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Eremurus  species, better known as ‘Foxtail Lily’ or ‘Desert Candle’, are important worldwide in landscaping and the cut-flower industry. One of the centers of highest diversity of the genus  Eremurus  is Iran, which has seven species. However, little is known about the genetic diversity within the genus  Eremurus . With the advent of genotyping-by-sequencing (GBS), it is possible to develop and employ single nucleotide polymorphism (SNP) markers in a cost-efficient manner in any species, regardless of its ploidy level, genome size or availability of a reference genome. Population structure and phylogeographic analyses of the genus  Eremurus  in Iran using a minimum of 3002 SNP markers identified either at the genus level or at the species level from GBS data showed longitudinal geographic structuring at the country scale for the genus and for the species  E. spectabilis  and  E. luteus , and at the regional scale for  E. olgae . Our analyses furthermore showed a close genetic relatedness between  E. olgae  and  E. stenophyllus  to the extent that they should be considered subspecies within an  E. olgae/stenophyllus  species complex. Their close genetic relatedness may explain why crosses between these two (sub)species have been found in the wild and are exploited extensively as ornamentals. Last, current species identification, while robust, relies on flower morphology. A subset of seven SNPs with species-specific (private) alleles were selected that differentiate the seven  Eremurus  species. The markers will be especially useful for cultivar protection and in hybrid production, where true hybrids could be identified at the seedling stage.

Intra- and interspecific diversity analyses in the genus Eremurus in Iran using genotyping-by-sequencing reveal geographic population structure