The expression of 1,613 transposable elements (TEs) represented in the Affymetrix Wheat Genome Chip was examined during cold treatment in crowns of four hexaploid wheat genotypes that vary in tolerance to cold and in flowering time. The TE expression profiles showed a constant level of expression throughout the experiment in three of the genotypes. In winter Norstar, the most cold-hardy of the four genotypes, a subset of the TEs showed a burst of expression after vernalization saturation was achieved. About 47% of the TEs were expressed, and both Class I (retrotransposons) and Class II (DNA transposons) types were well represented. Gypsy and Copia were the most represented among the retrotransposons while CACTA and Mariner were the most represented DNA transposons. The data suggests that the Vrn-A1 region plays a role in the stage-specific induction of TE expression in this genotype. 1. Introduction Transposable elements (TEs) are DNA sequences that can move or transpose to new locations within the genome. Transposable elements are generally classified based on their mechanism of transposition. Class I TE, or retrotransposons, move by a “copy and paste” mechanism whereby the TE is transcribed into an RNA intermediate that is converted to DNA by RNA-dependent DNA polymerases before it reinserts itself in the genome. Class II TE, or DNA transposons, utilize the “cut and paste” mechanism wherein the TE element DNA itself is excised from the genome and reinserted in a new position. TE transposition has been shown to generate mutations that can alter gene expression, and to create gene deletions and duplications, chromosome breaks, and genome rearrangements [1]. Thus, TEs can be a powerful force for species adaptation to adverse biotic and abiotic challenges and a facilitator of speciation by creating potentially advantageous genetic variations upon which natural selection can act [2, 3]. Transposable elements are ubiquitous and can be found in both prokaryotic and eukaryotic genomes. In plants (especially cereals), TEs make up a large portion of the genome. In wheat, repetitive and transposable elements comprise more than 80% of the genomic sequence [4]. To prevent the potentially harmful effects of TE transposition, the host plant has evolved several mechanisms to repress TE expression [5, 6]. TE can be silenced before or after transcription. Transcriptional silencing of TE includes DNA methylation and chromatin remodeling, which renders the elements unavailable for transcription. On the other hand, posttranscription silencing involves small noncoding RNA
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