SSR and IRAP-based genetic diversity analysis for core collection of Idesia polycarpa

Idesia polycarpa, a promising woody oil crop, has abundant germplasm resources in Guizhou Province. To promote effective conservation and utilization, a core collection was established. The genetic diversity of 120 accessions from seven populations was evaluated using 42 polymorphic primers (18 SSRs, 24 IRAPs). The markers showed high polymorphism (PPL: 100%). IRAPs outperformed SSRs in the number of loci per primer (17.76 vs. 9.56), Ne (1.43 vs. 1.31), H (0.27 vs. 0.20), I (0.61 vs. 0.46), and PIC (0.71 vs. 0.89). The Mantel test indicated that both markers provided complementary information (r = 0.424, p < 0.001). Genetic diversity varied significantly among populations, with the Guizhou northwest region (LPS) the most diverse and the Guizhou southeast region (QDN) the least. Analysis showed moderate to low genetic differentiation (Gst = 0.126) and moderate gene flow (Nm = 1.73). UPGMA, PCoA, and STRUCTURE analyses revealed a distinct genetic structure with some local admixture. A core collection of 30 accessions was successfully established, retaining 96.7% of the total alleles. DNA fingerprints using IRAP primers (RT19 + RT34) achieved 100% discrimination among individuals. This study provides valuable genetic insights and technical support for the conservation, breeding, and sustainable use of Idesia polycarpa.