite for genome sequencing. Wheat polyploidy and large genomes require the use of novel strategies in the physical mapping of its chromosomes. Instead of attempting to construct wheat physical maps globally, the physical maps of the chromosomes of Aegilops tauschii, the diploid ancestor of the wheat D genome, will be constructed first. These maps will then be used as templates for the construction of the physical maps of three individual chromosomes of the wheat D genome in the cultivar Chinese Spring (CS). This step will be facilitated by international collaboration with the Institute of Experimental Botany (IEB), Czech Republic, which developed a technique for the isolation of individual wheat chromosomes by chromosome flow-sorting. This project complements ongoing national and international work toward wheat genome sequencing and it provides opportunities for training of US postdoctoral researchers and students at several educational levels.Sequence-ready physical maps of the three CS chromosomes will make it theoretically possible to initiate wheat genome sequencing at the end of this project. While it will take other projects and an unknown number of years before the full wheat genomic sequence will be available to the research community, the anchored physical maps generated in this project will provide a valuable resource for genetic and genomic projects and studies of polyploid genome evolution. Research planned in this project parallels several other national and international projects aiming at knowledge acquisition or resource development needed for the completion of the physical maps of all 21 CS chromosomes. Synergy among these projects will greatly broaden their individual impacts. To broaden further the impact of this project, the following specific activities will be organized: nationally advertised internships for undergraduate students in each of the participating laboratories, a nationally advertised workshop at UC Davis in fingerprinting and physical mapping for graduate students and postdoctoral trainees, and a nationally advertised international internship for US graduate students and postdoctoral trainees at IEB to acquire skills in plant chromosome isolation by flow-sorting, currently unavailable in this country, and other plant molecular cytogenetic techniques. Finally, several project laboratories will host high school and junior college students supported by summer research programs in genomics and biotechnology in the home institutions.The project database(WheatDB) will be accessible at http://wheatdb.ucdavis.edu:8080/wheatdb/index.jsp. This public database will be the initial repository of fingerprints, physical mapping information and all other deliverables generated by the project. It also provides the tools for easy access, display, and analysis of the generated data. The project data will also be integrated into GrainGenes (http://wheat.pw.usda.gov/GG2/index.shtml) and Gramene (http://www.gramene.org/), both curated public websites. GrainGenes provides a compilation of molecular and phenotypic information on wheat and other cereals. Gramene is an open-source, data resource for comparative genome analysis in the grasses.