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. |
|
Contact:
VIB / UGent Bioinformatics & Evolutionary Genomics Technologiepark 927 B-9052 Gent BELGIUM +32 (0) 9 33 13807 (phone) +32 (0) 9 33 13809 (fax) |
You are visiting an outdated page of the BEG/Van de Peer Lab site.
Not all pages have been ported, so these archived pages are still available.
Redirect to the new website?