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

Hanieh Hadizadeh; Bochra A Bahri; Peng Qi; H Dayton Wilde; Katrien M Devos

doi:10.1038/s41438-020-0265-9

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

Hortic Res. 2020 Mar 2:7:30. doi: 10.1038/s41438-020-0265-9. eCollection 2020.

Authors

Hanieh Hadizadeh^#¹, Bochra A Bahri^#^{2

3

4}, Peng Qi³, H Dayton Wilde⁵, Katrien M Devos³

Affiliations

¹ 1Department of Horticulture, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran.
² 2Laboratory of Bioaggressors and Integrated Protection in Agriculture, The National Agronomic Institute of Tunisia, University of Carthage, 1082 Tunis, Tunisia.
³ 3Institute of Plant Breeding, Genetics and Genomics (Department of Crop and Soil Sciences), and Department of Plant Biology, University of Georgia, Athens, GA 30602 USA.
⁴ 5Present Address: Department of Plant Pathology, University of Georgia, Griffin, GA 30223 USA.
⁵ 4Institute of Plant Breeding, Genetics and Genomics (Department of Horticulture), University of Georgia, Athens, GA 30602 USA.

^# Contributed equally.

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.

Keywords: Genetic variation; Next-generation sequencing.