Copia-like retrotransposons in rice: sequence heterogeneity, species distribution and chromosomal locations

Degenerated oligonucleotide primers were used to amplify, clone, and analyze sequence heterogeneity and chromosomal distribution of 23 PCR fragments corresponding to the reverse transcriptase domain of copia-like retrotransposons in rice. Of the 23 fragments 22 could be aligned by their deduced amino acid sequences and were divided into 6 groups according to the phylogenetic and Southern blot analyses. Amino acid sequence differences among the 22 aligned fragments ranged from 1 to 64%. Southern blot analysis of 10 rice accessions including indica, japonica and common wild rice, using these 23 fragments as probes, showed that copia-like retrotransposons were present in moderate to high copy numbers in all the rice genome although the exact copy number cannot be determined. The major difference revealed by southern analysis is a differentiation between the four indica varieties as one group and the four japonica varieties and the two wild rice accessions as another group. Polymorphisms were also detected among the indica and japonica varieties by major bands and repeatable minor bands. Five hybridization bands were mapped to chromosomes 3, 4, 8, and 9, respectively. All the five bands were inherited in a dominant Mendelian fashion and were not allelic with each other, indicating that the same element did not reside on the same location in different rice accessions. No transcript of the copia-like reverse transcriptase was detected on northern blot. The results suggest that the sequence heterogeneity and distributional variability of retrotransposons may be one of contributory factors causing genetic diversity in rice.