Origins of Allium ampeloprasum horticultural groups and a molecular phylogeny of the section Allium (Allium: Alliaceae)

The subgenus Allium section Allium includes economically important species, such as garlic and leek, as well as other polyploid minor crops. Phylogenetic studies within this section, with a focus on horticultural groups within A. ampeloprasum, were performed on 31 accessions of 17 species using the nuclear ribosomal DNA internal transcribed spacer (ITS) region and the chloroplast trnL-F and trnD-T regions. The results confirmed the monophyly of section Allium. Four main clades were identified on all ITS analyses but the relationships among those and the remaining species studied within section Allium remained unresolved. Trees based on cpDNA recovered two major clades and a topology only partly congruent with that of the ITS tree. Intra-individual polymorphism of the ITS region proved useful in tracking putative parent species of polyploid taxa. The allopolyploid origin of great headed garlic (GHG), A. iranicum and A. polyanthum was confirmed. No signs of hybridization in leek or kurrat were detected but possible introgression events were identified in pearl onion and bulbous leek. Although GHG is often used as a garlic substitute, molecular analysis revealed only a distant relationship with garlic. We also clarified the previous incorrect classification of cultivated forms within A. ampeloprasum, by showing that leek, kurrat, pearl onion, and bulbous leek should be considered separately from GHG.     

Chemical constituents and medicinal properties of Allium species

Allium species, belonging to Alliaceae family, are among the oldest cultivated vegetables used as food. Garlic, onions, leeks and chives, which belong to this family, have been reported to have medicinal properties. The Allium species constituents have been shown to have antibacterial and antioxidant activities, and, in addition, other biological properties. These activities are related to their rich organosulfur compounds. These organosulfur compounds are believed to prevent the development of cancer, cardiovascular, neurological, diabetes, liver diseases as well as allergy and arthritis. There have also been reports on toxicities of these compounds. The major active compounds of Allium species includes, diallyl disulfide, diallyl trisulfide, diallyl sulfide, dipropyl disulfide, dipropyl trisulfide, 1-propenylpropyl disulfide, allyl methyl disulfide and dimethyl disulfide. The aim of this review is to focus on a variety of experimental and clinical reports on the effectiveness, toxicities and possible mechanisms of actions of the active compounds of garlic, onions, leek and chives.

     

Phylogenetic relationships among cultivated Allium species from restriction enzyme analysis of the chloroplast genome

Summary The genus Allium contains many economically important species, including the bulb onion, chive, garlic, Japanese bunching onion, and leek. Phylogenetic relationships among the cultivated alliums are not well understood, and taxonomic classifications are based on relatively few morphological characters. Chloroplast DNA is highly conserved and useful in determining phylogenetic relationships. The size of the chloroplast genome of Allium cepa was estimated at 140 kb and restriction enzyme sites were mapped for KpnI, PstI, PvuII, SalI, XbaI, and XhoI. Variability at restriction enzyme sites in the chloroplast DNA was studied for at least three accessions of each of six cultivated, old-world Allium species. Of 189 restriction enzyme sites detected with 12 enzymes, 15 mutations were identified and used to estimate phylogenetic relationships. Cladistic analysis based on Wagner and Dollo parsimony resulted in a single, most-parsimonious tree of 16 steps and supported division of the species into sections. Allium species in section Porrum were distinguished from species in sections Cepa and Phyllodolon. Two species in section Rhiziridium, A. schoenoprasum and A. tuberosum, differed by five mutations and were placed in separate lineages. Allium cepa and A. fistulosum shared the loss of a restriction enzyme site and were phylogenetically closer to each other than to A. schoenoprasum. This study demonstrates the usefulness of restriction enzyme site analysis of the chloroplast genome in the elucidation of phylogenetic relationships in Allium.     

Chromosome Dynamics Visualized with an Anti-Centromeric Histone H3 Antibody in Allium

Due to the ease with which chromosomes can be observed, the Allium species, and onion in particular, have been familiar materials employed in cytogenetic experiments in biology. In this study, centromeric histone H3 (CENH3)-coding cDNAs were identified in four Allium species (onion, welsh onion, garlic and garlic chives) and cloned. Anti-CENH3 antibody was then raised against a deduced amino acid sequence of CENH3 of welsh onion. The antibody recognized all CENH3 orthologs of the Allium species tested. Immunostaining with the antibody enabled clear visualization of chromosome behavior during mitosis in the species. Furthermore, three-dimensional (3D) observation of mitotic cell division was achieved by subjecting root sections to immunohistochemical techniques. The 3D dynamics of the cells and position of cell-cycle marker proteins (CENH3 and α-tubulin) were clearly revealed by immunohistochemical staining with the antibodies. The immunohistochemical analysis made it possible to establish an overview of the location of dividing cells in the root tissues. This breakthrough in technique, in addition to the two centromeric DNA sequences isolated from welsh onion by chromatin immuno-precipitation using the antibody, should lead to a better understanding of plant cell division. A phylogenetic analysis of Allium CENH3s together with the previously reported plant CENH3s showed two separate clades for monocot species tested. One clade was made from CENH3s of the Allium species with those of Poaceae species, and the other from CENH3s of a holocentric species (Luzula nivea). These data may imply functional differences of CENH3s between holocentric and monocentric species. Centromeric localization of DNA sequences isolated from welsh onion by chromatin immuno-precipitation (ChIP) using the antibody was confirmed by fluorescence in situ hybridization and ChIP-quantitative PCR.     

Genetic mapping of expressed sequences in onion and in silico comparisons with rice show scant colinearity

The Poales (which include the grasses) and Asparagales [which include onion (Allium cepa L.) and other Allium species] are the two most economically important monocot orders. Enormous genomic resources have been developed for the grasses; however, their applicability to other major monocot groups, such as the Asparagales, is unclear. Expressed sequence tags (ESTs) from onion that showed significant similarities (80% similarity over at least 70% of the sequence) to single positions in the rice genome were selected. One hundred new genetic markers developed from these ESTs were added to the intraspecific map derived from the BYG15-23×AC43 segregating family, producing 14 linkage groups encompassing 1,907 cM at LOD 4. Onion linkage groups were assigned to chromosomes using alien addition lines of Allium fistulosum L. carrying single onion chromosomes. Visual comparisons of genetic linkage in onion with physical linkage in rice revealed scant colinearity; however, short regions of colinearity could be identified. Our results demonstrate that the grasses may not be appropriate genomic models for other major monocot groups such as the Asparagales; this will make it necessary to develop genomic resources for these important plants. Electronic Supplementary Material Supplementary material is available for this article at     

Cytogenetical evidences for hybrid structure and origin of diploid and triploid shallots (Allium cepa var.viviparum,Liliaceae) from Dalmatia (Croatia)

Two viviparous strains of common onion (Allium cepa) denoted asAllium cepa var.viviparum (syn.Allium ×proliferum), traditionally cultivated in the seaside regions of Croatia were found to be diploid (2n = 2x = 16) and triploid (2n = 3x = 24), respectively. The triploid cultivated onion Ljutika has not been previously reported in Europe. Using Feulgen and Giemsa C-banding methods both karyotypes were shown to be of hybrid constitution. Results obtained in this work indicate that Dalmatian viviparous onions arose from spontaneous hybridization ofA. cepa withA. fistulosum.     

Botrytis sinoallii: a new species of the grey mould pathogen on Allium crops in China

A study was conducted to identify Botrytis spp. isolated from bulb onion, green onions, garlic, and garlic chives grown in Hubei Province of China. Based on colony morphology and conidial characteristics, 367 strains of Botrytis spp. were identified as five distinct species, namely, B. cinerea, B. squamosa, B. porri, B. byssoidea, and an undescribed Botrytis species (Botrytis sp.), which accounted for 64.3, 29.9, 3.3, 0.3, and 2.2%, respectively. The previously undescribed species is herein described as a new species, B. sinoallii sp. nov., which is characterized by production of numerous small sclerotia on potato dextrose agar. Phylogenetic analysis using partial sequences of three nuclear genes (G3PDH, HSP60, and RPB2) showed that B. sinoallii forms a unique lineage, which is closely related to B. squamosa, a well-known species on Allium crops, but distantly related to the other species of Botrytis on Allium crops, including B. cinerea, B. porri, B. aclada, B. allii, B. byssoidea, B. globosa, and B. sphaerosperma. Results of inoculation tests showed that B. sinoallii is a newly identified agent that can cause leaf blight of green onion, garlic, and garlic chives. Potential impact of B. sinoallii on production of Allium crops in China is discussed.     

Factors influencing <Emphasis Type="Italic">Agrobacterium</Emphasis>-mediated transformation of monocotyledonous species

Summary Since the success of Agrobacterium-mediated transformation of rice in the early 1990s, significant advances in Agrobacterium-mediated transformation of monocotyledonous plant species have been achieved. Transgenic plants obtained via Agrobacterium-mediated transformation have been regenerated in more than a dozen monocotyledonous species, ranging from the most important cereal crops to ornamental plant species. Efficient transformation protocols for agronomically important cereal crops such as rice, wheat, maize, barley, and sorghum have been developed and transformation for some of these species has become routine. Many factors influencing Agrobacterium-mediated transformation of monocotyledonous plants have been investigated and elucidated. These factors include plant genotype, explant type, Agrobacterium strain, and binary vector. In addition, a wide variety of inoculation and co-culture conditions have been shown to be important for the transformation of monocots. For example, antinecrotic treatments using antioxidants and bactericides, osmotic treatments, desiccation of explants before or after Agrobacterium infection, and inoculation and co-culture medium compositions have influenced the ability to recover transgenic monocols. The plant selectable markers used and the promoters driving these marker genes have also been recognized as important factors influencing stable transformation frequency. Extension of transformation protocols to elite genotypes and to more readily available explants in agronomically important crop species will be the challenge of the future. Further evaluation of genes stimulating plant cell division or T-DNA integration, and genes increasing competency of plant cells to Agrobacterium, may increase transformation efficiency in various systems. Understanding mechanisms by which treatments such as desiccation and antioxidants impact T-DNA delivery and stable transformation will facilitate development of efficient transformation systems.     

AlLTPs from Allium species represent a novel class of lipid transfer proteins that are localized in endomembrane compartments

Lipid transfer proteins (LTPs) are widely distributed in the plant kingdom, but their functions remain elusive. The proteins AlLTP2-4 were isolated from three related Allium plants: garlic (A. sativum L.), Welsh onion (A. fistulosum L.), and Nanking shallot (A. ascalonicum L.). These novel proteins comprise a new class of LTPs associated with the Ace-AMP1 from onion (A. cepa L.). The AlLTP genes encode proteins harboring 132 common amino acids and also share a high level of sequence identity. Protein characteristics and phylogenetic analysis suggest that LTPs could be classified into five distinct groups. The AlLTPs were clustered into the most distantly related plant LTP subfamily and appeared to be restricted to the Allium species. In particular, the number of amino acids existing between the fourth and fifth Cys residue was suggested as a conserved motif facilitating the categorization of all the LTP-related proteins in the family. Unlike other LTPs, AlLTPs harboring both the putative C-terminal propeptide and N-terminal signal peptide were predicted to be localized to cytoplasmic vacuoles. When a chimeric GFP protein fused with both N-terminal and C-terminal AlLTP2 signal peptides was expressed in rice cells, the fluorescence signal was detected in the endomembrane compartments, thereby confirming that AlLTPs are an unprecedented intracellular type of LTP. Collectively, our present data demonstrate that AlLTPs are a novel type of LTP associated with the Allium species.     

Restriction enzyme analysis of the chloroplast and nuclear 45s ribosomal DNA ofAllium sectionsCepa andPhyllodolon (Alliaceae)

Estimates of the phylogenetic relationships among cultivated and wildAllium species would benefit from identification of molecular characters. Restriction enzyme analysis of the chloroplast DNA (cpDNA) of the bulb onion (Allium cepa), Japanese bunching onion (A. fistulosum), wildAllium species in sect.Cepa andPhyllodolon, and the outgroupsA. ampeloprasum andA. tuberosum detected 39 polymorphisms.Allium cepa andA. vavilovii were identical for all characters. Cladistic analysis generated three most-parsimoniousWagner trees of 44 steps differing only in a zero-length branch.Allium fistulosum andA. altaicum (sect.Phyllodolon) comprised a monophyletic lineage separated from theA. cepa andA. vavilovii of sect.Cepa. The unresolved node was composed ofA. galanthum, A. roylei, and the lineage containingA. cepa, A. vavilovii, A. fistulosum, andA. altaicum. The clade containingA. altaicum, A. cepa, A. fistulosum, A. galanthum, A. roylei, andA. vavilovii remained resolved for strict consensus ofWagner trees of 48 steps or less.Allium pskemense andA. oschaninii were increasingly distant.Allium oschaninii has been proposed as the progenitor of the bulb onion, but was more closely related to the common progenitor of all species in sect.Cepa andPhyllodolon. Phylogenies estimated from cpDNA characters usingDollo parsimony resulted in a single most-parsimonious tree of 46 steps and agreed with phylogenies based onWagner parsimony. Polymorphic restriction enzyme sites in the 45s ribosomal DNA were not used to estimate phylogenies because of uncertain homologies, but are useful for identifying interspecific hybrids. The maternal phylogenies estimated in this study help to distinguish wildAllium species closely related to the bulb onion. Although not in agreement with classifications based on morphology, the phylogenies closely reflected crossability among species in sect.Cepa andPhyllodolon.     

Quercetin-4′-glucoside: a physiological inhibitor of the activities of dominant glutathione <Emphasis Type="Italic">S</Emphasis>-transferases in onion (<Emphasis Type="Italic">Allium cepa</Emphasis> L.) bulb

The onion (Allium cepa L.) bulb has a high level of glutathione S-transferase (GST) activity, and it is a rich source of sulfur compounds as well as flavonoids. To investigate interactions between onion bulb GSTs and metabolites, we separated onion bulb GSTs (GSTa and GSTb as minor GSTs and GSTc, GSTd and GSTe as dominant GSTs) by DEAE-cellulose chromatography. In Western blot analysis with anti-CmGSTF1 antiserum, GSTc and GSTd fractions showed a thick band. A cDNA (AcGSTF1) corresponding to GSTc was immunoscreened with the same antiserum from an onion bulb cDNA library and its bacterial expression product was also subjected to investigation. Among the sulfur compounds, nonphysiological compounds, S-hexyl glutathione (GSH) and S-butyl GSH, showed strong inhibitory effects on 1-chloro-2,4-dinitrobenezene (CDNB)-conjugating activities of GSTa, GSTb and GSTe. However, physiological sulfur compounds, S-methyl GSH, S-propyl GSH, S-lactoyl GSH and S-ethyl-l-cysteine sulfoxide, had small or almost no inhibitory effects. Therefore, onion sulfur compounds might have the least possibility to be substantial inhibitors of onion GSTs. On the other hand, the activities of GSTc, GSTd and AcGSTF1 were strongly inhibited by flavonoids, quercetin, luteolin, apigenin and kaempferol. Ethylacetate (EtOAc) extract of onion bulb contained quercetin-4′-glucoside as a major inhibitory substance. The strong inhibitory effects of quercetin-4′-glucoside on GSTc and GSTd as well as on AcGSTF1 (50% inhibitory concentration (IC₅₀): 9.5, 7.5 and 11.2 μM, respectively) along with its high concentration (226 μM) in the onion bulb indicates that quercetin-4′-glucoside is a physiological inhibitor of dominant GSTs in the onion bulb.     

Genetic diversity in the top onion,Allium ×proliferum (Alliaceae), analysed by isozymes

Polymorphisms for six enzyme systems (GPI, IDH, PDG, PGM, SKD, and TPI) were analysed in the top onion,Allium ×proliferum. Five multilocus isozyme genotypes were found. The banding patterns of top onions were compared with those ofA. ×wakegi, A. cepa, A. fistulosum, A. altaicum, and artificial hybrids between these three species. One top onion type and one artificial hybrid had identical banding patterns. Shallots andA. altaicum, the wild progenitor ofA. fistulosum, cannot be distinguished from the common onion andA. fistulosum, respectively; these species are also potential contributors to the top onion's gene pool.     

Simplified rapid differentiation of Liriomyza chinensis Kato (Diptera; Agromyzidae) genotypes A and B using PCR-RFLP

The stone leek leafminer Liriomyza chinensis Kato is one of the most important pests of Allium spp. In recent years, a new genotype of L. chinensis, genotype B, has been shown to cause more severe damage to Allium spp. compared with the native genotype A in Japan. Thus, identification of the genotypes is important for establishing L. chinensis control strategies. In this study, we developed a simple and rapid method of genotype identification using PCR-restriction fragment length polymorphism (RFLP). Primers were designed to mitochondria cytochrome oxidase subunit I gene (mtCOI) nucleotide sequences from both genotypes. Genotypes A and B were successfully identified using the restriction enzymes PvuI and DdeI, respectively. Using PCR-RFLP, we identified the genotype of L. chinensis samples (n = 108) collected in seven Japanese bunching onion fields in Ibaraki Prefecture, Japan. All individuals were shown to be genotype B, as expected.     

Diseases caused by <Emphasis Type="Italic">Ganoderma</Emphasis> spp. on perennial crops in Pakistan

Ganoderma applanatum (Pres. Wallr) Pat. and G. lucidum (Leyss. ex Fr.) Karst attack species of Pinus, Dalbergia, Artocarpus, Morus, Cedrus, Melia, Quercus, Populus and other trees in Pakistan causing stem, butt and root rot diseases. A research institution to manage the diseases of perennial crops in general and of trees yielding edible oil in particular such as coconut and oil palm needs to be established in Pakistan.     

The effect of Cl- upon the sensitivity of starch-containing and starch-deficient stomata and guard cell protoplasts towards potassium ions,fusicoccin and abscisic acid

Chloride ions are necessary to compensate for the positively charged potassium ions imported into guard cells of Allium cepa L. during stomatal opening. Therefore an external Cl^- supply of intact Allium plants is important. But high levels of chloride have been found to reduce the sensitivity of the starch-lacking stomata and isolated guard cell protoplasts (GCPs) from Allium to potassium ions, fusicoccin and abscisic acid. Furthermore, with high levels of chloride, malate anions disappear from the guard cells of Allium, a finding which contrasts with situation in Vicia where the stomatal sensitivity to K⁺ ions, fusicoccin and ABA is not influenced by Cl^- ions and malate levels are unaffected. It is suggested that the absence of malate as a proton yielding primer inhibits the mechanism of H⁺/K⁺ exchange in Allium.Abbreviations ABA abscisic acid - FC fusicoccin - GCPs guard cell protoplasts     

Bioactive Saponins from Allium and Aster Plants

Plants belonging to the genera Allium and Aster are widely distributed in nature and have been used as food and/or medicine. Their wide use was mainly due to the medicinal properties attributed to these plants since ancient times, recently supported by epidemiological and laboratory studies. Saponin compounds, responsible for many pharmacological activities, are quite abundant in these plants. Thus, a deep knowledge about the saponin composition of these vegetables appears to be essential and could promote the discovery of new potential leads. As part of our continuing research aimed at the identification of bioactive metabolites, we have addressed our attention to several Allium and Aster species. The study resulted in the isolation of over fifty saponins of furostane, spirostane, cholestane, and oleane-type structures. Some of the isolated compounds exhibited promising antiproliferative, antifungal, and antispasmodic activities. Their structure, distribution and bioactivity will be reported here together with a brief overview of the literature on Allium and Aster saponins.     

Salmonella contamination of vegetables irrigated with untreated wastewater

The irrigation of vegetables with raw wastewater has been practised in El Azzouzia, the wastewater-spreading field of Marrakesh city (Morocco), for many years. This water was found to be contaminated with different serogroups of Salmonella. B and C were the most frequently isolated groups. These same serogroups were detected on vegetables irrigated with these wastewater effluents. The crops whose edible product develops on the ground surface, such as lettuce and parsley, were more contaminated than those which grow, above the soil surface, like tomatoes and pimento. Except on lettuce, Salmonella on crops did not persist beyond 3 days after irrigation.     

The cytogeographical distribution pattern ofAllium (Alliaceae) in the Greek Peninsula and Islands

Greece is considered as a secondary centre of evolution for the genusAllium since it possesses about 50% of the species known from the whole Flora Europaea area. In the present investigation 44 GreekAllium spp. have been studied and new chromosome counts are reported from 40 populations and 17 species. The distribution of the different cytotypes (x = 7, x = 8, x = 11 and 2n = 2x, 3x, 4x, 5x, 6x, 7x) in Greece is discussed. From the four phytogeographical subdivisions recognized, South continental Greece shows the greatest species and karyotype diversity. This phenomenon is probably due to the geographical position and to the geological history of this area which has received species and populations from different directions. Subsequently, hybridization apparently has been of evolutionary importance.The genusAllium in Greece I.