Gene regulation and evolution mediated by retrotransposons associated with rice genes

Retrotransposons constitute a major class of transposons in higher plant genomes, which can transpose via a RNA intermediate. In an effort to study how retrotransposons associated with genes evolve, presence/absence polymorphisms of retrotransposons in six rice genes and five promoters of rice genes across 95 cultivated and wild rice genotypes were analyzed. Different insertion times and conservation patterns were observed. Chapter 2 describes their insertion patterns in genes which were dated as recent as the ancestral divergence of temperate japonica from the other groups of O. sativa and as old as the ancestral divergence of wild rice O. granulata (GG) from O. ridleyi (HHJJ). Retrotransposons displayed different evolutionary rates depending on their location. Nucleotide substitution rates of retrotransposons inserted in introns were found to be higher than non-retrotransposon sequences. When retrotransposon sequence was across intron and exon regions, intron part of retrotansposons evolved faster than exon part. Chapter 3 describes presence/absence polymorphisms of the selected retrotransposons inserted in promoter regions in 95 cultivated and wild rice genotypes. Insertion times varied from AA genome ancestor to O. officinalis ancestor. Sequence of retrotransposons in most promoters evolved at a slower rate compared to other sequences in the promoter region. Chapter 4 describes the effect of retrotransposon insertions in four rice promoter regions on downstream gene regulation using promoter-reporter gene constructs with and without retrotransposons. Transcription level differences of gus gene were detected by real-time RT-PCR and differences in protein levels were detected by histochemical GUS staining assays in transgenic Arabidopsis and transient expression studies in rice. The different extent of conservation of these four insertions correlates with the function of downstream genes. The molecular mechanism of how these retrotransposons affect downstream gene regulation needs to be elucidated.