A repetitive sequence specific to Oryza species with BB genome and abundant in Oryza punctata Kotschy ex Steud

Molecular markers are capable of discriminating specific constituents of genome and monitoring genomic introgression of interspecific hybrids. In this study, we isolate and characterize a BB genome specific RAPD, Opun210, from Oryza punctata Kotschy ex Steud (W1593), an African native wild rice. We demonstrate the Opun210 as a highly species-specific marker. The Opun210 sequence is 789 base pairs in length and estimated at 5.3 × 104 copies in O. puntata (W1593) haploid genome, which contains the most repeats of Opun210 among Oryza species. The results of DNA sequence alignments among Opun210 and a few hits in the GenBank found that a relatively high similarity was in position ~500 nucleotides regions at the 5' ends, but a low similarity was in the rest of the nucleotides at the 3' ends. SCAR-PCR profiles indicates that this fragment was specific to BB genome. Furthermore, the Opun210 sequence at position 430~480 nucleotides putatively encodes a peptide with 88% identity to a Ty3-gypsy retrotransposon protein or a peptide with 94% identity to a hypothetical protein. The results of Southern hybridization and fluorescent in situ hybridization (FISH) indicated that the repetitive Opun210 sequences dispersed throughout the entire genome of O. punctata. The origin and divergence of the Opun210 sequence in genus Oryza is discussed based on the investigations in this study.

Cheng, Y.-Y., Fang, S.-A., Lin, Y.-C., Chung, C. (2007) A repetitive sequence specific to Oryza species with BB genome and abundant in Oryza punctata Kotschy ex Steud. Bot. Stud. 48:263-72.









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