A LARGE-SCALE SEQUENCE-READY PHYSICAL MAP OF THE RICE GENOME

¹ Department of Soil and Crop Sciences, Crop Biotechnology Center, Texas A&M University, College Station, TX 77843-2123 USA

² Institute of Genetics, Chinese Academy of Sciences, Beijing 100101, P.R. China

Integrative physical mapping is central to future genomics research. One aspect is genome physical mapping, the reconstruction of genomes from DNA fragments that are cloned, ordered and permanently maintained in forms of DNA libraries. Integration of a physical map with genetic and/or cytogenetic maps creates a genomics "freeway" that will greatly accelerate all kinds of genomics research, including rapid mapping of most plant genes (ca. 60,000), development of any kinds of DNA markers for agronomic genes and quantitative trait loci (QTLs), isolation of a large number of genes and QTLs, studies of gene and QTL action modes, and large-scale genome sequencing. To rapidly develop integrated physical maps of genomes with large-insert bacterial clones, we prevously developed a complete set of technologies for integrative physical mapping of genomes, by which an integrated physical map for an organism with a genome size of 1000 Mb can be developed within 2 - 3 years in a single laboratory and at a cost for development of a moderate density RFLP map. We also experimentally demonstrated the feasibility of genome physical mapping with large-insert bacterial clones. Using these technologies, we have developed a large-scale sequence-ready physical map of the rice genome from the three complementary indica cv. Teqing BAC libraries. A total of 24,576 BACs were fingerprinted using the Fpase I kit (Invention No.: TAMUS 1228) and by DNA sequencing gel electrophoresis. The informative BACs, having an average insert size of 140 kb and covering 6.8x haploid rice genomes, were used for assembling the physical map of the rice genome with the FPC3.2 software package (Soderlund et al. CABIOS 13:523, 1997). At the present time, the physical map consists of 298 contigs, ranging from several hundred kilobases to > 20 Mb (1.5 to > 80 cM) with an average contig length of > 1.4 Mb (5.7 cM) and covers > 97% of the rice genome. Analysis of the physical map contigs with different methods has indicated that the physical map is highly reliable and therefore, will provide a powerful framework for genomics research of gramineous crops.