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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 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.
Our analyses furthermore showed a close genetic relatedness between E. 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.
Download PDF Introduction 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.
Eremurus species are important commercially as ornamental plants for landscaping and cut-flower markets 2. In addition to their ornamental value, Eremurus species have been used in traditional medicine and are potential sources for anti-inflammatory, antibacterial, and antiprotozoal drugs 3 , 4 , 5.
Other Eremurus products, such as bio-oil 6 and adhesives 7 , have industrial applications. A better understanding of the genetic variation within and among Eremurus species would facilitate breeding for ornamental traits and other properties. Naderi Safar and colleagues 8 used genetic variation obtained by amplicon sequencing of the plastid trnL-F and nuclear rDNA ITS regions to conduct a molecular phylogenetic study of three Asphodelaceae genera, including Eremurus.
This study showed that Eremurus species grouped into the paraphyletic subgenus Henningia and the monophyletic subgenus Eremurus. However, information on the genetic diversity within Eremurus species is lacking. Recent developments in next 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 , Both diploid E.
Flow cytometry of the diploid E. Iran is the third largest diversity center of the genus Eremurus, after the Soviet Union and Afghanistan There are seven Eremurus species and three subspecies found in Iran, with the greatest species diversity located in the northeastern part of the country. Eremurus stenophyllus Boiss. Eremurus stenophyllus subsp. Bieb subsp. Hybrids between E. Eremurus species are generally insect-pollinated, although self-fertilization is possible and wind dispersal of pollen has been observed in desert habitats where pollinator activity is unreliable 17 , In this study, we investigated the interspecific and intraspecific diversity in Eremurus spp.
In addition to the biological significance of our research, this is the first report of the use of GBS on species of the Asphodelaceae, none of which have been sequenced to date, the first use of GBS on an angiosperm species with a genome size 1C larger than 8 Gb and no reference genome, and one of the few applications of GBS to plants of ornamental interest. Furthermore, we demonstrate the use of GBS to study intraspecific variation as well as interspecific variation in Eremurus spp.
Because the reference building was carried out across species, we required each reference tag to be present in only two accessions in order to be included in the reference. The assembled GBS reference consisted of , tags. The average number of reads for the remaining 88 accessions was 1.
The final number of SNPs used for the diversity analyses across the seven Eremurus species was A SNP resampling analysis showed that a subset of randomly selected SNPs had the same power to distinguish all multilocus genotypes as the full set of SNPs, indicating that our SNP set was adequate to determine the diversity between Eremurus species Supplementary Fig.
The subpopulation division was largely by species Fig. Eremurus inderiensis, E. Colored vertical bars indicate the percentage membership to different subpopulations. Interrelationships between the superclades were unresolved in the NJ tree Fig. Superclade 1 comprised E. Superclade 2 comprised two sister clades corresponding to E. With the exception of a few branches, relationships between accessions within species had low bootstrap values Fig. The genus Eremurus in Iran was geographically structured according to an East-West transect.
All species sampled within subgenus Henningia originated from the eastern part of Iran except E. This represents The highest number of private alleles was found in E. No private alleles were identified for E. The highest frequency of any diagnostic allele in E. A total of 82 and alleles were private and diagnostic, respectively, for the E. The number of private and diagnostic alleles per subpopulation is given in Table 1. Four morphological traits, tepal color, tepal nerve, tepal tip, and flower shape, were singly able to distinguish the two subgenera, Eremurus and Henningia, as defined by Wendelbo 15 Supplementary Table S6.
In addition, tepal color, tepal tip and flower shape used in combination were able to differentiate the seven species. The two most morphologically diverse species were E. Table 2 Summary of morphological diversity across species within the genus Eremurus Full size table Eremurus spectabilis, E. White, yellow, and orange tepal colors were diagnostic for E. No variation was observed within species for tepal nerve, tepal tip, flower shape, bract margin, fruit shape, or leaf margin and surface indumentum.
In contrast, inflorescence length displayed variation within all Eremurus species Supplementary Table S6. Overall, 55 morphotypes matrices consisting of all 16 morphological characters were recorded and all of them were specific to one of the studied species Supplementary Table S8.
Specific morphotypes were also recorded for each clade of E. One trait out of the 16 evaluated tepal color was able to differentiate E. The first coordinate of the PCoA explained The second coordinate, explaining The second coordinate also separated the species within subgenus Henningia into three groups represented by E. The third coordinate explained 9.
Adjacent SNPs were also removed. This concurs with E. The majority The lower number of shared tags when considering only the SNP-carrying tags used in the analyses compared with all reference tags can be explained by the fact that common reference tags are not necessarily polymorphic in all subpopulations.
Trees within a E. For accessions belonging to E. Both species were collected from the eastern part of Iran Fig. Discrepant placement in the two analyses was found for E. Eremurus stenophyllus was the only species that had flower color variants. In addition to the typical yellow color, some accessions had orange or white flowers. All E. Within E. While all E. Three clades with unresolved relationships were identified in E. Clade I comprised five species collected at the same location N Clade II, also sampled in eastern Iran, consisted of two sister subclades, one comprising four species collected at N Discussion Genotyping-by-sequencing for phylogenetic analysis across species within a genus Genotyping-by-sequencing has been used in a number of species without a reference genome to identify SNP markers for genetic mapping or diversity analyses, e.
Furthermore, using GBS references generated either across species or within species, the same GBS reads can be used to provide markers suitable for cross-species and intraspecific applications, respectively. To generate a reduced representation genome reference from GBS reads using the UGbS-Flex pipeline, we first clustered reads within accessions, extracted consensus sequences from each cluster, and then clustered the consensus sequences across accessions We then used blast all-vs.
This reference consisted of , sequences. As expected, however, little bootstrap support was obtained for the majority of relationships between accessions within a species. To increase the resolution at the accession level, we extracted the raw reads for the three largest subpopulations obtained with STRUCTURE, which essentially corresponded to the species E. Genetic relationships between and within Eremurus species We used STRUCTURE 20 , which applies a Bayesian iterative algorithm, to determine the most likely number of genetic groups and the membership of each Eremurus accession to these groups.
We obtained five clusters Fig. In , Baker divided the genus Eremurus into three subgenera, Eremurus verus, Ammolirion, and Henningia Wendelbo 15 recognized only two genera, Eremurus, which comprised sections Eremurus and Ammolirion, and Henningia, which comprised section Henningia. Naderi Safar and colleagues 8 subsequently showed using plastid trnL-F and ribosomal internal transcribed spacer ITS sequences that subgenus Henningia was paraphyletic, with E.
Our results largely agree with Naderi Safar et al. S5 , while E. Our data also bring into question some of the current species delineations. In contrast, these values are 0. Furthermore, E. The SNP data obtained from both the across-species and intraspecies analyses of the GBS reads demonstrated that accessions typically group by geographic location. Interestingly, E.
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 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. Our analyses furthermore showed a close genetic relatedness between E. 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.
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