Genomic in situ hybridization was used to detect introgressed segment from Oryza australinesis onto the chromosomes of introgression line derived from the hybrid O. sativa x O. australinesis. Genomic DNA from Oryza australinesis was labeled with biotin and hybridized to the homologous sequences on the O. sativa chromosomes. The probe hybridization fluoresced green and non labeled O. sativa chromosomes appeared red or blue due to counterstaining with propidium iodide (PI) or 4,6-diamidino-2-phenylindole (DAPI). This differential painting of chromosomes unequivocally detected the introgressed
segment. Among the 200 cells analyzed, 6.5% of the cells showed hybridization signal. Signal appeared on one chromosome in 5%, on two homologous chromosomes in 1% and on sister chromatids in 0.5%
of the cells. Hybridization was seen on the short arm of the chromosome 12 of the introgression line.