Transpositional reactivation of two LTR retrotransposons in rice‐Zizania recombinant inbred lines (RILs)

摘要

Transposable elements (TEs) which include transposons (class II TEs) and retrotransposons (class I TEs) are ubiquitous genomic components of all studied eukaryotes, and are particularly abundant in plants. Retrotransposons transpose via an RNA intermediate by a “copy-and-paste” mechanism (Bennetzen 2000). As a result, they are a major cause for genome size difference between related plant species. For example, about 17–22% of the rice genome is occupied by retrotransposons, and the proportions are even greater in plants with large genomes like Zea mays (> 80%) and common wheat (≈ 90%) (McCarthy et al. 2002; Gao et al. 2004; Kashkush et al. 2007). Retrotransposons can be classified into two major categories, i.e. LTR (long terminal repeat) and non-LTR retrotransposons (Bennetzen 2000). LTR retrotransposons can be further divided into two major groups, Ty1-copia-like and Ty3-gypsy-like, based on the order of the internal domains (Bennetzen 2000).Mounting evidence has indicated that TEs have contributed significantly to the evolution of genome structure and function. TEs can be transpositionally activated and produce insertional mutagenesis and enhance ectopic genomic recombination under various biotic and abiotic stresses, such as tissue culture, pathogen attack, wounding and cold stress (Wessler et al. 1995; Grandbastien 1998; Lisch 2007; Shapiro 2010). McClintock envisioned in the 1980s that species crossing represents a genetic stress which may cause reactivation of quiescent TEs in parental species and cause genomic restructuring (McClintock 1984). Indeed, accumulating though circumstantial evidence indicated that at least in certain species crossings, previously cryptic parental TEs can be transcriptionally and/or transpositionally reactivated (O'Neill et al. 1998; Labrador et al. 1999; Liu and Wendel 2000; Shan et al. 2005; Ungerer et al. 2006). In addition, the phenomenon of hybrid dysgenesis that occurs between certain intraspecific crossings in Drosophila represents a classical example of hybridization-induced TE activity (Kidwell 1985).Introgressive hybridization occurs widely between related natural plant populations, and is believed as playing important roles in genome evolution of many plant groups (Stebbins 1959; Arnold 1992; Wendel 2000; Rieseberg et al. 2003). In plant breeding, introgression of alien chromatin segments from wild species into crops is widely used and represents one of the most effective methods for creating new germplasm. Although the major and immediate effect of introgression is direct transfer of useful alleles from the donor species into the recipient one, several studies suggested that introgression may also impact the recipient genome by novel means. For example, it was found that introgression of uncharacterized foreign DNA segments into cultured animal cells may cause genome-wide perturbation of DNA methylation patterns and changes in gene expression (Remus et al. 1999). Another similar example showed that introgression of minute chromatin segments of Zizania latifolia into rice has caused extensive and wide-ranging genetic and epigenetic changes in the resultant recombinant inbred lines, or RILs (Liu et al. 1999; Wang et al. 2005), as well as transpositional activation of at least three TEs, a copia-like retrotranspon Tos17, a MITE mPing and a class II TE belonging to the hAT superfamily, called DartDart, in the resulting RILs (Liu and Wendel 2000; Shan et al. 2005; Wang et al. 2010).During characterization of several rice–Zizania RILs by the amplified fragment length polymorphism (AFLP) marker, two variant bands were found to be homologous to two transposition-competent LTR-retrotransposons based on sequence analysis against the whole genome of Nipponbare (). We report here that both elements were actually transpositionally activated in the studied RILs, although the new retrotransposon insertions did not associate with expression changes of the adjacent genes.