Recent amplification of Osr4 LTR-retrotransposon caused rice D1 gene mutation and dwarf phenotype

A novel rice d1 mutant was identified using map-based cloning and comparative analysis of known d1 mutants. The mutant (d1-a) shows a mild dwarf trait, which differs only slightly from the wildtype in plant height at the tillering stage. The d1-a mutant is different from other d1 mutants. We found that it was interrupted by an Osr4 long terminal repeat (LTR)-retrotransposon, which resulted in the loss of exon 7 in the mutant D1 mRNA. A paralog of the D1 gene, D1-like, was revealed. D1-like is a truncated gene that might have resulted from recombination between retrotransposons. We identified 65 Osr4 LTR-retrotransposons in Nipponbare, and found more LTR variants in contrast to coding DNA sequence (CDS) in the retrotransposons. We also identified five possible regulatory motifs in LTRs which may control the expression of the retrotransposons. In addition, we predicted six putative functional Osr4 retrotransposons that contain complete CDSs and all important elements. Osr4 retrotransposons were classified into 4 groups, and this type of retrotransposon only appears to be present in monocots. Members of group I-1, which included all putative functional retrotransposons, showed a high similarity with each other. The retrotransposons were expressed in all tissues, at especially higher levels in some leaves and seeds. These findings imply that transpositions of group I-1 members might have occurred frequently and recently.