Genome-Wide Restriction Map of Rice by Optical Mapping

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The grasses provide more than 80% of the world's edible dry matter. Among the grasses, rice has become the model monocot plant, having a relatively small genome (430 Mb), the ability to be transformed, high density genetic maps based on molecular markers, and physical maps from large fragment clones under development. Comparative analysis among the grasses has shown that large grass genomes of important crop plants such as wheat, barley, maize, sorghum, oat and sugarcane share extensive synteny with the genome of rice, thus making detailed study of the rice genome relevant to all grasses. This award supports the construction of an optical restriction map of the genome of rice (O. sativa L. japonica variety Nipponbare) as a first step toward development of a comprehensive understanding of the genome organization of O. sativa L. This variety has been selected by the international plant genome community as the template for a rice genome sequencing effort. Direct restriction mapping of the rice genome will be performed on large, random fragments of genomic DNA, isolated cells, or nuclei mounted on specially prepared surfaces. Ordered restriction maps prepared from individual DNA molecules will be assembled into a continuous map covering the entire genome. Successful application of this approach has already led to the rapid development of optical restriction maps for the genomes of Escherichia coli (4.3 Mb) and Plasmodium falciparum (26 Mb). Efforts are currently underway to map the human genome (3,000 Mb). It is anticipated that a complete optical restriction map of diploid rice can be accomplished in 3 years. The resulting map will be linked to available genetic and physical maps through comparison of restriction fragment patterns of selected BAC clones of Nipponbare DNA, developed elsewhere, and by localization of existing molecular markers in the rice genetic map to these clones. This approach will complement those currently underway by providing critical linking data to fill gaps in BAC contigs as well as a means to organize DNA sequence information generated from a random genome sequencing approach.