Analysis of selected singleton transposable elements (SSTEs) and their application for the development of land PATE markers in Magnaporthe oryzae

Transposable elements (TEs) are distributed throughout the genome and play an important role in genome variation of the rice blast fungus, Magnaporthe oryzae . TE-associated molecular markers have been developed and used extensively for diversity analysis in natural populations. Here, we investigated the genomic distribution of a selected group of TEs that are dispersed as singletons, and each is of a size feasible for PCR validation, designated as SSTEs, in the genome of the reference laboratory strain, 70-15. The 75 SSTEs identified were distributed evenly on seven chromosomes of the M. oryzae genome. Approximately 40 % of SSTEs were located either in the coding or promoter regions of the predicted genes. The presence or absence of each SSTE at the respective locus was assessed, resolving significant presence/absence polymorphism among 11 rice blast strains collected from different locations worldwide. The presence/absence (P/A) polymorphism of SSTEs in different strains suggests that they may be useful for developing map-based land PATE markers for genetic analysis in M. oryzae.