Advances 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.