Genome organization and non-colinear distribution of the knob-associated sequences in maize

The maize (Zea mays L.) genome contains abundant of repetitive elements. In this study, fluorescence in situ hybridization (FISH) was used to reveal the distribution of the knob-associated 180-bp repeats and TR-1 elements among eleven maize inbred lines. Non-colinear distribution of the knob-associated sequences was detected, and a distinct FISH pattern for each maize inbred line was constructed. This result confirmed that FISH using the knob-associated sequences as probes may be a rapid method to identify maize germplasm resources. The 180-bp repeats were more numerous and widely distributed than the TR-1 elements in the maize genome, which provided cytogenetical evidence for the hypothesis that the TR-1 elements were derived from the 180-bp repeats. The knob-associated sequences were concentrated in the satellite of chromosome 6. The signals of the TR-1 elements were readily detected in the satellites of all the maize inbred lines, and the signals of 180-bp repeats were detected in the satellites of six maize inbred lines. This finding indicated that the TR-1 elements tend to accumulate in regions of exceedingly low recombination.