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

A novel primer (FaSt-R) targeting the Prunus-specific Falling Stone (FaSt) non-autonomous transposon was combined with start-codon-targeted (SCoT) primers to assess genetic diversity in 12 cultivars from six Prunus 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 FaSt 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 FaSt elements localized in UTRs and introns of genes with key physiological functions. Comparative analysis indicated a biased distribution of FaSt elements between the Cerasus and Prunus subgenera. In silico findings suggest that FaSt elements are more fragmented in cherry species, potentially contributing to subgeneric divergence. Overall, the SCoT–FaSt marker system is effective for evaluating Prunus genetic diversity, reconstructing phylogenetic relationships, and elucidating the genomic impact of an active Mutator-like transposon.