Abstract
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.
Highlights
Eremurus, the largest genus in the Asphodelaceae, is comprised of some 45 species of herbaceous perennial plants that are native to central Asia and Caucasia[1]
To analyze diversity in Eremurus at the genus level, a reference was assembled from GBS reads (‘GBS reference’) across 96 accessions belonging to seven Eremurus species collected across Iran (Supplementary Table S1; Supplementary Fig. S1)
We obtained a total of 12,535 single nucleotide polymorphism (SNP) markers across the 96 samples after alignment of the reads from each accession to the GBS reference and SNP calling, removal of adjacent SNPs and filtering for biallelic SNPs, SNPs with a quality depth (QD) ≥ 10, and SNPs with
Summary
The largest genus in the Asphodelaceae, is comprised of some 45 species of herbaceous perennial plants that are native to central Asia and Caucasia[1]. Eremurus species are important commercially as ornamental plants for landscaping and cut-flower markets[2] Due to their large and colorful floral spikes, Eremurus species are known in the international horticulture trade as “Foxtail Lily” or “Desert Candle”. Recent developments in generation sequencing technologies have enabled the detection of single nucleotide polymorphism (SNP) markers at the whole genome level in non-model species, including those that lack a sequenced genome, using reduced representation sequencing[9,10,11] These approaches have not yet been applied to identify SNP markers across species within an angiosperm genus comprised of species with very large genomes (>8 Gb) and no reference genome.
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