Figure 4.

Fiber-FISH Analysis of Rice Centromeric DNA.

(A) BAC clone RC8-1 (red) is located ∼50 kb away from the CentO locus in rice chromosome 8 (CentO-8). Fiber-FISH signals derived from CentO-8 (green) can be identified unambiguously and measured using RC8-1 as a reference marker. The top signal is from var Nipponbare rice; the bottom signal is from var Zhongxian 3037 rice. Note that the red signals within the CentO-8 loci were derived from the CRR sequences contained in BAC RC8-1. Bar = 10 μm.

(B) Representative fiber-FISH signals demonstrate highly variable densities and nesting of the CRR elements (red signals) within CentO arrays (green signals). An ∼400-kb CentO signal (fiber i) contains no CRR insertion. Fiber ii (∼200 kb) shows five insertions (arrowheads). Long CRR signals (>20 kb) inserted into CentO satellite DNA are detected within fibers iii and iv. A CRR signal independent of CentO satellite DNA (fiber v) contains ∼100-kb CRR-related sequences. The long CRR signals most likely are derived from nested CRR elements. Bar = 10 μm.

(C) A fiber-FISH signal consists of interspersed signals from CRR and CentO. The top fiber signal (green) is from CentO; the middle fiber signal (red) is from CRR; and the bottom fiber signal is a merged image. Bar = 10 μm.