We used 22 fragments corresponding to the reverse transcriptase domain of copia-like retrotransposons as representatives to study the organization and distribution of these elements in the rice genome. The loci detected by these 22 fragments were assigned to 47 locations in the molecular-linkage map involving all 12 chromosomes. The distributional features of copia-like retrotransposons found in the rice genome indicated that (i) the loci detected were located mainly in one arm of each chromosome; (ii) one fragment usually detected several loci that were mapped to similar locations of different chromosomes; (iii) retrotransposons sharing high identity in nucleotide sequences were usually assigned to similar locations of the chromosomes; and (iv) concurrences of multiple loci, detected by different fragments, in similar locations or stretches of different chromosomes were common in the rice genome. We also determined that the copy number of copia-like retrotransposons in rice genome may be as low as ≈100 per haploid genome. The restricted distribution, along with low copy number, suggested that copia-like retrotransposons in rice were relatively inactive during evolution compared with those in other plants. The distributional features of the copia-like retrotransposons suggested the existence of possible lineages among the rice chromosomes, which in turn suggested that chromosome duplication and diversification may be a mechanism for the origin and evolution of the rice chromosomes. The information provided by fine mapping of the retroelements in the genetic linkage map may also be useful for gene tagging and molecular cloning
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