Insertion site-based polymorphism: A Swiss army knife for wheat genomics

Transposable elements (TEs) are prevalent in the genomes of all plants. They are ubiquitous, in high-copy number, evenly distributed in the genome, in both hetero- and euchromatin, and show insertional polymorphism both between and within species1,2. These genetic properties have recently allowed the development of several TE-based molecular marker types, such as S-SAP, IRAP, REMAP and RBIP3,4. These molecular markers have successfully been used to establish phylogenies, study biodiversity and generate linkage maps for agronomically important traits in several species such as barley, pea, rice and tobacco4-6. In wheat, TEs account for more than 70% of the genome2,7 and play a major role in the structure and evolution of the genome. It is likely that TEs have driven wheat genome evolution in diverse ways, including genome expansion and contraction, segmental duplication, and exon shuffling. It has been proposed that TE-induced genomic rearrangements tend to promote both cytological and genetic diploidization of polyploid genomes8,9. Therefore, TE-based molecular markers represent ideal tools to study the structure and evolution of the hexaploid wheat genome.