Molecular characterization of GATA/GACA microsatellite repeats in tomato

Microsatellite repeats like GATA or GACA display a degree of variability that allows their use in cultivar identification. Southern hybridization with oligonucleotide probes complementary to these microsatellites were used for the detection of polymorphisms. To understand the molecular structure of the detected DNA, fragments hybridizing to GATA and GACA probes were cloned and sequenced. In the four clones analyzed, repeats of GATA and GACA were found intertwined. The GATA and GACA arrays were not perfect but were heavily degenerated, in that they contained many tetranucleotides that might have been derived by a single point mutation from GATA or GACA. Some of these derived sequences, like GGTA and GGAT, were present as relatively long stretches that also contained some point mutations. This supports the hypothesis that long stretches of repeats are stabilized by the accumulation of point mutations. Analysis of the flanking sequences of the fragments obtained with the GACA probe showed that one of them was homologous to a Lilium henryi retrotransposon and the other to a sequence upstream of a potato patatin gene. The two fragments obtained using the GATA probe were flanked by DNA that had no homology to any known sequence but they were highly homologous to each other. This DNA was frequently associated with GATA elements and was present in the tomato genome in approximately 4300 copies. The function of this new class of repetitive DNA, here termed U30, is presently unknown.