A comparative study of the Barley yellow dwarf virus species PAV and PAS: distribution,accumulation and host resistance

This study investigated the distribution and characteristics of the Barley yellow dwarf virus (BYDV) species BYDV‐PAS, which was recently separated from BYDV‐PAV, the most commonly studied BYDV species. Throughout 3 years of experimental monitoring of BYDV incidence, PAS was the most frequently occurring species infecting cereals and grasses in the Czech Republic. Furthermore, Rhopalosiphum maidis and Metopolophium dirhodum were recorded as BYDV‐PAS vectors, even though M. dirhodum does not usually transmit BYDV‐PAV. In field experiments with barley and wheat, where virus accumulation, symptoms and effect on the yield were tested, BYDV‐PAV was more severe than PAS. Infection with the BYDV‐PAV isolate resulted in greater expression of symptoms and also in a greater reduction in plant height and grain weight per spike than BYDV‐PAS. In a sensitive cultivar of barley (Graciosa), the amount of viral RNA of BYDV‐PAV was also significantly higher than that of BYDV‐PAS. In a tolerant line (Wbon‐123), however, no such differences were found. In conclusion, although BYDV‐PAS seems to be dominant in the Czech Republic, BYDV‐PAV has the potential to cause more significant crop losses in barley and wheat.     

Plant community diversity influences vector behaviour and Barley yellow dwarf virus population structure

The species composition of a plant community can affect the distribution and abundance of other organisms including plant pathogens. The goal of this study was to understand the role of host diversity in the transmission of two Barley yellow dwarf virus (BYDV) species that share insect vectors and hosts. Greenhouse experiments measured the transmission rate of BYDV species PAV and PAS from infected oat plants to healthy agricultural and wild grasses and from these species back to healthy oat seedlings. In the field component of the study, the rate of spread of PAV and PAS was measured in monoculture plots planted with agricultural grasses. In greenhouse experiments, the aphid vector more readily transmitted PAV from agricultural grasses and more readily inoculated PAS to the wild grass species assayed. In the field experiment, disease prevalence was greater in wheat, but there was no difference in the rate of spread of PAV and PAS. These results indicate an interaction between vector and host genotype that selects for greater PAV transmission in grain crops, contributes to differences in disease prevalence between grass types, and maintains pathogen diversity within the larger plant community (i.e. agricultural and non‐agricultural hosts).     

The invasive weed Ventenata dubia is a host of Barley yellow dwarf virus with implications for an endangered grassland habitat

Ventenata dubia (African wiregrass), a winter annual weed, is a non‐native species invading grasslands, rangelands and pastures throughout the USA. Limited information is available on its suitability as a host to pathogens and insects in its invaded range. The barley/cereal yellow dwarf virus (B/CYDV) complex occurs ubiquitously in Poaceae species. In non‐managed grasslands, BYDV infection influences competitive dynamics between native and invasive grasses and facilitates invasion by non‐native annual weeds. The Palouse prairie of south‐eastern Washington and northern Idaho, USA, is an endangered ecosystem. Surveys of V. dubia in Palouse prairie and neighbouring Conservation Reserve Program (CRP) habitats were conducted to determine whether B/CYDV viral species are present. Laboratory tests examined the suitability of V. dubia to host BYDV‐PAV and serve as an inoculum source. Plant growth and weight parameters were measured to gauge the impact of BYDV‐PAV on V. dubia. Infection of V. dubia in Palouse prairie and CRP habitats with two species of BYDV, PAV and SGV, was detected for the first time. The ability of BYDV‐PAV to infect V. dubia in the laboratory and transmission from infected V. dubia to barley were demonstrated. BYDV‐PAV‐infected V. dubia showed reductions in plant height, number of leaves and tillers per plant, and above‐ground dry weight, suggesting that V. dubia is sensitive to BYDV. Results demonstrate that V. dubia is a host to BYDV and may serve as a virus inoculum source with potential implications for its management, competitive dynamics between invasive and native grasses and future conservation of endangered grasslands.     

Occurrence of barley yellow dwarf viruses in some common grasses (Gramineae) in south west England

The incidence and distribution of aphid transmitted barley yellow dwarf (BYD) viruses (PAV-, RPV- and MAV-like isolates) are described in 14 species of common pasture and hedgerow grasses from five localities of south-west England during 1987 and 1988. Isolates were identified by indirect 'sandwich' ELISA using the monoclonal antibodies MAC91, MAC92 and MAFF2. More infection was detected in 1987 than in 1988 but this was mainly due to a sharp decline at one site. Intensity of infection was greater in Poa annua and Lolium perenne populations than in most other species. BYD was not detected in Arrhenatherum elatius Elymus repens Agrostis canina and A. stolonifera . All three isolates of BYD were widespread. MAV was associated more with localities further north and RPV more with those further south. PAV was common only at the southern-most site. This geographical distribution was reasonably consistent in both years. Given these trends, susceptible grass species fell broadly into three groups with respect to isolate frequency, those predominently infected by RPV and MAV (seven spp.), those equally infected by all isolates (two spp.) and a single species, Poa annua , infected mainly by PAV. Some implications of these findings for the epidemiology and control of BYD viruses are briefly considered.     

Occurrence of barley yellow dwarf virus in pastures of western France

As pasture grasses are preponderant in the agriculture of western France, their role as reservoirs of barley yellow dwarf virus (BYDV) and its aphid vectors has been studied from 1984 to 1986. Aphids were observed on most crops of five pasture grass species (brome grass, cocksfoot, tall fescue, Italian and perennial ryegrass) but in very low numbers. Rhopalosiphum padi was the most numerous species. The incidence of BYDV was high, with levels of infection ranging from 6 to 80% depending on the species of pasture grasses. Fescue pastures were highly infected with BYDV, whereas the virus was not detected in cocksfoot pastures. PAV-, RPV-, MAV-like isolates of BYDV were detected in pasture grasses, but RPV- and MAV-like isolates were only detected from ryegrass and brome grass, respectively. The role of these grasses as source of viruliferous aphids infecting cereals is discussed.     

Reducing tillage intensity affects the cumulative emergence dynamics of annual grass weeds in winter cereals

Annual grass weeds such as Apera spica‐venti and Vulpia myuros are promoted in non‐inversion tillage systems and winter cereal‐based crop rotations. Unsatisfactory weed control in these conditions is often associated with a poor understanding of the emergence pattern of these weed species. The aim of this study was to investigate, understand and model the cumulative emergence patterns of A. spica‐venti, V. myuros and Poa annua in winter cereals grown in three primary tillage regimes: (i) mouldboard ploughing, (ii) pre‐sowing tine cultivation to 8–10 cm soil depth and (iii) direct drilling. Direct drilling delayed the cumulative emergence of A. spica‐venti and V. myuros (counted together) in contrast with ploughing, while the emergence pattern of P. annua was unaffected by the type of tillage system. The total density of emerged weed seedlings varied between the tillage systems and years with a higher total emergence seen under direct drilling, followed by pre‐sowing tine cultivation and ploughing. The emergence patterns of all species were differently influenced by the tillage systems, suggesting that under direct drilling, in which these species occur simultaneously, management interventions should first and foremost consider that A. spica‐venti and V. myuros emerge over a longer period to avoid control failures.     

A generic RT‐PCR assay for the detection of Luteoviridae

This study, using RT‐PCR, is the first comprehensive assessment since 1991 of a generic detection method for the Luteoviridae. Thirteen Luteoviridae species were detected using three separate sets of low‐degeneracy generic primers with RT‐PCR to amplify 68‐, 75‐ and 129/156‐bp regions of the Luteoviridae coat‐protein gene. Species detected include all members of the genus Luteovirus [Barley yellow dwarf virus (BYDV)‐PAV, BYDV‐PAS, BYDV‐MAV (129 and/or 156 bp amplicons), Soybean dwarf virus, Bean leafroll virus (68 bp amplicon)] and eight of nine species from the genus Polerovirus [Beet western yellows virus, Beet chlorosis virus, Beet mild yellowing virus, Turnip yellows virus, Potato leafroll virus, Cucurbit aphid‐borne yellows virus, Cereal yellow dwarf virus‐RPV (68‐bp amplicon) and Sugarcane yellow leaf virus (75‐bp amplicon)]. These primers were not able to detect Carrot red leaf virus, Sweet potato leaf speckling virus (both belong to unassigned Luteoviridae) and Pea enation mosaic virus‐1 (genus Enamovirus). A synthetic positive control containing all primer sequence priming sites was designed to facilitate this method as a generic tool for use with a variety of host plants. The Luteoviridae primers described in this study present a simple infection‐detection tool of benefit to biosecurity authorities in nursery‐stock surveillance, disease management or outbreak prevention, and may also be useful in detection of as‐yet undiscovered species within the Luteovirus and Polerovirus genera.     

Impacts of soil moisture level and organic matter content on growth of two Juncus species and Poa pratensis grown under acid soil conditions

The abundance of Juncus effusus (soft rush) and Juncus conglomeratus (compact rush) has increased in coastal grasslands in Norway over recent decades, and their spread has coincided with increased precipitation in the region. Especially in water‐saturated, peaty soils, it appears from field observations that productive grasses cannot compete effectively with such rapidly growing rush plants. In autumn–winters of 2012–2013 and 2013–2014, a four‐factor, randomised block greenhouse experiment was performed to investigate the effect of different soil moisture regimes and organic matter contents on competition between these rush species and smooth meadow‐grass (Poa pratensis). The rush species were grown in monoculture and in competition with the meadow‐grass, using the equivalent of full and half the recommended seed rate for the latter. After about three months, above‐ and below‐ground dry matter was measured. J. effusus had more vigorous growth, producing on average 23–40% greater biomass in both fractions than J. conglomeratus. The competitive ability of both rush species declined with decreasing soil moisture; at the lowest levels of soil moisture, growth reductions were up to 93% in J. conglomeratus and 74% in J. effusus. Increasing water level in peat–sand mixture decreased competivitiveness of meadow‐grass, while pure peat, when moist, completely impeded its below‐ground development. These results show that control of rush plants through management may only be achieved if basic soil limitations have been resolved.     

Differences in MAT gene distribution and expression between Rhynchosporium species on grasses

Leaf blotch is a globally important disease of barley crops and other grasses that is caused by at least five host‐specialized species in the fungal genus Rhynchosporium. The pathogen R. commune (specialized to barley, brome‐grass and Italian ryegrass) has long been considered to reproduce only by asexual means, but there has been accumulating evidence for recombination and gene flow from population genetic studies and the detection of complementary MAT1‐1 and MAT1‐2 isolates in a c. 1:1 ratio in the field. Here, it is demonstrated that 28 isolates of the closely related species R. agropyri (on couch‐grass) and R. secalis (on rye and triticale), collected from Europe, were also either of MAT1‐1 or MAT1‐2 genotype and that the distribution of mating types did not deviate significantly from a 1:1 ratio. Evidence is then provided for MAT1‐1‐1 and MAT1‐2‐1 gene expression during mycelial growth for all three species. By contrast, 27 isolates of the more distantly related R. orthosporum (on cocksfoot) and R. lolii (on Italian and perennial ryegrasses) from Europe were exclusively of the MAT1‐1 genotype, and expression of the MAT1‐1‐1 gene could not be detected during mycelial growth. These data suggest that cryptic sexual cycles are more likely to exist for R. commune, R. agropyri and R. secalis than for either R. orthosporum or R. lolii. A phylogenetic analysis of partial MAT1‐1 idiomorph sequences resolved these five species into two distinct groups (R. commune, R. agropyri and R. secalis versus R. orthosporum and R. lolii) but provided only limited resolution within each group.     

Transmission of barley yellow dwarf virus by cereal aphids collected from different habitats on cereal farms

Cereal aphids were collected from cereal crops, from Poa annua within cereal fields, from Lolium perenne pastures and from wild grasses in hedge bottoms and around farm buildings. The frequency of barley yellow dwarf virus (BYDV) transmission was assessed by aphid transmission tests. There were differences in transmission rates between aphid species, between host species and between years. The transmission rates of Rhopalosiphum padi from the different host species were broadly similar whereas for Sitobion avenae, P. annua within cereal fields was significantly better than the other host species. Wild grasses other than P. annua were relatively poor sources of virus. A large percentage of aphids frequently transmitted more than one strain, suggesting that host plants are often infected with more than one BYDV strain.     

Sequence analyses of Wheat dwarf virus isolates from different hosts reveal low genetic diversity within the wheat strain

Wheat dwarf virus (WDV) causes disease in wheat (Triticum aestivum) and barley (Hordeum vulgare) in many parts of Europe. The host range also includes many species of the family Poaceae. WDV is only transmitted by the leafhopper Psammotettix alienus. During a five‐year period (2001–2005), grass samples were collected in central Sweden in the vicinity of fields with WDV‐infected winter wheat. Screening with ELISA and PCR identified WDV in a low number of samples (8/1098) from only three grass species: Apera spica‐venti, Avena fatua and Poa pratensis. In addition, triticale was found to be positive. Fourteen WDV isolates from Avena fatua, Apera spica‐venti, Triticum aestivum, Lolium multiflorum, Poa pratensis, triticale and the insect vector Psammotettix alienus, were partially sequenced (ca. 1200 nucleotides), providing the first published WDV sequences from the insect vector. All isolates belonged to the wheat strain of WDV and the genetic diversity was low. Phylogenetic analyses showed no clear grouping according to geographical location or host species. The results suggest that the same WDV genotypes are infecting both wheat and grasses in Sweden. Interestingly, one group of isolates (subtype B) formed a distinct clade in the phylogenetic tree. Subtype B was always found in mixed infection with the main genotype. Complete sequencing of a subtype B isolate showed that it was 98·6% identical to a typical wheat isolate from the same plant.     

从麦类种质资源中筛选大麦黄矮病毒(BYDV)抗原

用 ELISA 法鉴定了小麦近缘种赖草属(Leymus)、披碱草属(Elymus)、鹅冠草属(Roegneria)3个属的21个种,其中17个种抗 BYDV。21145份小麦品种中筛选到症状轻、病毒含量高的耐病品种忻县冬麦、江西早等29份。3604份大麦品种中筛选到症状轻、病毒含量低的抗病品种C13208、小麦近缘种(Agropyronintemedium)和普通小麦杂交的异源八倍体中4无芒,中5,远中7,陇远45、46,远中1001,忻4079以及附加系 L1。现已获得抗 BYDV 的以中4无芒、L1为亲本的杂交后代。     

Assessing the efficacy and impact of management of an invasive species in a protected area: Poa annua on sub‐Antarctic Macquarie Island

Plant eradication is difficult, particularly in remote, protected areas. The Southern Ocean Islands are very isolated and highly protected, but the flora contains many alien plants. Small restricted populations have been eradicated, but eradication of established species has proven difficult. A better understanding of the efficacy of control methods at sub‐Antarctic temperatures and their off‐target impacts may increase eradication success. With interest in controlling non‐native Poa annua in the region, we aimed to determine if physical and chemical methods can control P. annua (the sub‐Antarctic biotype) in sub‐Antarctic conditions and examined their impact on native plants. We quantified the effectiveness of physical control methods on P. annua in situ on sub‐Antarctic Macquarie Island through field‐based experiments and assessed their selectivity on P. annua compared with native grasses. We also quantified the effectiveness of several herbicides on P. annua at sub‐Antarctic temperatures and assessed their selectivity on native grasses. Of the four physical disturbance methods tested, none effectively reduced P. annua cover as one‐off treatments. Of the herbicide treatments, glyphosate and trifloxysulfuron sodium were effective and were less damaging to native grass species, indicating potential selectivity. Physical control was of limited effectiveness, but did not affect native species richness. An integrated weed management programme utilising the strategic use of selective herbicides with follow‐up chemical and physical intervention may balance control and biodiversity outcomes. This research highlights the importance of site‐specific testing of control methods and understanding off‐target impacts of control when managing alien plant species in protected areas.     

Insights into the genetic diversity and evolution of Little cherry virus 1

Little cherry virus 1 (LChV‐1), a member of the recently proposed genus Velarivirus, is a sweet cherry pathogen that has been recently reported to infect other Prunus species and is associated with various plant disorders. In this work the incidence of the virus on its putative hosts and possible mechanisms driving its evolution were investigated. Due to problems encountered with LChV‐1 detection, a new nested RT‐PCR assay was developed and applied. The virus was found to be prevalent in cherry plantations in Greece and only occasionally detected in other Prunus species. Sequences corresponding to the partial RNA‐dependent RNA polymerase (RdRp), heat‐shock protein homologue (HSP70h) and coat protein (CP) genes were determined from Greek LChV‐1 isolates originating from different hosts; these were analysed, along with published homologous genomic regions from other isolates. Phylogenetic analysis of the three genes revealed the segregation of four evolutionary distinct groups showing no host or geography‐based clustering. Mean genetic distances among the four groups were high with the CP region showing the highest divergence, although intragroup variability levels were low. Nevertheless, estimations of the mean ratio of nonsynonymous substitutions per synonymous site to synonymous substitutions per synonymous site (dN/dS) for the partial RdRp, HSP70h and CP indicated that these genomic regions are under negative selection pressure. Interestingly, a recombination event was identified at the 3′ end of RdRp on a Greek virus isolate, thus highlighting the role of this mechanism in the evolutionary history of LChV‐1.     

Identification and differentiation of Phyllosticta species causing freckle disease of banana using high resolution melting (HRM) analysis

Freckle disease of banana is caused by three closely related species of Phyllosticta, namely P. musarum, P. maculata and P. cavendishii. In this study, a high resolution melting (HRM) analysis assay was developed and its potential to identify these three fungal species is reported. The assay, which targets the ITS of the nuclear rDNA of the fungal species, generates three distinct melt profiles for the three Phyllosticta species. It is also able to distinguish a combination of up to three co‐infecting species by generating a deviant melt curve. Thirty‐five fungal cultures and infected herbarium leaf specimens, previously characterized using nucleotide sequencing as belonging to one of the three Phyllosticta species, were used for validation of the HRM analysis assay. The normalized curves generated differentiated all samples, with samples from each species correctly identified. The assay was further evaluated against 18 uncharacterized infected leaf specimens from various geographic locations and the results were verified by subsequent nucleotide sequencing. This HRM analysis assay allows rapid identification and differentiation of the three Phyllosticta species using a single primer pair in a one‐step closed‐tube system without labelled fluorescence probes. This novel assay format has potential for simultaneously identifying and differentiating other closely related species of plant pathogens, as well as the classification of infected historic specimens.     

Occurrence of barley yellow dwarf virus in cereals and grasses of the low-rainfall wheatbelt of South Australia

South Australia is in the dry temperate zone where most cereal crops are grown in an area of low rainfall, with a crop-free season from December to April. The incidence of barley yellow dwarf virus (BYDV) was assessed by ELISA from 1989 to 1991 in wheat crops and irrigated pastures of South Australia. The incidence of BYDV was low in most wheat crops of the low-rainfall area in 1989 and 1990 (less than 1% of plants infected), but moderate levels of infection (1–10%) were observed in some early-sown crops. BYDV infection was more widespread in the high-rainfall area (south east of South Australia). A high incidence of BYDV was observed in the irrigated pastures of the three areas surveyed (4–86%). Of the five previously described strains, the Rhopalosiphum padi/Sitobion avenae strain (PAV) was the most common in wheat samples (> 90%). PAV and the R. padi-specific strain (RPV) were found in pasture grasses, alone or in mixed infection. Virus incidence was greater in Festuca spp. (56%) and Lolium perenne (30%) than in other species (2-–9%).     

Characterization of the first two viruses described from wild populations of hammer orchids (Drakaea spp.) in Australia

Sequences representing the genomes of two distinct virus isolates infecting wild plants of two members of the genus Drakaea (hammer orchids) in Western Australia are described. The virus isolated from Drakaea livida has a bipartite genome of 4490 nt (RNA1) and 2905 nt (RNA2) that shares closest sequence and structural similarity to members of the genus Pecluvirus, family Virgaviridae, described from legumes in the Indian subcontinent and West Africa. However, it differs from pecluviruses by lacking a P39 protein on RNA2 and having a cysteine‐rich protein gene located 3′ of the triple gene block protein genes. It is the first peclu‐like virus to be described from Australia. The name Drakaea virus A is proposed (DVA; proposed member of the family Virgaviridae, genus unassigned). The second virus isolate was identified from Drakaea elastica, a species classed as endangered under conservation legislation. The genome sequence of this virus shares closest identity with isolates of Donkey orchid symptomless virus (DOSV; proposed member of the order Tymovirales, family and genus unassigned), a species described previously from wild Caladenia and Diuris orchids in the same region. These viruses are the first to be isolated from wild Drakaea populations and are proposed to have an ancient association with their orchid hosts.     

Arabidopsis thaliana,an experimental host for tomato yellow leaf curl disease‐associated begomoviruses by agroinoculation and whitefly transmission

Tomato yellow leaf curl disease is one of the most devastating viral diseases affecting tomato crops worldwide. This disease is caused by several begomoviruses (genus Begomovirus, family Geminiviridae), such as Tomato yellow leaf curl virus (TYLCV), that are transmitted in nature by the whitefly vector Bemisia tabaci. An efficient control of this vector‐transmitted disease requires a thorough knowledge of the plant–virus–vector triple interaction. The possibility of using Arabidopsis thaliana as an experimental host would provide the opportunity to use a wide variety of genetic resources and tools to understand interactions that are not feasible in agronomically important hosts. In this study, it is demonstrated that isolates of two strains (Israel, IL and Mild, Mld) of TYLCV can replicate and systemically infect A. thaliana ecotype Columbia plants either by Agrobacterium tumefaciens‐mediated inoculation or through the natural vector Bemisia tabaci. The virus can also be acquired from A. thaliana‐infected plants by B. tabaci and transmitted to either A. thaliana or tomato plants. Therefore, A. thaliana is a suitable host for TYLCV–insect vector–plant host interaction studies. Interestingly, an isolate of the Spain (ES) strain of a related begomovirus, Tomato yellow leaf curl Sardinia virus (TYLCSV‐ES), is unable to infect this ecotype of A. thaliana efficiently. Using infectious chimeric viral clones between TYLCV‐Mld and TYLCSV‐ES, candidate viral factors involved in an efficient infection of A. thaliana were identified.     

Survival of seeds from perennial biomass species during commercial‐scale anaerobic digestion

Tall perennial grass species can be utilised as bioenergy feedstocks, but some are considered invasive species. Using biomass from such species as feedstocks for anaerobic digestion (AD) may introduce the risk of disseminating viable seeds onto agricultural lands during digestate application. To evaluate this risk, we investigated the survival rates of perennial grass seeds obtained from biomass species during AD. After removal from the digester, seeds were germinated and stained with tetrazolium chloride to determine viability. During three experimental runs, batches of 100 seeds from four species were exposed to 0, 2, 6, 12, 24, 48, 72 and 168 h of mesophilic (38°C) AD within a commercial‐scale digester. Seed viability of Phalaris arundinacea, Phragmites australis, Panicum virgatum and Solanum lycopersicum was reduced by 95% (LT₉₅) after 29, 52, 98 and 105 h of AD respectively. Commercial digesters that utilise perennial grasses as a feedstock typically have retention times ranging from 240 to 1480 h, which greatly exceeds the LT₉₅ values found in this study. Anaerobic digestion resulted in the rapid death of seeds in all species tested, suggesting unwanted dissemination of perennial grass species via digestate application to agricultural land is unlikely.     

Pathogenicity of 21 newly described Phytophthora species against seven Western Australian native plant species

The pathogenicity of some Phytophthora species recently described from Western Australia, together with P. cinnamomi as a control, was tested against seven Western Australian native plant species in the glasshouse. Host species were Banksia grandis, B. littoralis, B. occidentalis, Casuarina obesa, Corymbia calophylla, Eucalyptus marginata and Lambertia inermis. Twenty‐two Phytophthora species were grown on a vermiculite, millet seed and V8 substrate and used as soil inoculum when the plant hosts were approximately 3 months old. Pathogenicity was assessed after 6 weeks and plants were scored for death, root damage, and percentage reduction of shoot growth compared with control plants. The pathogenicity of P. cinnamomi was confirmed. Phytophthora niederhauserii was shown to be similar to P. cinnamomi in pathogenicity and of concern ecologically. Other species that killed one or more hosts were P. boodjera, P. constricta, P. elongata, P. moyootj and P. rosacearum, while P. condilina, P. gibbosa, P. gregata, P. litoralis and P. ‘personii’ caused significant reduction to shoot and/or root growth, but did not kill plants. Host species susceptible to the highest number of Phytophthora species were B. grandis, B. littoralis, B. occidentalis and E. marginata. No Phytophthora species tested killed C. calophylla.