Carlavirus isolates from cultivated Allium species represent three viruses

From 12 cultivated and mostly vegetatively propagatedAllium species and varieties tested for carlavirus infections, 94 virus isolates were obtained which varied greatly on indicator hosts.Chenopodium amaranticolor, C. quinoa, Celosia argentea var.plumosa Geisha,Nicotiana hesperis accession 67A andN. occidentalis accession P1 proved valuable for detection, isolation and propagation of part of the isolates. The latter three species are new experimental hosts for carlaviruses ofAllium species. Other isolates could only be transmitted toAllium species such as crow garlic (A. vineale) leek (A. ampeloprasum var.porrum) and onion (A. cepa var.cepa). The isolates were grouped into three viruses by differential hosts and host reactions and their reaction with four antisera.Shallot latent virus (SLV) was found in ever-ready onion (A. cepa var.perutile), grey shallot (unidentifiedAllium species), multiplier onion (A. cepa var.aggregatum), pearl onion (A. ampeloprasum var.sectivum), rakkyo (A. chinense), shallot (A. cepa var.ascalonicum), and Welsh onion (A. fistulosum). Virus isolates from garlic and Asian shallot, fully reacting with antiserum to SLV but differing in host reactions from the SLV type-isolate, are now described as garlic strain (SLV-G) and Asian shallot strain of the virus, respectively. The garlic latent virus from garlic described in Japan is now considered identical with SLV-G.A carlavirus almost universal in garlic, and also found in great-headed garlic (A. ampeloprasum var.holmense), in an unidentifiedAllium species, and occasionally in leek, did not react with the antisera to SLV and the Japanese garlic latent virus, and is now described as the new garlic common latent virus (GCLV). It appeared identical to a virus erroneously identified in Germany as garlic latent virus.The new Sint-Jan's-onion latent virus (SjoLV) from Utrechtse Sint-Jan's onion (unidentifiedAllium species) from the Netherlands and similar crops originating from other countries, did not induce reactions in test plants and could only be detected by electron microscope decoration tests. It reacted equally wellwith the antisera to SLV and GCLV. It was also present together with SLV in ever-ready onion, pearl onion, rakkyo, shallot, and Welsh onion. Garlic latent virus reported in Japan from hosts other than garlic should be regarded as SLV, SjoLV, or a mixture of these viruses.The carlaviruses were not detected in wild plants of ramsons (A. ursinum), and of the predominantly vegetatively propagated crow garlic (A. vineale), field garlic (A. oleraceum), and sand leek (A. scorodoprasum), collected in the Netherlands.Severe reactions in the indicator hosts incidentally revealed soil-borne viruses in shallot (the nepovirusesArabis mosaic virus (ArMV) and tomato black ring virus) and crow garlic (ArMV and the tobravirus tobacco rattle virus). Tobacco necrosis virus (necrovirus) was detected in roots of shallot.     

<Emphasis Type="Italic">Pseudomonas syringae</Emphasis> pv. <Emphasis Type="Italic">alliifistulosi</Emphasis> pv. nov., the causal agent of bacterial leaf spot of onions

In 1972, bacterial leaf spot of onion (BLSO) was first recorded in Japan by Goto. The pathogen was considered as a pathovar of Pseudomonas syringae specifically causing disease on onion and Welsh onion, but it has not been taxonomically investigated in detail. In 2012 and 2014, a disease suspected as BLSO re-emerged on onion in Shizuoka and Hyogo Prefectures, Japan, respectively. A pathogenic bacterium isolated from the infected onions was thought to be the BLSO agent after preliminary examinations. Strains isolated from BLSO in 1969, 1986, 1987, 2012 and 2014 were characterized and compared with the causal agent of bacterial blight of leek (P. syringae pv. porri), which causes similar symptoms on Allium plants. The result of rep-PCR distinguished the BLSO agent from P. syringae pv. porri. Multilocus sequence analysis on housekeeping genes and hrp genes encoding the type-III secretion system revealed that the strains of the BLSO agent clustered independently of P. syringae pv. porri. The BLSO agent and P. syringae pv. porri also differed in utilization of erythritol, dl-homoserine, glutaric acid and other bacteriological characteristics and caused different reactions on onion, Welsh onions, chives, shallot, rakkyo, leek, garlic and Chinese chive. Thus, the BLSO agent clearly differs from P. syringae pv. porri and is considered to be a new pathovar of P. syringae. The name P. syringae pv. alliifistulosi is proposed with pathotype strain ICMP3414.     

Double-edged effects of the cryogenic technique for virus eradication and preservation in shallot shoot tips

Plant virus eradication is a prerequisite for the use of virus-free propagules for sustainable crop production. In contrast, virus preservation is required for all types of applied and basic research of viruses. Shoot tip cryopreservation can act as a double-edged strategy, facilitating either virus eradication or virus preservation in cryoderived plants. Here, we tested the efficacies of shoot tip cryopreservation for virus eradication and preservation in shallot (Allium cepa var. aggregatum). In vitro stock shallot shoots infected with onion yellow dwarf virus (OYDV) and shallot latent virus were thermotreated for 0, 2, and 4 weeks at a constant temperature of 36℃ before shoot tip cryopreservation. Results showed that viruses were preserved in recovered shoots when thermotherapy was not applied. Although thermotherapy lowered the regrowth levels of cryotreated shoot tips, the efficiency of virus eradication increased from 5% to 54%. Immunolocalization of OYDV and histological observation of cryotreated shoot tips showed the high frequency of virus preservation was due to the viral invasion of cells close to the apical meristem and the high proportion of cells surviving. Four weeks of thermotherapy drastically decreased the distribution of OYDV, as well as the percentage of surviving cells within the shoot tips, thereby promoting virus eradication. Virus-free plants obtained from combining thermotherapy with cryotherapy showed significantly improved vegetative growth and bulb production. The present study reports how thermotherapy can act as a trigger to facilitate either the safe preservation of Allium viruses or the production of virus-free shallot plants.     

A new pathovar of <Emphasis Type="Italic">Pseudomonas syringae</Emphasis>, pathovar <Emphasis Type="Italic">allii,</Emphasis> isolated from onion plants exhibiting symptoms of blight

Bacterial pathogens of onion (Allium cepa) plants and their undetected presence in seed can cause substantial losses to onion producers. In this study, 23 Pseudomonas syringae strains were isolated from five onion plants and 18 onion seeds. The symptoms on leaves and seed stalks were irregular lesions with necrotic centres and water soaked margins. The aim of the study was to characterize these P. syringae strains using Biolog GN III carbon source utilization, multilocus sequence typing (MLST) based on partial sequences of four housekeeping genes (cts, gapA, gyrB and rpoD), and to determine whether or not the strains were pathogenic on onion (cv. Granex 33), chive (Allium schoenoprasum cv. Grasiue), leek (Allium porrum cv. Giant Italian) and spring onion (Allium fistulosum cv. Salotte) plants. Both Biolog analysis and MLST analysis separated onion strains into two clusters, one supporting the existence of a new pathovar of P. syringae, and the other corresponding to P. syringae pv. porri. Pseudomonas syringae strains belonging to the new pathovar we pathogenic only on onion plants of the Allium spp. tested. The results of this study revealed that bacterial blight of onion in South Africa is caused by two pathovars of P. syringae sensu lato, namely, the newly described pathovar, allii, and P. syringae pv. porri. The symptoms caused by these two pathovars in the field were indistinguishable.     

Incidence of Viruses Infecting Allium Spp. in Greece

A survey identified viruses infecting garlic, leek and onion crops and wild Allium species in Greece. Virus identification was based on ELISA, immunoelectron microscopy, and occasionally on RT-PCR. Samples of cultivated Allium species were collected from five districts, whereas samples of twenty-seven wild Allium species were also collected from all over Greece. Onion yellow dwarf virus (OYDV) and Leek yellow stripe virus (LYSV) were identified in 98.5% and 83.7% of all samples, respectively, and were found in all regions. Allexiviruses were also detected in all regions and their incidence ranged from 62.5% to 70.5% (depending on region and type of allexivirus). Garlic common latent virus (GCLV) was detected in samples from Arcadia (97.6%) and Evia (18.0%) and in one field in Larissa (23.0%). Shallot latent virus (SLV) was found only in two areas (Evros and Theva) and in fields planted with imported propagative material, from Iran and China. The incidence of virus-like symptoms in leek crops ranged from 10.0% to 90.0% in different regions and fields and all symptomatic plants were found to be infected by LYSV. Onion yellow dwarf virus was only found in seven symptomatic onion samples from southern Greece. Allium ampeloprasum spp. ampeloprasum and Allium flavum, were the only wild Allium species found to be infected with LYSV. Finally Turnip mosaic virus (TuMV) was found in A. sphaerocephalon, A. guttatum, A. subhirsutum, and A. neapolitanum.     

Leek yellow stripe virus and its relationships to onion yellow dwarf virus; characterization,ecology and possible control

Since 1970 yellow stripe disease of leek (Allium porrum) has developed epidemically in the south-eastern part of the Netherlands coincident with increasing year-around cultivation of the crop. Many autumn and winter crops now become totally infected. Apparently similar attacks, first reported in Germany in 1937, are increasingly attracting attention in various European countries. This paper describes the leek yellow stripe virus (LYSV) as a new potyvirus related to onion yellow dwarf virus (OYDV), which was so far incompletely described. LYSV is hardly infectious to onion (A. cepa) and shallot (A. ascalonicum) and OYDV behaves similarly on leek. The leek virus further differs from OYDV in not being infectious toA. fistulosum and in causing distinct local lesions onChenopodium amaranticolor andC. quinoa. The two viruses closely resemble each other in external symptoms in their respective hosts, in persistence of infectivity in expressed sap, and in particle morphology and length (LYSV 820 nm; OYDV 833 nm). Intracytoplasmic inclusion bodies slightly differ. Further biophysical characters of the two viruses, such as sedimentation coefficient (OYDV 143 S), buoyant density in CsCl (LYSV 1.326; OYDV 1.306, or 1.258 in Cs₂SO₄), and molecular mass of coat protein subunit (LYSV 34000; OYDV 30000 dalton), are characteristic of the potyvirus group, but do not assist in judging their relationships. Serologically they are only distantly related if at all. The leek virus is not seed-borne. It is aphid-transmitted in the non-persistent manner and its main epidemic build-up is during late summer and autumn. The sole sources of infection are nearby leek crops. Awaiting the development of resistant leek cultivars, it is advised to avoid sowing leek seed beds and planting spring crops near overwintering leek, and to remove infected plants showing up during summer.     

Further Evidence that Shallot Yellow Stripe Virus (SYSV) Is a Distinct Potyvirus and Reidentification of Welsh Onion Yellow Stripe Virus as a SYSV Strain

ABSTRACT An antiserum to shallot yellow stripe virus (SYSV) was raised and used in combination with a range of other antisera to potyviruses of Allium spp. in electron microscopic decoration experiments. The serological results corroborated an earlier finding that the type isolates of SYSV and Welsh onion yellow stripe virus (WoYSV) are closely related to each other and only distantly related to onion yellow dwarf (OYDV) and leek yellow stripe (LYSV) viruses, the two other major potyviruses infecting Allium spp. Moreover, the decoration results indicated that Japanese potyviruses named OYDV and Wakegi yellow dwarf virus are isolates of SYSV. Sequence analysis of the 3'-terminal regions of the SYSV and WoYSV ge-nomes revealed coat protein (CP) amino acid and 3'-nontranslated region (3'-NTR) nucleotide sequence identities of 95 and 89%, respectively. The CP amino acid and 3'-NTR nucleotide sequences of these viruses differed from those of OYDV and LYSV by >25 and >67%, respectively. The serological and molecular studies showed that SYSV and WoYSV are different strains of a potyvirus distinct from OYDV and LYSV. For priority reasons, we propose that these strains together with the Wakegi-type isolates of OYDV described in Japan be referred to as SYSV and that SYSV isolates from Allium spp. other than shallot be designated as the Welsh onion strain of SYSV (SYSV-Wo).     

Mite-borne virus isolates from cultivated Allium species,and their classification into two new rymoviruses in the family Potyviridae

While testing several samples of onion and of vegetatively propagated garlic, sand leek and shallot from a number of countries, virus isolates with unusually flexuous particles were obtained by mite (Aceria tulipae) or sap transmissions. No aphid-borne poty-or carlavirus was transmitted by mites, and mite-borne virus isolates could not be transmitted by aphids. The mite-borne isolates did not react with antisera to aphid-borne potyviruses ofAllium spp. or with the Agdia potyvirus group monoclonal. In contrast to the mite-borne onion and garlic mosaic viruses reported in the literature, our mite-borne isolates induced no visible or only very mild symptoms inAllium spp., except isolates from shallot ‘Santé’ which caused diffuse striping. Heavily mite-infested test plants or plant samples showed streaking and malformation due to mite feeding (tangle-top). The mite-borne virus isolates could be classified with test plants and a discriminating antiserum into three groups, representing two viruses and a strain of one of them. They are tentatively named onion mite-borne latent virus (OMbLV), garlic strain of this virus (OMbLV-G), and shallot mite-borne latent virus (SMbLV). Mite transmission, length of virus particles (ca. 700 to 800 nm), and the presence of granular inclusion bodies in infected tissue indicate that the viruses belong to the mite-borne genusRymovirus of the familyPotyviridae. OMbLV from shallot and onion, and OMbLV-G from garlic and sand leek, can be assayed onChenopodium murale but differ in their natural hosts. They are very common. SMbLV, to whichC. murale does not react, was isolated from shallot originating from Asia and Russia.     

Root exudates of potato onion are involved in the suppression of clubroot in a Chinese cabbage-potato onion-Chinese cabbage crop rotation

Clubroot, caused by Plasmodiophora brassicae, has emerged as a serious disease threatening cruciferous crop production throughout the world. Crop rotation with non-host species is commonly practised to avoid clubroot, but it is not known whether rotation crops can control clubroot when the resting spores of P. brassicae remain unaffected. Pot experiments were performed to investigate the response of clubroot in Chinese cabbage to crop rotation with potato onion. The results showed that Chinese cabbage rotated with potato onion exhibited less clubroot disease than Chinese cabbage monoculture. Compared with residues from potato onion, the addition of root exudates from potato onion significantly decreased the disease incidence and index of clubroot (p ≤ 0.05). Potato onion root exudates decreased the number of secondary plasmodia of P. brassicae and the expression of the PRO1 gene of P. brassicae. These results suggest that root exudates from potato onion may play an important role in suppressing clubroot in a Chinese cabbage-potato onion-Chinese cabbage rotation system.     

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).     

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.     

Molecular characterization of <Emphasis Type="Italic">Ditylenchus dipsaci</Emphasis> on Onion in Turkey

Ditylenchus dipsaci is a species complex including diploid and polyploid individuals. The onion race of D. dipsaci is a sensu stricto group and has a wide range of host spectrum. Identification of the D. dipsaci onion race is difficult using morphological and morphometrical methods. Species specific primers are mostly used in molecular approaches for identification of D. dipsaci populations. Fifty one morphologically selected Ditylenchus spp. populations from onion production areas in Turkey were subjected to molecular identification using four D. dipsaci species specific primer sets (PF1-PR1, PF2-PR2, DdpS1-rDNA2, DitNF1- rDNA2, H05-H06) targeting 5.8S and 18S rDNA, ITS1 and flanking ITS regions. Thirty nine percent of the nematode samples were positive with four primers tested, while four of the nematode samples gave specific bands with H05-H06 primers. Ditylenchus dipsaci sensu stricto was identified with specific primer sets in Adana, Hatay, Tekirdag, Bursa, Aksaray, Karaman, Eskisehir and Ankara provinces in Mediterranean, Trace, Aegean and Central Regions in Turkey.     

First report of leaf spot caused by <Emphasis Type="Italic">Alternaria alternata</Emphasis> on <Emphasis Type="Italic">Drimia maritima</Emphasis>

Drimia maritima (squill) is a historically important medicinal plant. During the spring of 2016, small, yellow leaf spots, which became brown and finally necrotic, were observed on squill plants in Kohgiluyeh and Boyer-Ahmad Provinces in Iran. A fungus was consistently isolated from infected leaves and identified as Alternaria alternata based on morphological and phylogenetic analyses. Pathogenicity tests confirmed A. alternata to be the causal agent of the newly observed leaf spot disease. This is the first report of leaf spot on D. maritima caused by A. alternata in the world.     

Check-list for scientific names of common parasitic fungi. Supplement Series 2b (additions and corrections): Fungi on field crops: Cereals and grasses

This paper suplements Series 2b (Neth. J. Pl. Path. 83 (1977) 165–204) and documents the nomenclature of an additional 10 parasitic fungi. The data on 25 fungi (teleomorph and/or anamorph) previously treated in Series 2b have been brought up to date and in accordance with the recent changes in the International Code of Botanical Nomenclature. The selected names include one new variety and two new infraspecific combinations, viz.Tapesia yallundae var.acuformis Boerema et al., anam.Ramulispora herpotrichoides var.acuformis (Nirenberg) Boerema et al. andUstilago tritici (Pers.) Rostrup f. sp.hordei (Schaffnit) Boerema et al.     

A myosin passenger protein gene (<Emphasis Type="Italic">FaSmy1</Emphasis>) is an essential regulator of cell development,pathogenicity, DON biosynthesis,and resistance to the fungicide phenamacril in <Emphasis Type="Italic">Fusarium asiaticum</Emphasis>

Wheat streak mosaic virus (WSMV) and Triticum mosaic virus (TriMV) are important viruses of wheat (Triticum aestivum L.) in the Great Plains of United States. In addition to agronomic practices to prevent damage from these viruses, temperature sensitive resistance genes Wsm1, Wsm2 and Wsm3, have been identified. However, threshold temperatures for Wsm1 and Wsm3 have not been clearly defined. To better understand these two resistance genes, wheat lines C.I.15092 (Wsm1), KS96HW10–3 (Wsm1), and KS12WGGRC59 (Wsm3) were evaluated for WSMV resistance at 27, 30, 33 and 35 °C and for TriMV resistance at 18, 21, 24, 27, 30, 33 and 35 °C. The results showed that only C.I.15092 remained resistant at 30 °C for both viruses. This line also tolerated TriMV at 33 and 35 °C with less sever symptom and lower infection rates. Wheat lines KS96HW10–3 and KS12WGGRC59 hold resistance to TriMV up to 21 °C. Molecular marker results suggested that the resistance in C.I.15092 is most probably conditioned by the resistance gene Wsm1 and additional gene(s) other than Wsm2 and Wsm3.     

Association of <Emphasis Type="Italic">Pantoea ananatis and Pantoea agglomerans</Emphasis> with leaf spot disease on ornamental plants of Araceae Family

During a survey in 2011–2012, three ornamental plants of Araceae namely Aglaonema nitidum, Syngonium podophyllum and Dieffenbachia amoena showing foliar disease symptoms were collected from central region of Iran. Infected plants exhibited spots on their leaves which appeared as yellow and water-soaked with chlorotic haloes and necrotic center. To investigate the etiology of this disorder, symptomatic leaves were collected from affected plants and six bacterial strains (B2Y, J3Y, SY, E60Y, E68Y and E5MM) were isolated and identified as Pantoea ananatis or P. agglomerans based on morphological, physiological, biochemical and molecular characters. The pathogenicity tests of the isolates demonstrated that they were not host specific. Furthermore, 16S rRNA gene sequencing revealed that the strains were phylogenetically closely related to genus Pantoea. Multilocus sequence analysis (MLSA) of concatenated partial atpD, gyrB and rpoB gene sequences of the six isolates showed a high similarity of B2Y, J3Y, and SY strains to P. ananatis and also of E60Y, E5MM and E68Y strains to P. agglomerans. These results were confirmed by phylogenetic analysis. To the best of our knowledge, this is the first report of leaf spot and necrosis of A. nitidum, S. podophyllum and D. amoena caused by the genus Pantoea.