Development of a quantitative pachytene chromosome map in Oryza sativa by imaging methods

A higher GC content region of an Oryza sativa chromosome can be specifically visualized by double staining with propidium iodide (PI) and 4, 6-diamidino-2-phenylindole (DAPI). This procedure allows identification of chromosome 9 from the other rice chromosomes at the pachytene stage. Using rice chromosome 9 as a model, an imaging method to construct a pachytene chromosomal map was developed by quantifying the fluorescence profile (FP) of each chromomere. The pachytene map of chromosome 9 consists of twenty-two chromomeres including four chromomeres within the nucleolar organizing region (NOR) and satellite region. The pachytene map was compared with the corresponding somatic prometaphase map and the linkage map. The differences among the three maps indicate that each map depicts specific biological information, which is difficult to be substituted by the other maps.