Ivanovska Beti, Onlamun Thanyarat, Halász Júlia, Hegedűs Attila
Group of Horticultural Plant Genetics, Department of Plant Biotechnology, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, Ménesi út 44., 1118 Budapest, Hungary.
Int J Mol Sci. 2025 Apr 23;26(9):3972. doi: 10.3390/ijms26093972.
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.
一种靶向特定的（）非自主转座子的新型引物（FaSt-R）与起始密码子靶向（SCoT）引物相结合，用于评估来自六个物种的12个品种和欧洲李的28个品种的遗传多样性。与仅进行SCoT分析相比，SCoT-FaSt组合产生的总条带较少，但多态性条带的百分比更高，同时在多态性信息含量、分辨能力、基因多样性和香农指数方面保持相当的值。SCoT-FaSt标记产生的条带大小范围更广，这使得凝胶图谱密度更低，从而能够更准确地检测差异扩增片段。邻接法和主成分分析证实，SCoT-FaSt标记在种间和种内水平上都提供了足够的系统发育分辨率。对32个SCoT-FaSt扩增子的测序揭示了26个片段中的元件，其中SCoT引物优先退火到富含GC的外显子和基因间区域。部分鉴定出17个蛋白质编码基因和1个RNA编码基因，元件位于具有关键生理功能的基因的UTR和内含子中。比较分析表明元件在和亚属之间存在偏向分布。电子分析结果表明，元件在樱桃物种中更加碎片化，这可能导致亚属分化。总体而言，SCoT-FaSt标记系统对于评估遗传多样性、重建系统发育关系以及阐明活性Mutator样转座子的基因组影响是有效的。
