The Combination of Start-Codon-Targeted (SCoT) and () Transposon-Specific Primers Provides an Efficient Marker Strategy for Species.

A novel primer (FaSt-R) targeting the -specific () non-autonomous transposon was combined with start-codon-targeted (SCoT) primers to assess genetic diversity in 12 cultivars from six species and 28 cultivars of European plum. Compared to SCoT-only analyses, the SCoT-FaSt combination produced fewer total bands but a higher percentage of polymorphic bands, while maintaining comparable values for polymorphism information content, resolving power, gene diversity, and Shannon's index. SCoT-FaSt markers generated bands across a broader size range, which made gel patterns less dense, enabling the more accurate detection of differentially amplified fragments. Neighbor-joining and principal component analyses confirmed that SCoT-FaSt markers provided sufficient phylogenetic resolution at both interspecific and intraspecific levels. The sequencing of 32 SCoT-FaSt amplicons revealed elements in 26 fragments, with SCoT primers preferentially annealing to GC-rich exonic and intergenic regions. Seventeen protein-coding and one RNA-coding gene were partially identified, with elements localized in UTRs and introns of genes with key physiological functions. Comparative analysis indicated a biased distribution of elements between the and subgenera. In silico findings suggest that elements are more fragmented in cherry species, potentially contributing to subgeneric divergence. Overall, the SCoT-FaSt marker system is effective for evaluating genetic diversity, reconstructing phylogenetic relationships, and elucidating the genomic impact of an active Mutator-like transposon.