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

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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.