GENOME STRUCTURE AND FUNCTION DISTRIBUTION OF SHORT INVERTED REPEATS FLANKING DNA FRAGMENTS IN CEREAL CHLOROPLAST GENOMES AND THEIR

Cultivated in temporary area grasses have evolved from common ancestor about 1.5 million years ago and maintain many similarities especially in cytoplasm genome. Chloroplast genome of those grasses consist of some 135,000 bp and approximately 100 functional genes. Genetic similarity of chloroplast genomes was evaluated by DNA hybridization with conservative probes and by sequencing of hot spots in intergeneric regions. Those methods are less useful for intraspecies studies, and PCR-fingerprinting was offered for this particular case. Information content of PCR markers may be increased by application of primers complementary to (a) DNA repeats abundant in genome or (b) DNA fragments participating in modification events. Distribution of small (7-10bp) inverted DNA repeats located in 100-4000bp from each other and thus capable to serve as PCR primers was studied in complete cereal genomes. The repeats flanking from 10 to 30 PCR-able fragments of the chloroplast DNA were chosen as AP-PCR primers and real PCR fingerprints obtained for wheat and 15 alloplasmic barley lines were compared to expected ones. Comparing to PCR analysis with random primers (RAPD), the selected primers produced bands of significantly (3-4 folds) higher PIC (Polymorphism Information Content), and GD (Genetic Diversity). Thus, PCR-fingerprinting with primers homologous for selected from sequence inverted repeats proved to be useful for genome variability studies