Structures and distribution of p-SINE1 members in rice genomes

Abstract

 We determined copy numbers of p-SINE1, a short interspersed element (SINE) in rice, and found that p-SINE1 was distributed in the Oryza sativa genome with an average spacing of about 1 member per 70 kb. We identified 31 p-SINE1 members located at different loci by cloning and characterized them by sequencing. Comparison with a consensus sequence derived from their sequences revealed that all of the p-SINE1 members contained base substitution mutations at various positions. In addition to the substitutions, some members contained deletions, insertions and tandem duplications of a few bases or of a large DNA segment. These mutations seem to have occurred to inhibit transcription from each p-SINE1 member by RNA polymerase III. PCR using a pair of primers that hybridize with the sequences flanking each p-SINE1 member revealed that many of the p-SINE1 members were present at corresponding loci in strains belonging to all rice species carrying the AA genome. Several of them were, however, present at corresponding loci in strains belonging to a limited number of species or in a limited number of the strains belonging to a rice species. These p-SINE1 members are supposed to be useful in the identification and classification of various rice strains with the AA genome. Simple tandem repeats of a trinucleotide (CAT) or dinucleotide (AG) sequence existed in the flanking regions of 2 p-SINE1 members. Such repeats, called microsatellite DNA, varied in number even in the cultivated rice strains examined, suggesting that microsatellite DNA is useful for the identification and classification of cultivars.