VISUALIZATION OF THE DNA STRETCHES IN A RICE GENOME BY EXTENDED DNA FIBER-FISH.

¹ Graduate School of Science and Technology, Niigata University, Nigata 950-2181, Japan

² Hokuriku National Agricultural Experiment Station, Joetsu 943-0193, Japan

³ National. Food Research Institute, Tsukuba 305-8642, Japan

⁴ Faculty of Engineering, Graduate School of Osaka University, Suita 565-0871, Japan

To develop a high resolution, fluorescence in situ hybridization method which enables analysis of positional relationship between genes, we performed FISH on the extended DNA fibers isolated from the nuclei of the rice young leaves and quantitative analyses of the length of fluorescent signal tracks using an image analysis method (CHIAS III). The materials that we used were Oryza sativa L. ssp. indica cv. IR8 and ssp. japonica cv. Nipponbare and 5S ribosomal RNA gene (5S rDNA) and telomere sequences as the probes in fiber-FISH. It was revealed that the copy number of 5S rDNA and telomere sequences in IR8 are 1.3 and 3 times longer than Nipponbare, respectively. Our results corresponds to the fact that the total DNA contents of IR8 is larger than Nipponbare. It is suggested that the genome size depends on the number and size of the repetitive sequence. Fiber-FISH method enables to quantitatively analyze the copy number of repetitive sequences among even the rice subspecies. Therefore it is included that the important information on the quantitative volume of the repetitive sequences could give the clue to understand the rice diversity. We also performed to develop contig map using the multicolor-FISH on the DNA fibers. This method would provide us a powerful tool to solve the various problems in genome research such as the gap between contigs on a chromosome map.