Plant Molecular Biology 33: 1051–1058, 1997.
1997 Kluwer Academic Publishers. Printed in Belgium.
Copia-like retrotransposons in rice: sequence heterogeneity, species
distribution and chromosomal locations
, Qifa Zhang
, P.J. Maughan
and M.A. Saghai Maroof
National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070,
author for correspondence);
Department of Crop and Soil Environmental Sciences, Virginia Polytechnic
Institute and State University, Blacksburg, VA 24061, USA
Received 30 July 1996; accepted in revised form 17 January 1997
Key words: genetic diversity, indica, japonica, mapping, reverse transcriptase
Degeneratedoligonucleotideprimers were used to amplify, clone, and analyze sequence heterogeneity and chromo-
somal distribution of 23 PCR fragments corresponding to the reverse transcriptase domain of copia-like retrotrans-
posons in rice. Of the 23 fragments 22 could be aligned by their deduced amino acid sequences and were divided
into 6 groups accordingto the phylogenetic and Southernblot analyses. Amino acid sequence differencesamong 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.
Retrotransposons are widely distributed in plants.
Retrotransposons can be divided into three major
classes according to the structural organization and
the amino acid sequences of the encoded reverse tran-
scriptase [4, 26]. Two of the three classes, the copia-
like and gypsy-like retrotransposons, are characterized
by the ﬂanking long terminal direct repeats (LTRs).
And the third class, LINE (long interspersed nuclear
elements)-like retrotransposons, does not have LTRs.
Recent studies have shown that copia-like retrotrans-
posons are ubiquitous among plants [5, 24], and these
The nucleotidesequencedata reported will appear in the EMBL,
GenBank and DDBJ Nucleotide Sequence Databases under the
accession numbers Z75496 (Rrt1) to Z75518 (Rrt23).
elements exhibit extensive DNA sequence diversity
both within and among plant species [6, 14, 19, 24]. It
has been estimated that the divergence of the deduced
amino acid sequences of copia-like retrotransposons
ranges from 8 to 71% among different plant species
[12, 24] and from 5 to 74% among copies within the
potato genome .
In rice, Hirochika et al.  studied the struc-
ture of retrotransposons and estimated that there are
about 1000 copies of the retrotransposons in the rice
genome. They also cloned ten PCR fragments ampli-
ﬁed using primer sequences deduced from copia-like
retrotransposon, and classiﬁed them into two famil-
ies according to their amino acid sequence similar-
ity. However, information is still lacking regarding the
extent of the sequence heterogeneity among different
GR: 201001889, Pips nr. 133225 BIO2KAP
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