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 .