The use of FISH in chromosomal localization of transgenes in rice

Chromosomal location and local chromatin structure are thought to play important roles in the stability of transgene expression. Fluorescence in situ hybridization (FISH) is a cytogenetic technique that allows the localization of specific DNA sequences on chromosomes. It provides an excellent means to analyze the chromosomal environment of integrated transgenes, helping to assess the effect of position on gene expression. FISH analyses have been conducted on nuclear chromosomal DNA at metaphase, interphase, meiotic prophase (pachytene) and on extended chromatin fibers (DNA fiber-FISH) and naked DNA molecules. Despite the small size of rice chromosomes, FISH has been successfully accomplished to detect unique and repetitive DNA sequences. A detailed FISH procedure for the detection of small and single copy transgenes within the rice genome is described and the application of FISH to evaluate chromosomal location and the local chromatin structure of transgenes as parameters that could affect their expression is discussed.