The distribution and copy number of copia-like retrotransposons in rice (Oryza sativa L.) and their implications in the organization and evolution ofthe rice genome

We used 22 fragments corresponding to the reverse transcriptase domain of c opia-like retrotransposons as representatives to study the organization and distribution of these elements in the rice genome. The loci detected by th ese 22 fragments were assigned to 47 locations in the molecular-linkage map involving all 12 chromosomes. The distributional features of copia-like re trotransposons found in the rice genome indicated that (i) the loci detecte d were located mainly in one arm of each chromosome; (ii) one fragment usua lly detected several loci that were mapped to similar locations of differen t chromosomes; (iii) retrotransposons sharing high identity in nucleotide s equences were usually assigned to similar locations of the chromosomes; and (iv) concurrences of multiple loci, detected by different fragments, in si milar locations or stretches of different chromosomes were common in the ri ce genome. We also determined that the copy number of copia-like retrotrans posons in rice genome may be as low as approximate to 100 per haploid genom e. The restricted distribution, along with low copy number, suggested that copia-like retrotransposons in rice were relatively inactive during evoluti on compared with those in other plants. The distributional features of the copia-like retrotransposons suggested the existence of possible lineages am ong the rice chromosomes, which in turn suggested that chromosome duplicati on and diversification may be a mechanism for the origin and evolution of t he rice chromosomes. The information provided by fine mapping of the retroe lements in the genetic linkage map may also be useful for gene tagging and molecular cloning.