- Short interspersed nuclear elements (SINEs) are non-autonomous non-LTR retroelements, present in most eukaryotic species. While SINEs are intensively investigated in humans and other animal systems, they are poorly studied in plants, especially in wheat. We used quantitative PCR of various wheat species to determine the copy number of a wheat SINE family, termed Au SINE, combined with computer-assisted analyses of the publicly available 454-pyrosequencing database of T. aestivum. In addition, we utilized site specific PCR on 57 Au SINE insertions, transposon methylation display and transposon display on newly formed wheat polyploids to assess retrotranspositional activity, epigenetic status and genetic rearrangements in Au SINE, respectively. We have retrieved 3706 different insertions of Au SINE from the 454-pyrosequencing database of T. aestivum and found that most of the elements have inserted in A/T rich regions, while ~38% of the insertions were associated with transcribed regions, including known wheat genes. We observedtypical retrotransposition of Au SINE in the second generation of a newly formed wheat allohexaploid and massive hypermethylation in CCGG sites surrounding Au SINE in the third generation. Finally, we have observed huge differences in the copy numbers in diploid Triticum and Aegilops species and a significant increase of the copy numbers in natural wheat polyploids, while in two out of three newly formed allopolyploid combinations used in this study, no significant increase in the copy number of Au SINE in the first four generations. Our data indicate that SINEs may play a prominent role in the genomic evolution of wheat through stress-induced activation. This article is protected by copyright. All rights reserved.