INTEGRATIVE PHYSICAL MAPPING OF GENOMES WITH LARGE-INSERT BACTERIAL CLONES: THE 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

Development of genome physical maps is essential to efficient genomics research. Physical mapping of a genome is typically achieved by reconstruction of the genome from DNA fragments permanently maintained in an ordered DNA library. Integration of a physical map with genetic and/or cytogenetic maps allows the physical map to serve as a genomic "freeway" for 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 physical maps of genomes with large-insert bacterial clones, we previously developed a complete set of technologies for physical mapping of genomes, by which a physical map for an organism with a genome size of 1000 Mb can be developed within 1 - 2 years in a single laboratory - at a cost similar to that for a moderate density RFLP map. We have also experimentally demonstrated the feasibility of physical mapping of genomes with large-insert bacterial clones. Rice is a desirable model species for genomics research of gramineous crops and a leading crop worldwide, in which indica rice accounts for 90% of world rice production. Using the technologies that we developed, we have developed a large-scale sequence-ready physical map of the rice genome, covering > 97% of the rice genome, from the three complementary indica BAC libraries by fingerprint analysis. 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). Analysis of the physical map contigs indicates that the physical map is highly reliable, and thus will greatly facilitate structural, functional and evolutionary research of gramineous genomes.