GarlicESTdb: an online database and mining tool for garlic EST sequences

Background  

Allium sativum., commonly known as garlic, is a species in the onion genus (Allium), which is a large and diverse one containing over 1,250 species. Its close relatives include chives, onion, leek and shallot. Garlic has been used throughout recorded history for culinary, medicinal use and health benefits. Currently, the interest in garlic is highly increasing due to nutritional and pharmaceutical value including high blood pressure and cholesterol, atherosclerosis and cancer. For all that, there are no comprehensive databases available for Expressed Sequence Tags(EST) of garlic for gene discovery and future efforts of genome annotation. That is why we developed a new garlic database and applications to enable comprehensive analysis of garlic gene expression.     

Identification of Botrytis spp. on Plants Grown in Iran

A total of 363 isolates were collected from all over Iran. They were isolated from apple, arum lily, briar rose, bride wort, broad bean, camellia, canola, carnation, cucumber, egg plant, feijoa, geranium, gerbera, gladiolus, grape, guilder rose, hibiscus, iris, kiwifruit, oleander, onion, orange, pear, pomegranate, primrose, quince, redbud, robinia, rose, rubber plant, sow thiste, spathe flower, strawberry, tomato, violet, wall flower and wheat. To identify the species, morphological characters such as conidiophore length, conidial and sclerotial dimensions were measured. According to morphological and cultural characters, eight Botrytis species were identified: B. aclada sensu lato, B. cinerea, B. fabae, B. convoluta, B. gladiolorum, B. paeoniae, B. pelargonii and B. porri. As far as we are aware, this is the first report of the last five species from Iran. These species were examined by polymerase chain reaction (PCR) using necrosis and ethylene‐inducing protein (NEP2) and C729 primers. A 835 bp band was amplified in B. cinerea, B. fabae and B. pelargonii, using NEP2, but not in others. However, C729 primers amplified a 700 bp band in B. cinerea and B. pelargonii and a 600 bp in B. fabae.     

Aspects of interspecific hybridization within edible <Emphasis Type="Italic">Alliaceae</Emphasis>

Crossing experiments within the genus Allium have been carried out for many years. Usually, with the aim of widening genetic variation, edible Alliaceae such as bulb onion, Japanese bunching onion, leek, garlic and shallot have been crossed with each other or with distant vegetable Allium crops. Interspecific hybridization, especially with wild relatives is considered as the best way of introgression desirable traits to the crops. By using sexual or somatic hybridization, many important characters, such as: disease and pest resistance, important metabolites and cytoplasmic male sterility have been transferred to other Allium crops. This review summarises some aspects of the directions of interspecific hybridization in edible Alliaceae and the significance and perspectives of using these hybrids in breeding programmes.     

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.     

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.     

Mechanism of action of the plant resistance inducer β-aminobutyric acid in <Emphasis Type="Italic">Allium cepa</Emphasis>

The mechanism of action of β-aminobutyric acid (BABA) as an inducer of resistance to the necrotrophic fungi Botrytis spp. in three different varieties of onion (Allium cepa) is investigated. It is shown that low concentrations of BABA are capable of inducing resistance in onion to neck rot induced by Botrytis allii and that induced by B. cinerea. By means of fluorescence microscopy it is established that treatment of the bulb of onion with BABA leads to priming defensive callose deposition, the principal mechanical barrier against penetration of the pathogen. However, the priming response was not discovered in the Sterling onion variety, which does not exhibit BABA-induced resistance to Botrytis fungi.     

Control of Botrytis cinerea and Botrytis squamosa in overwintered salad onions by fungicide sprays

In 1974/75, 13 sprays of 0·2% a.i. thiram applied at 14 day intervals to overwintered salad onions reduced the incidence of Botrytis cinerea and significantly increased onion yields. In 1977/78 both B. cinerea and B. squamosa occurred, and 12 iprodione sprays at 0·1% a.i. applied at 14-day intervals or 6 sprays at 0·2% a.i. applied at 28-day intervals gave good control of B. cinerea and B. squamosa and significantly increased onion yields. Benomyl (0·1% a.i. at 14-day intervals, or 0·2% a.i. at 28-day intervals) failed to control either pathogen because of the development of carbendazim-insensitive strains of the fungi. Effective control of both pathogens and increased yields were obtained with an application of 0·4% a.i. thiram in October and November followed by an application of 0·2% a.i. iprodione in December and January.     

Studies on the biology of Botrytis species on overwintered salad onions

In the years 1973/4–1974/5, Botrytis cinerea was responsible for losses of 26% and 37% respectively in overwintered salad (green) onion crops grown at Wellesbourne. The fungus invaded the tips of cotyledonary and young true leaves and then grew downwards and inwards through the leaf axils to colonise the internal tissues and produce a collar rot which caused plants to collapse and die. More direct infection of the junction between an older and younger leaf produced a similar effect. Symptoms were rarely noticeable (except occasionally in the later stages of the disease) and affected plants disappeared unobtrusively. The incidence of collar rot increased as the rate of leaf production fell with the drop in temperatures in winter months but decreased as leaf growth resumed with increases in temperature in the spring. The fungus grew and sporulated well at low temperatures (5°C) and more inoculated seedlings developed collar rot when maintained at simulated winter temperatures (7°C) than when kept at simulated spring temperatures (15°C). B. squamosa occurred spasmodically producing white leaf lesions but caused no loss of plants. B. allii although present at a low incidence did not increase in the crops but in common with B. cinerea caused some damage to the bases of plants at harvest.     

Resistenz verschiedener Kultur- und Wildtomatenpflanzen (Lycopersicon spp.) gegenüber Botrytis cinerea Pers.

Resistance of different cultivated and wild tomato plants (Lycopersicon spp.) to Botrytis cinerea Pers. 20 provenances of different cultivated and wild tomato plants (Lycopersicon spp.) were screened for resistance to Botrytis cinerea Pers. using an in vitro-leaf necrosis test. The Botrytis resistance decreased with increasing age of the leaves corresponding to their insertion height (relative youth resistance respectively senescence susceptibility). The 6 B. cinerea-isolates used for inoculation differed significantly in virulence. With increasing inoculum age a virulence reduction of the various B. cinerea-isolates occurred. Within the investigated test plant collection 2 wild species –L. columbianum and L. hirsutum– proved to be resistant in each stage of development to all B. cinerea-isolates and additionally showed field resistance.     

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.

     

Discrimination amongst Alliums using an electronic nose

Pyruvic acid content determination and, to lesser extents, thiosulphinates determination and organoleptic tests are used for assessing the eating characteristics of onions and other Allium spp. Each of these methods has inherent limitations, especially when large numbers of samples are to be evaluated. With a view to developing a more convenient quality evaluation method, an electronic nose was used to discriminate flavour and aroma characteristics amongst garlic, leek, shallot, bulb onion and spring onion. Differences in relative sensor response to headspace volatiles over macerated samples of these five different Allium types were recorded. Principal Component Analysis (PCA) showed some separation among the five types. PCA and Mahalanobis' D² statistic suggested similarities in headspace volatiles for shallot, spring and bulb onions and differences for leek and, especially, garlic. Multiple linear regression analyses (Y =α+β₁X₁+β₁X₂; N_{(x, Y)}=5) of the first two principal component values (PCA 1 [X₁] and PCA 2 [X₂]) accounted for not less than 90% of the total variation in pyruvic acid concentration (Y1), total soluble solids content (Y2) and percentage dry matter content (Y3) of the Allium types. These relationships suggest that electronic nose discrimination was on the basis of quality characteristics that relate to Allium flavour. This work has shown that the electronic nose has potential for flavour characteristic‐based discrimination amongst Allium types. Future work will explore this potential within a single Allium spp.     

Botrytis species: relentless necrotrophic thugs or endophytes gone rogue?

Plant pathology has a long‐standing tradition of classifying microbes as pathogens, endophytes or saprophytes. Lifestyles of pathogens are categorized as biotrophic, necrotrophic or hemibiotrophic. Botrytis species are considered by many to be archetypal examples of necrotrophic fungi, with B. cinerea being the most extensively studied species because of its broad host range and economic impact. In this review, we discuss recent work which illustrates that B. cinerea is capable of colonizing plants internally, presumably as an endophyte, without causing any disease or stress symptoms. The extent of the facultative endophytic behaviour of B. cinerea and its relevance in the ecology and disease epidemiology may be vastly underestimated. Moreover, we discuss the recent discovery of a novel Botrytis species, B. deweyae, which normally grows as an endophyte in ornamental daylilies (Hemerocallis), but displays facultative pathogenic behaviour, and is increasingly causing economic damage. We propose that the emergence of endophytes ‘gone rogue’ as novel diseases may be related to increased inbreeding of hybrid lines and reduced genetic diversity. These observations lead us to argue that the sometimes inflexible classification of pathogenic microbes by their lifestyles requires serious reconsideration. There is much more variety to the interactions of Botrytis with its hosts than the eye (or the plant pathologist) can see, and this may be true for other microbes interacting with plants.     

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.     

A serological test for detecting Botrytis allii, the cause of neck rot of onion bulbs

Polyclonal antisera for the immunological detection of Botrytis allii, the cause of onion neck rot, were raised from cell wall and cytoplasmic fractions of the fungus, and from surface plate washings of two isolates of the pathogen. These antisera were used to develop an indirect ELISA for the detection of latent B. allii infection in stored onion bulbs. The antisera did not react with healthy onion tissue and showed only minimal recognition of fungi from other genera. Some cross-reactivity was observed with B. cinerea but not with other Botrytis spp. tested. In many instances following infection, fungal antigen could be detected earlier by ELISA than by direct culture. In tests on bulbs from a commercial store, the level of B. allii infection was found to be 3.3% by both ELISA and direct plating, but this result was achieved 7 days sooner by ELISA. In field tests, the indirect ELISA gave a good indication at harvest of the probable incidence during storage of neck rot in untreated and artificially inoculated plants, whilst culturing gave results consistently lower than the ELISA until bulbs had been in store for several months, when results for ELISA and culturing were the same. Spores applied to growing plants during the growing season led to greater levels of neck rot than did infested seed, indicating that field debris and waste from cold stores may be more important sources of inoculum in some years than seed contamination.     

Biological control of Botrytis cinerea on stem wounds with moderately halophilic bacteria

Infection of tomato stem wounds by Botrytis cinerea is an important problem which can cause severe economic losses in greenhouse tomato crops. Three moderately halophilic bacteria were tested for their ability to protect pruning wounds from attacks by B. cinerea under growth chamber conditions. The severity of the disease estimated by the length of the rotted stem was used to calculate the area under the disease progress curves (AUDPC). Bacterial antagonists (B1, B2 and B3) were very effective in controlling Botrytis-infection on the tomato stems during the first 6 days and later by the end of the experiment. Plants treated with Bacillus subtilis (B1) had the lowest AUDPC (0). It was followed by B. subtilis (B3) and Halomonas sp. (B2) with AUDPC of 9.8 and 17.02, respectively. While the B1 strain best inhibited grey mold development when applied as young culture (24 h), the B3 strain performed better as an older culture (48 h). In contrast to the results obtained with Bacillus species, the efficacy of the bacterial treatment B2 seems to be independent of the growth phase. The co-cultures with fungal spores and either B. subtilis (B1) or Halomonas sp. (B2) applied as a 24 h bacterial culture completely inhibited the germination of B. cinerea after 24 h at 21°C.     

Compounds from Allium species with cytotoxic and antimicrobial activity

Garlic (Allium sativum L.) is a bulb-shaped plant belonging to the Allium genus which also includes onions (Allium cepa L.), leek (Allium ampeloprasum L. var. porrum Gay), shallot (Allium ascalonicum L), scallion (A. fistulosum L.) and chives (Allium schoenoprasum L.). The biological activity of garlic has been known since ancient times. Babylonians, Egyptians, Phoenicians, Greeks and Romans used garlic as a remedy for intestinal disorders, respiratory infections, skin diseases, bacterial infections, worms, wounds and tumors. In particular, before the discovery of antibiotics, garlic has been used against amoebic dysentery and epidemic diseases such as typhus, cholera, diphtheria, and tuberculosis. To date, more than 3,000 publications scientifically supported the use of garlic in the ethno-medicine. But what makes garlic and Allium species effective against cancer? The effect of garlic may arise from its antibacterial properties or from its ability to block formation on cancer-causing substances, half the activation of cancer causing substances, enhance DNA repair, reduce cell proliferation or induce cell death. Epidemiological studies have found that an increase of consumptions of Allium spp. reduce the risk of prostate and gastric cancers and this has been mainly related to two main classes of compounds: the apolar sulphur compounds and the polar saponins. These latter compounds, compared to the more studied thiosulphinates, have the advantages of not being pungent and more stable during cooking. Recently, there has been increasing scientific attention given to such compounds. In this paper, the literature about the major volatile and non-volatile organic compounds of garlic and other Allium plants has been reviewed. Particular attention is given to the compounds possessing antibacterial and cytotoxic activity in garlic and in the other Allium species and their mechanism of action.     

Potential of Ulocladium atrum for biocontrol of onion leaf spot through suppression of sporulation of Botrytis spp.

Epidemics of onion leaf spotcaused by Botrytis spp. depend onnecrotic leaf tissue for inoculum build up inthe crop. Ulocladium atrum Preuss. is astrong competitor on necrotic above-groundplant tissues. The potential of the antagonistto reduce colonisation of necrotic leaf tissueby Botrytis spp. and subsequentsporulation was studied in two fieldexperiments. U. atrum colonised necrotictissues and consistently reduced thesporulation of fungal competitors. Althoughincidence of Botrytis spp. was low,significantly lower spore loads of Botrytis spp. were found on spore trapslocated within U. atrum treated onionplots as compared to untreated control plots.The number of leaf spots caused by Botrytis spp. was low in both fieldexperiments but was significantly reduced by60% after U. atrum applications in thesecond experiment. Spraying of the fungicideRonilan resulted in the same control level.Results show that U. atrum has apotential for biological control against diseases caused by Botrytis spp. in onions.     

Alternative Hosts for Fusarium spp. Causing Crown and Root Rot of Asparagus in Spain

Asparagus crown and root rot caused by Fusarium oxysporum f.sp. asparagi (Foa), F. proliferatum (Fp) and F. solani (Fs) result in early decline and loss of crop production. The role of several crop species on the survival of the Fusarium spp. was investigated. The root symptoms and plant weight of seven crop species were evaluated after inoculation with each of the three Fusarium spp. The number of colony‐forming units of the Fusarium spp. from root tissues was also determined. Garlic was shown to be a symptomatic host for Foa, Fp and Fs; Fs was also pathogenic to onion. Root colonization of garlic, onion, maize, wheat, potato and sunflower suggested that they are reservoirs of Foa, Fp and Fs from asparagus and demonstrated the importance of crop rotation on the development of this asparagus disease.     

Contribution of Pathogens to Peach Fruit Rot in Northern Greece and their Sensitivity to Iprodione, Carbendazim, Thiophanate-methyl and Tebuconazole Fungicides

This study identified the main pathogens causing fruit rots of mature peaches in northern Greece, the major peach producing area of Greece. The brown rot pathogen Monilinia laxa was responsible for approximately 70% and 78% of rotted peaches in 2005 and 2006 respectively. Serious damage (up to 5%) was also caused with the fungus Phomopsis amygdali. Other pathogens isolated from rotted peaches at a low percentage were Alternaria alternata, Aspergillus niger, Aspergillus flavus, Botrytis cinerea, Sclerotinia sclerotiorum, Fusarium spp., Colletotrichum gloeosporioides, Rhizopus stolonifer and Gilbertella persicaria. Most fungal isolates originated from the rotted peaches were tested for their sensitivity to the fungicides iprodione, carbendazim, thiophanate methyl and tebuconazole at label recommended concentrations. All fungicides inhibited the growth of M. laxa, A. niger, A. flavus, S. sclerotiorum, P. amygdali and B. cinerea on poisoned agar. Apart from iprodione, all other fungicides inhibited the mycelium growth of the pathogen Fusarium sp. The mycelium growth of Fusarium sp. was significantly less with iprodione than control. Only iprodione and tebuconazole were effective against A. alternata and R. stolonifer. Tebuconazole inhibited the mycelium growth of R. stolonifer, while iprodione reduced significantly in comparison to control. The mycelium growth of the fungus C. gloeosporioides was inhibited by tebuconazole and reduced significantly by the fungicides thiophanate methyl, carbendazim and iprodione. Among all the fungi tested, only M. laxa and B. cinerea isolates were found resistant to benzimidazoles [the EC50 (50% effective concentration) value was 100–200 mg/l and 200–300 mg/l for the largest number of thiophanate methyl‐ and carbendazim‐resistant M. laxa isolates respectively, while the biggest number of B. cinerea thiophanate methyl‐ and carbendazim‐resistant isolates showed EC50 value 200–300 mg/l and 300–400 mg/l, respectively]. However, these strains were sensitive to tebuconazole and iprodione. Therefore, these fungicides can be used as an alternative method to control benzimidazole‐resistant Monilinia and Botrytis isolates.