A LARGE-SCALE PLANT TRANSFORMATION- AND GENOME SEQUENCE-READY PHYSICAL MAP OF THE ARABIDOPOSIS THALIANA GENOME

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

Arabidopsis thaliana is a model species for plant genetic and biological studies because it has a small genome (145 Mb/1C). Although the Arabidopsis genome will be completely sequenced within a few years, a great effort hereafter will be needed to determine the biological functions of the DNA sequences. The purposes of this study are to establish a bridge between the DNA sequences and functional genomics, and develop a readily used system for large-scale studies of Arabidopsis genes: biological functions, gene organization, expression and gene-gene interaction. In previous studies we demonstrated the feasibility of physically mapping genomes with large-insert bacterial clones and developed a complete set of technologies for rapid development of integrated physical maps of genomes from these clones by fingerprint analysis. Using these technologies, we have developed a large-scale ready physical map of the rice genome. To develop a physical map of the Arabidopsis genome that will be integrated with the genome sequencing project and ready for large-scale functional genomics studies, we have developed two binary libraries of the Ecotype Columbia with Bam HI and Eco RI, respectively, the average insert size of the Bam HI library being 125 kb and that of the Eco RI library being 120 kb. These two binary libraries along with the TAMU BAC library (in Hind III site) utilized in the genome sequencing project were used in the development of the physical map. A total of 9,216 (24 384-well microtiter dishes, 7.8x genome coverages) large-insert clones have been fingerprinted, 2,304 from the TAMU BAC library, 4,608 from the Bam HI binary library, and 2,304 from the Eco RI binary library. At the present time we are assembling the physical map from these large-insert bacterial clone fingerprints. Since we have already successfully developed a large-scale sequence-ready physical map of the rice genome (430 Mb/1C) covering > 97% of the rice genome using this approach, it is expected that a desirable physical map of the Arabidopsis genome will be developed.