Survey and characterization of potyviruses and their strains of Allium species

Nearly 5700 plants of 14 cultivated and 8 wildAllium species and varieties from the Netherlands and other parts of the world, were tested for infection with aphid-borne potyviruses by ELISA, electron microscope decoration tests and/or inoculation onto test plants. This resulted in the detection of two known viruses, viz. leek yellow stripe virus (LYSV) and onion yellow dwarf virus (OYDV), and the discovery and characterization of two new viruses, viz. shallot yellow stripe virus (SYSV) and Welsh onion yellow stripe virus (WoYSV), and of six strains of these viruses. ‘Garlic mosaic’, ‘barlic yellow streak’, ‘onion mosaic’, ‘shallot mosaic’, ‘shallot X’, and ‘shallot yellows’ viruses, incompletely described in the literature, are now reidentified as well-known viruses or as strains or mixtures of such viruses. ‘Garlic yellow stripe virus’ is also a complex containing a potyvirus possibly differing from the viruses found in this survey. The symptoms of the potyviruses studied varied widely and ranged from mild to severe chlorotic to yellow striping of leaves, and they are of little diagnostic importance.LYSV was found in vegetatively propagated pearl onion (A. ampeloprasum var.sectivum) from Europe and Asia. It has decreased in leek crops (A. ampeloprasum var.porrum) in the Netherlands since the 1970, apparently due to resistance in new cultivars. OYDV was common in onion (A. cepa var.cepa) from the former USSR and North Africa, and in European cultivars of shallot (A. cepa var.ascalonicum), with the exception of the highly resistant ‘Santé’, but was not detected during this survey in Asian shallot. European samples of ever-ready onion (A. cepa var.perutile), multiplier onion (A. cepa var.aggregatum) and tree onion (A. cepa var.viviparum) contained OYDV. It was also found in sand leek (A. scorodoprasum) from european gene collections. A strain of OYDV from onion and shallot in Morocco and Spain was virulent on onion and shallot cultivars resistant to common OYDV, as reported early for a similar isolate in the USA.Asian shallot appeared generally infected with the new SYSV, similar to OYDV in host range and symptoms but serologically distinct. It was not detected in onion and shallot from Europe or North Africa. A virulent strain of this virus caused striping in sap-inoculated garlic (A. sativum) and Formosan lily (Lilium formosanum). The new WoYSV, infecting Welsh onion in Indonesia and Japan, was earlier described in Japan as OYDV from rakkyo and Welsh onion. It appeared serologically closely related to SYSV and distantly to OYDV, but differed in its host range.Host-specific strains of LYSV and OYDV were detected in garlic, wild garlic (A. longicuspis), an unidentifiedAllium species (suffix-G), and great-headed garlic (A. ampeloprasum var.holmense) (suffix-GhG)., LYSV-G and OYDV-G infected on average 45% and 73%, respectively, of the garlic samples of worldwide origin. Symptoms of isolates of both strains varied in severity, implying the necessity of serological tests for disease diagnosis and health certification. LYSV-GhG was the cause of yellow striping in 93% of the great-headed garlic plants tested, mainly from the Mediterranean area. One sample was also infected with OYDV-GhG.Many samples from vegetatively propagated crops grown from non-certified planting stock contained a few plants free of potyviruses, implying the possibility to obtain healthy (and possibly resistant) selections of such cultivars avoiding meristem-tip culture. Cross-protection of garlic sets by a mild potyvirus isolate seems to be an alternative to the use of vulnerable virus-free sets.Generally, viruses and virus strains could not be transmitted to anyAllium species other than their natural host, except to the highly susceptible crow garlic (A. vineale). This species, and other predominantly vegetatively propagating wildAllium spp. (field garlic,A. oleraceum; ramsons,A. ursinum; sand leek), were found not to be reservoirs of viruses that might infectAllium crops in the netherlands. Streaking in vegetatively propagated wild leeks (A. ampeloprasum and closely related species) originating from the Mediterranean area and Asia was due to an undescribed miteborne virus. The survey confirmed that spread of potyviruses inAllium crops in the Netherlands is from planting sets, and from a neighbouring crop only if of the same species.     

Viral dieback of carrot and other umbelliferae caused by the Anthriscus strain of parsnip yellow fleck virus,and its distinction from carrot motley dwarf

Viral dieback of carrot, chervil, coriander, dill and wild Umbelliferae is described. Disease incidence in carrot crops grown for seed is often high but low in ware carrot. There is no secondary spread in carrot crops.The causal virus was identified as theAnthriscus strain of parsnip yellow fleck virus (PYFV) transmitted byCavariella aegopodii from cow parsley(Anthriscus sylvestris). Nicotiana benthamiana was practically indespensable for isolation of PYFV by sap transmission from plants with viral dieback.No immunity was found in 12 carrot cultivars or in wild carrot. Disease control with a systemic insecticide had limited effect.Carrot red leaf virus and carrot mottle virus were commonly found in carrot, but they did not cause dieback symptoms. Cucumber mosaic virus, parsnip mosaic virus and a virus resembling that of carrot yellow leaf were occasionally isolated from carrot. Symptoms due to mycoplasma were also observed.Samenvatting Bij de zaadteelt van peen is in ons land reeds lang een schadelijke, vroeg in het seizoen optredende instervingsziekte bekend als voorjaarsziekte of het zwart. Planten vallen op door necrose van jonge spruiten (insterving). Soms gaat meer dan de helft van het gewas verloren. Voor consumptie geteelde peen wordt echter nauwelijks aangetast. De ziekte is nu ook gevonden bij dille, kervel, koriander en wilde schermbloemigen.Uit zieke planten en ook vaak uit symptoomloze fluitekruidplanten werd een virus geïsoleerd waarmee de insterving kon worden gereproduceerd. Het werd herkend als de fluitekruid-(ofAnthriscus-)stam van pastinakegeelvlekvirus (PYFV) op grond van waardplanten, symptomen, serologie en overdracht doorCavariella aegopodii met als onmisbare helper hetAnthriscus-vergelingsvirus (AYV), dat ook in fluitekruid voorkomt. Het gebruik vanNicotiana benthamiana als toetsplant maakte isolatie uit planten met virusinsterving mogelijk. Voor de ziekte wordt nu de naam virusinsterving van schermbloemigen voorgesteld.Peenroodbladigheid veroorzaakt door peenroodbladvirus, dat meestal samengaat met peenvlekkenvirus, bleek ook algemeen voor te komen. Deze twee virussen spelen geen rol bij het veroorzaken van virusinsterving, zoals wel werd aangenomen. Beide ziekten zijn geheel verschillend in symptomatologie en epidemiologie. Incidenteel werden komkommermozaïekvirus, pastinakemozaïekvirus en een virus gelijkend op peengeelbladvirus in aangetroffen. Ook werd eenmaal een aan een mycoplasma toe te schrijven ziekte geconstateerd.Virusinsterving bleek epidemiologisch te kunnen worden verklaard door de massale jaarlijkse migratie vanC. aegopodii in het voorjaar, waarbij PYFV van fluitekruid naar peen en andere schermbloemigen wordt verspreid. Door onvatbaarheid van peen voor het helpervirus (AYV) treedt in dit gewas geen secundaire verspreiding op.In geen van 12 peenrassen en wilde peen werd resistentie aangetroffen. Toepassing van een systemisch insekticide bleek in eerder onderzoek slechts een beperkt effect te hebben. Peenzaadteelt in gebieden met minder bladluizen, zoals het noorden des lands, lijkt aan te bevelen, maar verder lijkt de ziekte niet te bestrijden.Work in partial fulfillment of requirements for master's training at Agricultural University, Wageningen     

Viruses affecting tomato crops in Serbia

In a two-year survey (2011–2012), 3220 samples were collected and analyzed in order to determine the presence and distribution of viruses in tomato crops at 56 localities of 18 districts in Serbia. Out of 12 viruses tested, Cucumber mosaic virus (CMV), Potato virus Y (PVY), Alfalfa mosaic virus (AMV), Tomato spotted wilt virus (TSWV), Tomato mosaic virus (ToMV) and Tobacco mosaic virus (TMV) were detected in 42.1, 40, 11, 8.6, 2.3 and 1.3% of the total tested samples, respectively. The results revealed that CMV was prevalent in 2011 and PVY in 2012. CMV and PVY, apart from being predominant, were also the most widespread viruses. In general, single infections were the most frequent type of infection. Additionally, the most common mixed infections were double infections and the most prevalent combination was CMV and PVY. In 2011, the incidence of diseases and the percentage of all infection types were significantly higher than in 2012. Furthermore, in 2011, regardless of total single infections being prevalent compared to mixed infections, two prevailing viruses were commonly detected in mixed infections. The additional molecular testing of ELISA-negative samples using virus specific primers did not reveal the presence of Pepino mosaic virus (PepMV), Tomato yellow leaf curl virus (TYLC), Tomato infections chlorosis virus (TICV) and Tomato chlorosis virus (ToCV).     

Some experiments and considerations on the identification of witches' broom viruses,especially in clovers,in the Netherlands and Italy

Witches' broom phenomena (witches' broom growth + antholysis) observed inTropaeolum majus and in clovers in the Netherlands and in several wild and cultivated plants in Italy were demonstrated to be due to virus infection. The virus(es) could be transmitted by grafting, through dodder and by means of leaf-hoppers (Euscelis spp. primarily). The virus isolates found in both countries did not differ appreciably in the symptoms they caused. Many of the deviations concerned have been known for a long time as teratological phenomena. In the extensive literature considerable confusion exists concerning the identity of several witches' broom virus diseases. They constitute a good example of the problem of virus variability. A continuous splitting of witches' broom viruses on the basis of slight differences in symptom expression or of vector specificity does not seem justified. Since no intrinsic properties of the virus(es) concerned are known, the only conclusion that can be drawn from the information available is that the Dutch and the Italian isolates show a great similarity to aster yellows virus as well as to tomato big bud, stolbur and other witches' broom viruses.     

Conidial sporulation of <Emphasis Type="Italic">Stemphylium solani</Emphasis> under laboratory conditions and infectivity of the inoculum produced <Emphasis Type="Italic">in vitro</Emphasis>

Potato virus Y (PVY) is the type-species of the genus Potyvirus, family Potyviridae, being reported as a major tomato (Solanum lycopersicum L.) pathogen in several regions of the world. Pepper yellow mosaic virus (PepYMV) was originally described as a resistance-breaking Potato virus Y (PVY) isolate on Capsicum annuum L. cultivars, and afterwards it was also reported infecting tomatoes in Brazil. In the present work, a search for sources of resistance to both PepYMV and PVY was conducted in a collection of 119 accessions belonging to seven Solanum (section Lycopersicon) species. This germplasm was initially evaluated to PepYMV reaction by mechanical inoculation followed by symptom observations and ELISA. Potential PepYMV resistance sources were identified for the first time in S. habrochaites, S. peruvianum, S. corneliomuelleri, S. chilense, S. pimpinellifolium, and one accession derived from an interspecific cross (S. lycopersicum x S. peruvianum). A sub-group of 24 accessions with negative serology for PepYMV was also challenged with a PVY isolate, followed by serological and molecular detection with universal primers. Solanum habrochaites ‘L.03683’ and ‘L.03684’ were the only accessions found with stable resistance to both viruses. These results confirm S. habrochaites as the most important source of multiple resistance factor(s) to distinct Potyvirus species.     

Conidial density of <Emphasis Type="Italic">Monilinia</Emphasis> spp. on peach fruit surfaces in relation to the incidences of latent infections and brown rot

To evaluate the effect of conidial density of Monilinia spp. on the fruit surface on the incidence of latent infection and brown rot in peaches, eleven field surveys were performed in commercial orchards located in Cataluña, Spain over four growing seasons from 2002 to 2005, and nine surveys were conducted to determine the sources of overwintered Monilinia spp. inoculum. There was a significant positive relationship (r?=?0.69) between the numbers of conidia of Monilinia spp. on the fruit surface and the incidence of latent infections, but not with brown rot at harvest. Although mummified fruit, twigs and pits have been identified as being able to carry the pathogen from year to year in peaches grown in Spanish orchards, no relationships between any of these sources and the numbers of conidia on the fruit surface, or incidence of latent infection or brown rot were found. The effect of temperature (T), solar radiation (SR), rainfall (R) and wind speed (WS) on the area under the number of conidia of Monilinia spp. curve (AUncC) on peach surfaces was analysed. Regression analysis revealed that T, SR, R, and WS could account for 99% of the total variation in the area of the AUncC on peach surfaces. Thus, in order to reduce the incidence of latent infection and brown rot it is essential not only to remove the sources of primary inoculum but also to reduce the number of Monilinia spp. conidia on the fruit surface. Furthermore, the sources of airborne conidia of Monilinia spp. should be taken into consideration in disease management programmes in Spain.     

Fast detection by loop-mediated isothermal amplification (LAMP) of the three begomovirus species infecting tomato in Panama

Potato yellow mosaic Panama virus (PYMPV), Tomato leaf curl Sinaloa virus (ToLCSiV) and Tomato yellow mottle virus (TYMoV) of genus Begomovirus (family Geminiviridae) are the only three begomovirus species detected infecting tomato (Solanum lycopersicum L.) in Panama. PYMPV, ToLCSiV and TYMoV induce symptoms of stunting, yellowing, curling, distortion of leaves and reduction of fruit size and cause important economic loses. A loop-mediated amplification under isothermal conditions (LAMP) assay was developed for the individual detection of these three begomovirus species by using a set of three primer pairs specific per each one of them. Amplification products were visualized by gel electrophoresis or direct Gel-Red staining of DNA into the reaction tube. PYMPV, ToLCSiV and TYMoV were detected in total DNA extracts obtained from different plant tissues such as leaves, stems, flowers, fruits and roots of infected tomato plants collected in different production regions of Panama. LAMP sensitivity was similar to that of conventional PCR but, the first procedure was faster and cheaper than the last one. Moreover, all three viruses were successfully detected by LAMP and not by conventional PCR from sap extracts obtained from leaf tissues of infected tomato plants which were embedded into 3MM Whatman paper and stored several days, facilitating the samples processing as well as the material movement among different laboratories. Therefore, LAMP is a specific, rapid and cheap procedure to detect all three begomoviruses infecting tomato in Panama and it is suitable for field surveys and sanitation programs.     

Synergy between grapevine vitiviruses and grapevine leafroll viruses

An interactive relationship between vitiviruses and grapevine leafroll viruses was characterized in grapevine. Grapevine viruses A and B (GVA and GVB) were found more frequently in the presence of co-infecting Grapevine leafroll associated viruses (GLRaV-1, ?2 or ?3) than in their absence. The titers of the vitiviruses in co-infection with leafroll viruses were found to be higher than were their titers in the absence of leafroll virus infection. The occurrence of vitivirus-associated stem-pitting symptoms was correlated with leafroll virus co-infection. Specific pairing associations on the species level were found between different viti- and leafroll virus species: GVB was associated preferentially with GLRaV-2; GVA was associated preferentially with GLRaV-1 and GLRaV-3. In contrast to the increase in vitivirus titer seen with leafroll virus co-infection, the incidence and titer of grapevine leafroll virus appeared to be unaltered by vitivirus co-infection. The potential for a synergistic enhancement of grapevine disease in co-infected vines is discussed.     

Haplotypes of ‘<Emphasis Type="Italic">Candidatus</Emphasis> Liberibacter solanacearum’ identified in Umbeliferous crops in Spain

‘Candidatus Liberibacter solanacearum’ is a phloem-limited Gram-negative bacterium that causes serious damage to different crops of the botanical families Solanaceae and Apiaceae. Five haplotypes have been described: LsoA and LsoB are present in solanaceous crops in America and vectored by the tomato/potato psyllid Bactericera cockerelli; LsoC affects carrots from Northern and Central Europe, and is transmitted by the carrot psyllid Trioza apicalis; haplotypes LsoD and LsoE are present in Southern Europe and Morocco in carrot and celery, and are associated with the psyllid Bactericera trigonica. Thirty-four ‘Ca. L. solanacearum’ isolates were collected in six different regions of Spain from distinct Apiaceae hosts (carrot, celery, parsley and parsnip) in eight consecutive years and were analysed. Their haplotypes were determined by a sequence analysis of 16S ribosomal RNA, the 16S–26S ribosomal RNA intergenic spacer, and the 23S ribosomal RNA and rplJ and rplL genes. Both haplotypes LsoD and LsoE were found across Spain, and no host specificity appeared between these two haplotypes. This is the first report of ‘Ca. L. solanacearum’ associated with parsley and parsnip.     

Identification and partial characterization of a <Emphasis Type="Italic">Carica papaya</Emphasis>-infecting isolate of <Emphasis Type="Italic">Alfalfa mosaic virus</Emphasis> in Brazil

A Carica papaya plant with severe yellow leaf mosaic, leaf distortion, and systemic necrosis was found in the municipality of Piracicaba, state of São Paulo, Brazil. Transmission electron microscopy (TEM) analysis revealed the presence of potyvirus-like particles and bacilliform particles similar to those of the Alfamovirus genus. The potyvirus was identified as Papaya ringspot virus-type P (PRSV-P). Biological, serological, and molecular studies confirmed the bacilliform virus as an isolate of Alfalfa mosaic virus (AMV). Partial nucleotide and amino acid sequences of the coat protein gene of this AMV isolate shared 97–98% identity with the AMV isolates in the GenBank database. This report is the first of the natural infection of papaya plants by AMV.     

First interception of the asiatic Bamboo longhorn, <Emphasis Type="Italic">Chlorophorus annularis</Emphasis> (F., 1787) (Coleoptera,Cerambycidae) in Italy

This study provide information on the first occurrence in Italy of the Coleoptera Cerambycidae Chlorophorus annularis (Fabricius, 1787). It is a species naturally and widely distributed in Asia and in oriental tropical and subtropical areas. This cerambyx is a post-harvest pest of bamboo belonging to several genera as Bambusa, Dendrocalamus, Phyllostachys, Sinocalamus, but it can also infest cultivated plants as Citrus spp., Gossypium, Liquidambar spp., Saccharum officinarum L., Vitis spp., and Zea mays L.     

Identification and characterization of <Emphasis Type="Italic">Colletotrichum</Emphasis> spp. associated with chili anthracnose in peninsular Malaysia

Anthracnose fruit rot caused by Colletotrichum spp. is a serious post-harvest disease of chili fruits (Capsicum spp.). One hundred-thirty isolates of Colletotrichum spp. were isolated from anthracnose of green and red cayenne pepper (Capsicum annuum) and bird’s eye chili (Capsicum frutescens). The isolates were morphologically identified as Colletotrichum acutatum sensu lato (62 isolates), Colletotrichum truncatum (54 isolates), and Colletotrichum gloeosporioides sensu lato (14 isolates). Molecular identification and phylogenetic analyses were based on internal transcribed spacer regions, β-tubulin, actin, and glyceraldehyde-3-phosphate dehydrogenase genes, and the isolates were re-identified as C. scovillei (58 isolates), C. truncatum (54 isolates), C. siamense (11 isolates), C. fioriniae (four isolates), and C. fructicola (3 isolates). Maximum likelihood trees using combined sequences showed that isolates of the same species grouped in the same main clade with the isolates used for comparison. Pathogenicity testing showed that the tested isolates from each species were pathogenic towards green and red Capsicum annuum and Capsicum frutescens upon treatment of wounded fruit, using both the mycelial plug and conidial suspension methods. Only five isolates of C. truncatum and seven isolates of C. scovillei were found to be pathogenic upon treatment of unwounded fruit. The occurrence of five Colletotrichum spp. (C. siamense, C. fructicola, C. scovillei, C. fioriniae, and C. truncatum) associated with chili anthracnose in Peninsular Malaysia indicates that correct species identification is important to formulate not only effective disease management, but also effective quarantine policy.     

Biochemical,physiological, and molecular characterization of <Emphasis Type="Italic">Dickeya dianthicola</Emphasis> (formerly named <Emphasis Type="Italic"> Erwinia chrysanthemi</Emphasis>) causing potato blackleg disease in Japan

The taxonomic assignment of Japanese potato blackleg isolates of Dickeya spp. has not been confirmed after the changes in their former name, Erwinia chrysanthemi. Therefore, we investigated and identified 23 representative isolates of Dickeya spp. from symptomatic stems of potatoes in Japan, with biochemical tests and phylogenetic sequence analysis using recA, dnaX, rpoD, gyrB, and 16S rDNA sequences. Results of our biochemical tests showed that all isolates can be assigned to phenon 5 and biovar 1, which are associated with D. dianthicola. Based on the recA, dnaX, rpoD, gyrB, and 16S rDNA sequences, all isolates are in the same clade with D. dianthicola and were clearly distinguished from D. chrysanthemi, D. dadantii, D. dadantii subsp. dieffenbachiae, D. solani, D. zeae, and D. paradisiaca. Therefore, we conclude that Dickeya spp. isolated from potatoes with blackleg symptoms in Japan are D. dianthicola.     

Natural infection of <Emphasis Type="Italic">Nicandra physaloides</Emphasis> by <Emphasis Type="Italic">Tomato severe rugose virus</Emphasis> in Brazil

Nicandra physaloides, a common weed in South America, was found to be infected by an isolate of Tomato severe rugose virus (ToSRV), a bipartite begomovirus. The plants developed severe yellow rugose mosaic and were collected in São Paulo State, Brazil. This isolate of ToSRV was transmitted by Bemisia tabaci B biotype from infected plants of N. physaloides to healthy plants of N. physaloides and tomato in a glasshouse. This is the first report of natural infection of N. physaloides by ToSRV in Brazil.     

Construction of a recombinant strain of <Emphasis Type="Italic">Pseudomonas fluorescens</Emphasis> producing both phenazine-1-carboxylic acid and cyclic lipopeptide for the biocontrol of take-all disease of wheat

Four Neofabraea species are responsible for bull’s eye rot, which is an important postharvest disease of apples and pears. The species diversity of its causal agents in Europe has not been thoroughly explored using molecular genetic methods. Eighty-one Neofabraea isolates were obtained mostly from apples with bull’s eye rot symptoms in the Czech Republic over a two year period. The isolates were identified using PCR fingerprinting and DNA sequencing of the ITS rDNA region, the mitochondrial SSU rDNA and the β-tubulin and EF1α genes. The most common species was N. alba (89 %), followed by N. perennans (5 %) and N. kienholzii (5 %). This is the third published record of N. kienholzii in Europe. The species identity of the isolate CPPF507, which was placed close to N. kienholzii, remains unclear. EF1α was shown to be a suitable marker for the identification of species of the genus Neofabraea and was comparable to the previously used β-tubulin gene. Furthermore, the aggressiveness of individual species was compared and species distribution across Europe was summarized. N. perennans and isolate CPPF507 proved to be the most aggressive, whereas the least aggressive was N. kienholzii. Two N. alba isolates isolated from symptomless apple fruits and leaves were pathogenic to apples in the infection tests.     

Use of zoospores of Polymyxa betae in screening beet seedlings for resistance to beet necrotic yellow vein virus

A system to culture viruliferousPolymyxa betae and to produce zoospores is described. The zoo spores were used for inoculation of beet seedlings, grown in nutrient solution, in tests for resistance to beet necrotic yellow vein virus (BNYVV). On most occasions in a time course experiment, and with various zoospore cultures, the partially resistant cultivar Rima and the accession Holly-1–4 had virus concentrations similar to the susceptible cultivar Regina, but the virus concentration inBeta vulgaris ssp.maritima accession WB42 was significantly lower (P<0.05). ‘Regina’ could be distinguished from various resistant accessions by a significantly higher virus concentration (P<0.05) shortly after inoculation, or after transplanting the seedlings from the nutrient solution into sand. Results of screening for resistance to BNYVV, using zoospores for inoculation, did not correspond with results of a test in which infested soil was used.Tests in which seedlings are grown in nutrient solution and inoculated with zoospores are suitable for the detection of accessions with a high level of resistance to BNYVV. To obtain virus infection in all plants, the optimal density of the zoospore suspension should first be determined and plants should be assayed shortly after inoculation.