Abstract
Because transposable elements contribute significantly to diversification between and within plant species, transposon-based molecular markers could have special benefits for phylogenetic studies. Sequence-specific amplification polymorph-ism (S-SAP) technique uses transposon-related primers combined with AFLP primers. Among the Class II TEs CACTA elements are of special interest, having highly conserved ends and highly variable internal sequences. For our analysis Bot1-related TIR sequences were used. Combinations with different AFLP primers were tested for number of bands, polymorphism degree and reproducibility. With selected primer combinations the VIR Brassica rapa core collection of 96 accessions encompassing a wide range of morphological types and geographical origins was investigated. Twelve primer combinations generated 123 polymorphic markers. The mean PIC value of these markers was 1.47-fold that of 149 SSR alleles tested in the same core collection. The set of S-SAP markers was used for distance analysis to generate a phylogenetic tree as basis for association studies with morphological traits, metabolite content and resistance traits.
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