In situ hybridization of the TR-1 and 180-bp repeats to pachytene chromosomes of maize (Seneca 60). (A) The overall view of pachytene chromosomes stained with 4′,6-diamino-2-phenylindole (DAPI), the 180-bp repeat (green), and the TR-1 repeat (red) fluorescent images. The 180-bp repeats reveal strong hybridization signal to large knobs on chromosomes 5, 6, and 9, and the TR-1 elements reveal strong hybridization to the large knob on chromosome 4. Several additional small clusters of 180-bp repeats and TR-1 elements may be found in different sites on the chromosomes. (B) Distribution of hybridization signals over chromosomes 4 and 5. Overall view of 4′,6-diamino-2-phenylindole-stained chromosomes 4 and 5 (DAPI), the 180-bp repeat (green), and the TR-1 element (red) fluorescent images. The 180-bp repeat is detected in the large knob of chromosome 5 but not in the large knob of chromosome 4. However, there is a small cluster of 180-bp repeats at the terminus of chromosome 4. The TR-1 repeat is detected in both large knobs and in the small cluster at the terminus of chromosome 4. (C) Distribution of hybridization signals over chromosome 6. The overall view of 4′,6-diamino-2-phenylindole-stained chromosome 6 (DAPI), the 180-bp repeat (green), and the TR-1 element (red) fluorescent images. The 180-bp repeat and TR-1 element form two clusters: a big one in the knob at the terminus of the short arm and a small one probably in the first chromomere of the satellite of chromosome 6.