Plant, Animal & Microbe Genomes X Conference

January 12-16, 2002
Town & Country Convention Center
San Diego, CA

Poster: Genome Sequencing & ESTs
           

CURRENT STATUS OF SEQUENCE-READY PHYSICAL MAP CONSTRUCTION FOR RICE CHROMOSOMES 1, 2, 6, 7 AND 8

Rice Genome Research Program, National Institute of Agrobiological Sciences / Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries, Tsukuba, Ibaraki 305, Japan

RGP is now constructing sequence-ready physical maps of rice chromosomes 1, 2, 6, 7 and 8 as part of an international collaboration to sequence the rice genome. BAC clones with 5 x sequences provided by the Monsanto company were used after BLASTing the BAC sequences against about 8,000 RGP genetic and EST marker sequences to determine the position of the clones on these five chromosomes. The resulting physical maps showed a coverage of 35~50% varying in five chromosomes. In regions where no Monsanto BAC clones were confirmed, we used our STS / EST markers to screen the RGP PAC library by PCR and then fingerprinted the picked PAC clones. As a result, the coverage increased to 70~80% for each chromosome. At present, we are trying to fill the gaps by STC strategy using the CUGI (Clemson Univ. Genomics Institute) BAC clones. BLASTing our finished BAC/PAC sequences against the STC database of CUGI could also find out bridging clones thereby closing the gaps between contigs or elongating the contigs. The finally remaining gap regions correspond mainly to regions close to centromere and we are now making efforts to cover these regions by end-walking method. These combinatorial strategies should enable us to construct a minimum number of contigs covering the entire region of each chromosome to complete the rice genome sequence. This work is supported by the MAFF Rice Genome Project grant GS-1101.