The subgenus Rhizirideum in the genus Allium consists of 38 species worldwide and forms five sections (A. sect. Rhizomatosa, A. sect. Tenuissima, A. sect. Rhizirideum, A. sect. Eduardia, and A. sect. ...Caespitosoprason), A. sect. Caespitosoprason being merged into A. sect. Rhizomatosa recently. Previous studies on this subgenus mainly focused on separate sections. To investigate the inter-section and inter-subgenera phylogenetic relationships and adaptive evolution of A. subg. Rhizirideum, we selected thirteen representative species, which cover five sections of this subgenus and can represent four typical phenotypes of it. We conducted the comparative plastome analysis with our thirteen plastomes. And phylogenetic inferences with CDSs and complete sequences of plastomes of our thirteen species and another fifty-four related species were also performed. As a result, the A. subg. Rhizirideum plastomes were relatively conservative in structure, IR/SC borders, codon usage, and repeat sequence. In phylogenetic results, the inter-subgenera relationships among A. subg. Rhizirideum and other genus Allium subgenera were generally similar to the previous reports. In contrast, the inter-section relationships within our subgenus A. subg. Rhizirideum were newly resolved in this study. A. sect. Rhizomatosa and A. sect. Tenuissima were sister branches, which were then clustered with A. sect. Rhizirideum and A. sect. Eduardia successively. However, Allium Polyrhizum Turcz. ex Regel, type species of A. sect. Caespitosoprason, was resolved as the basal taxon of A. subg. Rhizirideum. Allium siphonanthum J. M. Xu was also found in clade A. subg. Cyathophora instead of clade A. subg. Rhizirideum. The selective pressure analysis was also conducted, and most protein-coding genes were under purifying selection. At the same time, just one gene, ycf2, was found under positive selection, and another three genes (rbcL, ycf1a, ycf1b) presented relaxed selection, which were all involved in the photosynthesis. The low temperature, dry climate, and high altitude of the extreme habitats where A. subg. Rhizirideum species grow might impose intense natural selection forces on their plastome genes for photosynthesis. In summary, our research provides new insights into the phylogeny and adaptive evolution of A. subg. Rhizirideum. Moreover, we suggest that the positions of the A. subg. Rhizirideum species A. polyrhizum and A. siphonanthum should be reconsidered.
A new species,
Allium negianum
(Amaryllidaceae), belongs to the genus Allium subg. Rhizirideum, sect. Eduardia is described here from the Uttarakhand Himalayan region of India. This taxon grows in ...Malari region of Niti valley in Chamoli district and Dharma valley of Pithoragarh district, Uttarakhand, India. It is a narrowly distributed species and morphologically more closer to
A. przewalskianum
Regel but differentiated by its tunic color of bulb, umbel with lax flowers, peduncle length, perigone colour, size and shape and leaf anatomy. Taxonomic delineation and relationship analysis based on nuclear ribosomal Internal Transcribed Spacers (ITS) region indicated that
A. negianum
is distinct and related to
A. przewalskianum
. This study provided a comprehensive description and comparison with
A. przewalskianum
, an identification key and notes on the distribution of the species.
Allium section Rhizirideum constitutes a group of approximately 24 species, distributed mostly in steppe areas of the Eurasian temperate zone. Its phylogenetic relationships are therefore relevant ...for understanding of the evolutionary and biogeographical patterns of the Eurasian steppes. Based upon DNA sequences from two plastid regions (trnQ-rps16 and trnL-rpl32) and the internal transcribed spacer region of nuclear ribosomal DNA, the phylogenetic relationships in Allium section Rhizirideum are investigated by using maximum parsimony and Bayesian inference. Dated phylogenies revealed (1) that diversification started in the upper Pliocene and further speciation events occurred during the Pleistocene and (2) a clear division of the section Rhizirideum into an "Asiatic" and "European" geographical group. Nomenclature, distribution maps and identification key for all species are provided. Origin and diversification within this section thus reflect the development and history of the modern Eurasian steppe.
Downy mildew resistance originating from Allium roylei Stearn provides a complete resistance to onions and is based on one, dominant gene. Since A. roylei can successfully be hybridized with onion ...(A. cepa L.), a breeding scheme aimed at the introgression of this gene was initiated ca. 20 years ago. Several setbacks in this programme were encountered, firstly the identified molecular marker linked to the downy mildew resistance locus became increasingly difficult to use and finally lost its discriminating power and secondly the final step, making homozygous introgression lines (ILs), turned out to be more difficult then was hoped. GISH analysis showed that the chromosomal region harbouring the resistance locus was the only remaining piece of A. roylei in the nuclear background of onion and it also confirmed that this region was located on the distal end of chromosome 3. It was hypothesized that some factor present in the remaining A. roylei region was lethal when homozygously present in an onion genetic background. The identification of an individual with a smaller and more distally located introgression fragment and homozygous ILs in its progeny validated this hypothesis. With the help of these nearly isogenic lines four AFLP® markers closely linked to the resistance gene were identified, which can be used for marker-aided selection. The introduction of downy mildew resistance caused by Peronospora destructor into onion is a significant step forward in the development of environmentally-friendly onion cultivars.
Pollen grains of 16 taxa of Allium L. belonging to sections Rhizirideum G. Don ex Koch., Codonoprasum Reichb. and Allium L. were investigated using light and scanning electron microscope, and pollens ...of four taxa were also examined with transmission electron microscope. Pollens were monosulcate and ellipsoidal. It was observed that the sulcus extends from distal to proximal in all taxa. The exine was semitectate and the tectum was perforate. Columellae were simplicolumellate. Exine sculpture was striate-perforate, striate-rugulate-perforate and rugulate-perforate. A. albidum Fischer ex Bieb. subsp. caucasicum (Regel) Stearn, A. rupicola Boiss ex Mouterde and A. asperiflorum Miscz. were seen to have an operculum. Key words: Allium; Codonoprasum; Rhizirideum; Alliaceae; Pollen morphology; Turkey DOI: 10.3329/bjb.v39i1.5524Bangladesh J. Bot. 39(1): 37-36, 2010 (June)
We have identified a set of informative STMS markers in onion (Allium cepa L.) and report on their application for genotyping and for determining genetic relationships. The markers have been ...developed from a genomic library enriched for microsatellites. Integrity of the microsatellite polymorphism was confirmed by amplicon sequencing. The microsatellite genotypes of 83 onion accessions and landraces from living onion collections were compared. As few as four primer pairs were sufficient to assign unique microsatellite patterns to the 83 accessions. Some of the microsatellite markers can be used for interspecific taxonomic analyses among close relatives of Allium cepa. Generally, our data support and extend results obtained from recently performed analyses using ITS, RAPD and morphology.PUBLICATION ABSTRACT
The chloroplast DNA diversity of 33 accessions belonging to 16 species of five sections in Allium subgenus Rhizirideum was studied by analysing the sequence of three fragments: the trnL-F intergenic ...spacer, the rps 16 intron and rbcL (rubisco large subunit). The three sections Cepa, Schoenoprasum and Rhizirideum, representing the majority of the included species, each possess a separate clade after phylogenetic analysis. Exceptions to this general rule are the placement of Allium pskemense (section Cepa) connected to Allium senescens (section Rhizirideum) and Alium roylei, taking an intermediate position between sections Cepa and Schoenoprasum. Both species were located in their own section after nuclear DNA analysis. A range of crossing experiments has been carried out. The different position of A. roylei when comparing cpDNA and nDNA diversity was not confirmed with the production of hybrid seeds after crossing A. roylei with species other than those of section Cepa. The different position of A. pskemense in the cpDNA and the nDNA tree can not be compared to its crossability, since only a few crossing experiments are reported for this species. The hypothesis that a shorter distance between two species in a cpDNA tree compared to their distance in a nDNA tree will indicate interfertility at a certain level, is neither confirmed nor rejected by the currently available results.
Amplified fragment length polymorphisms (AFLPs) for assessing nuclear DNA diversity have been used for the reconstruction of the phylogeny and evolution of several sections of Allium subgenus ...Rhizirideum. A dataset of 355 characters for 33 accessions belonging to 20 species has been compiled. The band-sharing of five interspecific hybrids and of an F^sub 2^ population between Allium cepa and Allium roylei with their parents indicated a heterozygosity level between 6 and 14%, which allows the use of dominant markers such as AFLPs for phylogeny reconstruction. A majority rule consensus tree based on 56 most-parsimonius trees (CI = 0.528) revealed a separate clade for each of the sections, Cepa, Rhizirideum and Schoenoprasum, and one clade combining the sections Oreiprason and Petroprason. An unweighted pair group mean average (UPGMA)-based dendrogram showed the same subdivision. The trees and the 'Hybrid Distance' approach both supported the assumption of a hybrid origin for A. roylei with considerable subsequent secondary evolution. The establishment of three alliances in the section Cepa and the close relationship of sections Oreiprason and Petroprason are now confirmed. The predictions of the Soybean domestication scenario, i.e. selection of a crop from one progenitor with subsequent narrowing of the genetic diversity of the crop, which applies to the cultigens A. cepa and Allium fistulosum, is supported by the Hybrid Distance approach.PUBLICATION ABSTRACT
Among 341 randomly amplified DNA sequences generated from 11 Allium species, 55 were purified by gel excision and subsequent reamplification by PCR. These were then used as probes in dot blot ...analysis to evaluate the relationships between 44 Allium accessions classified under the subgenus Rhizirideum. The hybridization signals were standardized and converted to Euclidean taxonomic distances. Unweighted Pair Group Mean analysis of the distance data generated a phyllogram which basically conformed to the classification system proposed by the Gatersleben (Germany) group. However, there was insufficient evidence to support the proposal to join A. chinense G. Don with A. virgunculae F. Maek. et Kitam. into sect. Sacculiferum or the recent suggestion to re-establish sect. Phyllodolon.
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