2 NEW GENOMES IN THE ORYZA COMPLEX IDENTIFIED ON THE BASIS OF MOLECULAR DIVERGENCE ANALYSIS USING TOTAL GENOMIC DNA HYBRIDIZATION

The genus Oryza to which cultivated rice belongs has 24 species (2n = 24 or 48), representing seven genomes (AA, BE, CC, EE, FF, BBCC and CC DD). The genomic constitution of five of these species is unknown. The se five species have been grouped into two species complexes, the tetr aploid ridleyi complex (O. ridleyi, O. longiglumis) and the diploid me yeriana complex (O. granulata, O. meyeriana, O. indandamanica). To eva luate the genomic structure of these species in terms of divergence at the molecular level vis-a-vis other known genomes of Oryza, we used t he total genomic DNA hybridization approach. Total genomic DNA (after restriction digestion) of 79 accessions of 23 Oryza species, 6 related genera, 5 outgroup taxa (2 monocots, 3 dicots) and 6 F(1)s and BC(1)s derived from crosses of O. sativa with wild species were hybridized i ndividually with P-32-labeled total genomic DNA from 12 Oryza species: O. ridleyi, O. longiglumis, O. granulata, O. meyeriana, O. brachyanth a, O. punctata, O. officinalis, O. eichingeri, O. alta, O. latifolia, O. australiensis, and O. sativa. The labeled genomic DNAs representing the ridleyi and meyeriana complexes cross-hybridized best to all the accessions of their respective species, less to those representing oth er genomes of Oryza and related genera, and least to outgroup taxa. In general, the hybridization differential measured in terms of signal i ntensities was >50-fold under conditions that permit detection of 70-7 5% homologous sequences, both in the presence and in the absence of O. sativa DNA as competitor. In contrast, when total DNAs representing o ther Oryza genomes were used as probes, species of the O. ridleyi and O. meyeriana complexes did not show any significant cross-hybridizatio n (<5%). These results demonstrate that the genome(s) of both of these complexes are highly diverged and distinct from all other known genom es of Oryza. We, therefore, propose new genomic designations for these two species complexes: cc for the diploid O. meyeriana complex and HH JJ for the allotetraploid O. ridleyi complex. The results also suggest that the uniqueness of these genomes is not restricted to species-spe cific highly repetitive DNA sequences, but also applies to dispersed s equences present in single or low to moderate copy numbers. Furthermor e these appear to share relatively more genome-specific repeat sequenc es between themselves than with other genomes of rice. The study also demonstrates the potential of total genomic DNA hybridization as a sim ple but powerful tool, complementary to existing approaches, for ascer taining the genomic makeup of an organism.