ISSR-assisted spatial genetic structure, population admixture, and biodiversity estimates across locally adopted saffron ecotypes from 18 different provenances of Iran

Here, genetic variability and spatial genetic structure patterns governing on a 90-sample collection of Iranian saffron ecotype gathered from 18 provenances were scrutinized using 20 ISSR markers. 17 out of 20 ISSR primers exhibited polymorphism with 130 polymorphic amplicons from 4 to 15 bands per primer, with an average of 7.647. Considering maximum values of PIC (0.37), discrimination power (D; 0.71), and expected heterozygosity (H; 0.497), both ISSR-7 and ISSR-9 primers were nominated to generate maximal discrimination and heterozygosity. Based on phylogenetic tree and PCoA, the ecotypes were classified into two major groups, but inconsistent with the geographical distribution. Similarly, via applying Bayesian population structure clustering, two sub-populations (K = 2) were observed, four ecotypes were admixture (Q < 0.70), and the rest were pure ecotypes (Q ≥ 0.70). Sub-population 1 was less genetically diverse (F_ST = 0.1658) than sub-population 2 (F_ST = 0.5593). As to AMOVA, 56.563% and 43.436% of total genetic variation were partitioned into inter- and intra-population variation, respectively. Based on spatial PCA (sPCA), robust signals of “global” and “local” structures were recognized, only the former was statistically significant (p < 0.001). Significant IBD patterns were also observed via Mantel test calculated between original/unbiased Nei’s genetic distances and geographic distances (p < 0.001) across full dataset. The results revealed ISSR capabilities in saffron DNA fingerprinting and biodiversity assessment, moderate-high genetic variability alongside significant global spatial genetic structure among saffron ecotypes, followed by low levels of gene flow (Nm = 0.2801) and admixture patterns.