El-nagish, A.; Dhar, M. K.; Mann, L.; An, R.; Houben, A.; Blattner, F.; Harpke, D.; Heitkam, T.

Summary (1) Background Saffron crocus (Crocus sativus) is the source of saffron, the most expensive spice in the world. It evolved about 3000 years ago as a sterile triploid clone in Greece. Since then, saffron has spread across the globe, where regionally distinct practices of saffron cultivation have developed. Despite differences in morpho-physiological traits, genetic variability is low, if present at all. Here, we aim to resolve chromosomal and sequence-associated variability across saffron crocus cultivars from the crop's main cultivation areas in Africa, Asia and Europe. (2) Methods We used genome-wide DNA polymorphisms obtained through genotyping-by-sequencing (GBS) of 33 saffron and 14 closely related Crocus accessions, which we place into a phylogenetic context. For karyotyping, we compare nine saffron accessions by multi-color fluorescent in situ hybridisation (FISH) with repetitive DNA probes. (3) Key results Phylogenetic analyses confirmed the single origin and clonal nature of all saffron accessions. We detected slight DNA differences among saffron crocus genotypes, which were minor compared with those in wild C. cartwrightianus populations. Still, the Iranian saffron accessions form a genetically very narrow group that differs from the other proveniences in population genetic analyses. However, chromosomes of some saffron accessions display variable FISH signals, likely resulting from gains and losses of tandemly repeated DNA. (4) Main conclusions Based on the high genetic identity and small karyotypic differences, we confirm the clonal origin of the saffron accessions. Nevertheless, as we detected small and regional chromosomal variability, we conclude that at least four somaclonal saffron lineages emerged after saffron's origin.