YIA-PGR: Comparative Genomics of Rice: reconstructing rice chromosome 1 in related species.

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Encoded in units called "genes" on linear structures known as "chromosomes" present in essentially every cell of every organism is the instruction set for that organism. The purpose of a genome project, such as the nearly complete Rice Genome Project, is to precisely locate and describe each gene. This is not the end of the story however. For the description generated may only hint at the function of a gene and gives little indication as to the interacting role any gene or group of genes plays in the overall functioning of the organism. At this point enters the discipline of genetic mapping-whereby traits may be localized to specific positions on a chromosome. To this end, in genomes related to rice, we will construct physical maps of regions homologous to rice chromosome 1. Libraries of genomes, called BAC libraries, which consist of bacteria containing large pieces of DNA from the genome of interest, will have been constructed for many of the species in the same genus as rice (Oryza). These BAC libraries are the substrate for genome sequencing and, in this case, building sequence-ready comparative maps to compare genomes. Approximately three-quarters of the nearly 5,000 predicted genes on chromosome 1 will be used to isolate and build comparative maps across this group of species. The end result will be the reconstruction of rice chromosome 1 in a group of related species. This will help us to better understand chromosome evolution and more efficiently utilize the rice sequence data for comparative mapping in more distantly related species, such as maize, sorghum and oat. In addition, by using the natural variation that occurs in this group of species, we will be able to begin assigning biological functions to many of the genes predicted to exist in rice based on the sequence data. Deliverables:All information on Overgo sequences, physical location, analysis and reconstruction of chromosome 1 will be available at:http://rice.genomics.purdue.edu Much of the marked up information will be migrated to:http://www.gramene.org. Information on the computational pipeline is also available at:http://rice.genomics.purdue.edu.