Evaluation of retrotranposons as molecular markers in wheat

Rerotransposons are the most abundant and widespread mobile genetic elements of eukaryotic genomes. Use of retrotransposons as molecular markers will be ideal regarding to their dispersion, ubiquity and prevalence in plant genomes. In order to developing retrotranpososns as molecular markers in wheat, 30 different retrotransposon families, previously detected in wheat and other plants evolutionary close to wheat, such as barley, oat, rice, maize and brachypodium were evaluated in wheat. All barley, oat and brachypodium retrotransposon based primers and most of rice and maize retrotransposon based primers amplified resoluble and scorable banding patterns in wheat. Rerotransposns Bare-1/Wis2-1A (wheat), Frodo TRIM (barley), oat LTRs, Sukkula (barley), Bagy2/Wilma (wheat), Daniela (wheat), Fatima (wheat) and Cerebera (barley) were active in wheat. Most primers designed based on conserved regions of retrotranpososn sequences, especially terminal regions of LTRs generated resoluble banding patterns. Desirable banding patterns produced by single and combinations of different retrotransposn primers demonstrating that the studied retrotransposon families are located in wheat genome in usual and nested status. Also, desirable banding patterns generated by single primer of 5' or 3' regions of LTR and primer combinations of 5' and 3' regions of different retrotransposon families in IRAP reactions implied head to head, tail to tail and head to tail situations of retrotranposons in wheat genome. Regarding to the results of this study, it is suggested to apply retrotranposon based molecular markers for genetic diversity, mapping and tagging of genes and traits in wheat and other crops.