MOLECULAR CHARACTERIZATION OF GATA GACA MICROSATELLITE REPEATS IN TOMATO/

Microsatellite repeats like GATA or GACA display a degree of variabili ty that allows their use in cultivar identification. Southern hybridiz ation with oligonucleotide probes complementary to these microsatellit es were used for the detection of polymorphisms. To understand the mol ecular structure of the detected DNA, fragments hybridizing to GATA an d GACA probes were cloned and sequenced. In the four clones analyzed, repeats of GATA and GACA were found intertwined. The GATA and GACA arr ays were not perfect but were heavily degenerated, in that they contai ned many tetranucleotides that might have been derived by a single poi nt mutation from GATA or GACA. Some of these derived sequences, like G GTA and GGAT, were present as relatively long stretches that also cont ained some point mutations. This supports the hypothesis that long str etches of repeats are stabilized by the accumulation of point mutation s. Analysis of the flanking sequences of the fragments obtained with t he GACA probe showed that one of them was homologous to a Lilium henry i retrotransposon and the other to a sequence upstream of a potato pat atin gene. The two fragments obtained using the GATA probe were flanke d by DNA that had no homology to any known sequence but they were high ly homologous to each other. This DNA was frequently associated with G ATA elements and was present in the tomato genome in approximately 430 0 copies. The function of this new class of repetitive DNA, here terme d U30, is presently unknown.