Role of recombination in the evolution of host specialization within bean yellow mosaic virus

Seven complete genomes and 64 coat protein gene sequences belonging to Bean yellow mosaic virus (BYMV) isolates from different continents were examined for evidence of genetic recombination using six different recombination-detection programs. In the seven complete genomes and a single complete genome of the related virus Clover yellow vein virus (ClYVV), evidence for eight recombination patterns was found by four or more programs, giving firm evidence of their presence, and five additional recombination patterns were detected by three or fewer programs, giving tentative evidence of their occurrence. When the nucleotide sequences of 64 BYMV and one ClYVV coat protein genes were analyzed, three firm recombination patterns were detected in 21 isolates (32%). With another six isolates (9%), tentative evidence was found for three further recombination patterns. Of the 19 firm or tentative recombination patterns detected within and between strain groups of BYMV, and with ClYVV, 12 involved a generalist group of isolates as a parent but none of the other BYMV groups acted as parents more than six times. These findings suggest that recombination played an important role in the evolution of BYMV strain groups that specialize in infecting particular groups of domesticated plants.

Phylogenetic Analysis of Bean yellow mosaic virus Isolates from Four Continents: Relationship Between the Seven Groups Found and Their Hosts and Origins

Genetic diversity of Bean yellow mosaic virus (BYMV) was studied by comparing sequences from the coat protein (CP) and genome-linked viral protein (VPg) genes of isolates from four continents. CP sequences compared were those of 17 new isolates and 47 others already on the database, while the VPg sequences used were from four new isolates and 10 from the database. Phylogenetic analysis of the CP sequences revealed seven distinct groups, six polytypic and one monotypic. The largest and most genetically diverse polytypic group, which had intragroup diversity of 0.061 nucleotide substitutions per site, contained isolates from natural infections in eight host species. These original isolation hosts included both wild (four) and domesticated (four) species and were from monocotyledonous and dicotyledonous plant families, indicating a generalized natural host range strategy. Only one of the other five polytypic groups spanned both monocotyledons and dicotyledons, and all contained isolates from fewer species (one to four), all of which were domesticated and had lower intragroup diversity (0.019 to 0.045 nucleotide substitutions per site), indicating host specialization. Phylogenetic analysis of the fewer VPg sequences revealed three polytypic and two monotypic groupings. These groups also correlated with original natural isolation hosts, but the branch topologies were sometimes incongruous with those formed by CPs. Also, intragroup diversity was generally higher for VPgs than for CPs. A plausible explanation for the groups found when the 64 different CP sequences were compared is that the generalized group represents the original ancestral type from which the specialist host groups evolved in response to domestication of plants after the advent of agriculture. Data on the geographical origins of the isolates within each group did not reveal whether the specialized groups might have coevolved with their principal natural hosts where these were first domesticated, but this seems plausible.

An epidemiological model for externally sourced vector-borne viruses applied to Bean yellow mosaic virus in lupin crops in a Mediterranean-type environment

A hybrid mechanistic/statistical model was developed to predict vector activity and epidemics of vector-borne viruses spreading from external virus sources to an adjacent crop. The pathosystem tested was Bean yellow mosaic virus (BYMV) spreading from annually self-regenerating, legume-based pastures to adjacent crops of narrow-leafed lupin (Lupinus angustifolius) in the winter-spring growing season in a region with a Mediterranean-type environment where the virus persists over summer within dormant seed of annual clovers. The model uses a combination of daily rainfall and mean temperature during late summer and early fall to drive aphid population increase, migration of aphids from pasture to lupin crops, and the spread of BYMV. The model predicted time of arrival of aphid vectors and resulting BYMV spread successfully for seven of eight datasets from 2 years of field observations at four sites representing different rainfall and geographic zones of the southwestern Australian grainbelt. Sensitivity analysis was performed to determine the relative importance of the main parameters that describe the pathosystem. The hybrid mechanistic/statistical approach used created a flexible analytical tool for vector-mediated plant pathosystems that made useful predictions even when field data were not available for some components of the system.

Molecular Genetic Characterization of Sweet potato virus G (SPVG) Isolates from Areas of the Pacific Ocean and Southern Africa

Sweet potato virus G (SPVG, genus Potyvirus, family Potyviridae) was detected in sweetpotato (Ipomoea batatas) storage roots sold in the local markets and storage roots or cuttings sampled directly from farmers' fields. Using serological and molecular methods, the virus was detected for the first time in Java, New Zealand, Hawaii, Tahiti, Tubuai, Easter Island, Zimbabwe, and South Africa, and also in an imported storage root under post-entry quarantine conditions in Western Australia. In some specimens, SPVG was detected in mixed infection with Sweet potato feathery mottle virus (genus Potyvirus). The coat protein (CP) encoding sequences of SPVG were analyzed for 11 plants from each of the aforementioned locations and compared with the CP sequences of 12 previously characterized isolates from China, Egypt, Ethiopia, Spain, Peru, and the continental United States. The nucleotide sequence identities of all SPVG isolates ranged from 79 to 100%, and amino acid identities ranged from 89 to 100%. Isolates of the same strain of SPVG had nucleotide and amino acid sequence identities from 97 to 100% and 96 to 100%, respectively, and were found in sweetpotatoes from all countries sampled except Peru. Furthermore, a plant from Zimbabwe was co-infected with two clearly different SPVG isolates of this strain. In contrast, three previously characterized isolates from China and Peru were phylogenetically distinct and exhibited <90% nucleotide identity with any other isolate. So far, the highest genetic diversity of SPVG seems to occur among isolates in China. Distribution of SPVG within many sweetpotato growing areas of the world emphasizes the need to determine the economic importance of SPVG.

Finding Wheat streak mosaic virus in south-west Australia

Between 2003 and summer 2006, 33 659 samples of wheat and grasses were collected from diverse locations in south-west Australia and tested for presence of Wheat streak mosaic virus (WSMV), but none was detected. In April–early May 2006, 2840 random samples of volunteer wheat from 28 fields on 24 farms in 6 districts in the grainbelt were tested. WSMV was detected for the first time, the infected samples coming from three fields, one in the Hyden and two in the Esperance districts. In ‘follow-up’ surveys in May 2006 in the same two districts, 8983 samples of volunteer wheat or grasses were tested, and the virus was detected on further farms, two in the Hyden and four in the Esperance districts. Incidences of infection in volunteer wheat were 1–8%, but WSMV was not found in grasses. By September 2006, when 1769 samples from further visits were tested, WSMV was detected in wheat crops or volunteer wheat plants at 2/3 of the original farms, with infection also found at one of them in barley, volunteer oats, and barley grass (Hordeum sp.). When samples of the seed stocks originally used in 2005 to plant five of the fields containing infected volunteer wheat at the three original infected farms were tested, seed transmission of WSMV was detected in four of them (0.1–0.2% transmission rates). In August–October 2006, 16 436 samples were collected in a growing-season survey for WSMV in wheat trials and crops throughout the grainbelt. WSMV was detected in 33% of ‘variety’ trials, 18% of other trials, 13% of seed ‘increase’ crops, and 52% of commercial crops. Incidences of infection were <1–100% within individual crops, <1–17% in trials, and <1–3% in seed increase crops. WSMV-infected sites were concentrated in the low-rainfall zone (east) of the central grainbelt. This area received considerable summer rains in 2006, which allowed growth of a substantial ‘green ramp’ of volunteer cereals and grasses, favouring infection of subsequent wheat plantings. WSMV was also detected at low levels over a much wider area involving all rainfall zones, from Dongara in the north to Esperance in the south. All 26 122 samples collected in January–May 2006 and 515 with possible WSMV symptoms collected in August–October 2006 were also tested for High plains virus (HPV), but it was not detected.

Further studies on Pea seed-borne mosaic virus in cool-season crop legumes: responses to infection and seed quality defects

Field and glasshouse experiments (3 of each) were done during 2003–06 to determine the responses of a range of genotypes belonging to 13 species of cool-season crop legumes to infection with Pea seed-borne mosaic virus (PSbMV). Seed quality defects were determined and genotypes of some species were also tested for seed transmission of the virus. In field experiments, of 39 genotypes of field pea (Pisum sativum) evaluated, 15 were ranked as highly susceptible, 10 susceptible, 9 moderately resistant, and 5 resistant, while all 7 lupin species (Lupinus spp.) tested were resistant. In glasshouse sap and graft inoculations with PSbMV to genotypes not found infected in the field and 2 additional lupin species, no virus was detected in any of the 9 lupin species or in 5 field pea genotypes tested. Thus, the lupins all appeared to be non-hosts and the 5 field pea genotypes had resistance to the 2 PSbMV isolates used to inoculate them. All 14 genotypes of faba bean (Vicia faba) evaluated in the field were ranked highly susceptible, while 12 out of 16 lentil (Lens culinaris) genotypes were ranked as highly susceptible and 4 as susceptible. Chickpea (Cicer arietinum) genotypes were moderately resistant (50) or susceptible (7). Once infected, plant sensitivities (symptom severities) ranged from low in some field pea and most lentil genotypes to high in most faba bean genotypes. Chickpea genotypes all were ranked as moderately sensitive. Seed lots harvested from PSbMV-infected plants of field pea, faba bean, and chickpea all showed severe seed quality defects, but lentil was usually less affected. The predominant seed symptoms were necrotic rings and line markings on the seed coat, malformation, reduced size, and splitting. Kabuli chickpea types also showed darkening of the seed coat. Seed transmission of PSbMV was detected in faba bean (0.2%) and field pea (5–30%). When PSbMV infection foci were introduced into plots of lentil cv. Nugget, the virus spread to the lentil plants and decreased shoot dry weight by 23%, seed yield by 96%, and individual seed weight by 58%. Seed transmission of PSbMV (6%) was detected in seed from the infected lentil plants. In a survey for possible viral seed symptoms, all seed lots of kabuli chickpea (5) and field pea (70), and 10 of 18 of faba bean were affected, but none of the 23 of lentil. When seedlings from 16 faba bean and 7 field pea seed lots were tested for 3 viruses, neither Broad bean stain virus nor Broad bean true mosaic virus was detected, but PSbMV was found in 5 field pea seed lots at incidences of <1–14%. PSbMV was detected in commercial field pea seed stocks of cvv. Kaspa (33) and Parafield (12) at incidences of 0.5–47% and 0.3–30%, respectively. The implications of these findings in terms of genotype susceptiblility and sensitivity to PSbMV infection and their importance for the management of PSbMV in legume crops are discussed.

The epidemiology of Wheat streak mosaic virus in Australia: case histories, gradients, mite vectors, and alternative hosts

Wheat streak mosaic virus (WSMV) infection and infestation with its wheat curl mite (WCM; Aceria tosichella) vector were investigated in wheat crops at two sites in the low-rainfall zone of the central grainbelt of south-west Australia. In the 2006 outbreak, after a preceding wet summer and autumn, high WCM populations and total infection with WSMV throughout a wheat crop were associated with presence of abundant grasses and self-sown ‘volunteer’ wheat plants before sowing the field that became affected. Wind strength and direction had a major effect on WSMV spread by WCM to neighbouring wheat crops, the virus being carried much further downwind than upwind by westerly frontal winds. Following a dry summer and autumn in 2007, together with control of grasses and volunteer cereals before sowing and use of a different seed stock, no WSMV or WCM were found in the following wheat crop within the previously affected area or elsewhere on the same farm. In the 2007 outbreak, where the preceding summer and autumn were wet, a 40% WSMV incidence and WCM numbers that reached 4800 mites/ear at the margin of the wheat crop were associated with abundant grasses and volunteer wheat plants in adjacent pasture. WSMV incidence and WCM populations declined rapidly with increasing distance from the affected pasture. Also, wheat plants that germinated early had higher WSMV infection incidences than those that germinated later. The alternative WSMV hosts identified at these sites were volunteer wheat, annual ryegrass (Lolium rigidum), barley grass (Hordeum sp.), and wild oats (Avena fatua). In surveys outside the growing season at or near these two sites or elsewhere in the grainbelt, small burr grass (Tragus australianus), stink grass (Eragrostis cilianensis), and witch grass (Panicum capillare) were identified as additional alternative hosts.

Discussion paper: The naming of Potato virus Y strains infecting potato

Potato virus Y (PVY) strain groups are based on host response and resistance gene interactions. The strain groups PVY(O), PVY(C) and PVY(N) are well established for the isolates infecting potato in the field. A switch in the emphasis from host response to nucleotide sequence differences in the virus genomes, detection of isolates recombining sequences of different strains, and the need to recognize isolates that cause necrotic symptoms in potato tubers have led to the assignment of new acronyms, especially to isolates of the PVY(N) strain group. This discussion paper proposes that any newly found isolates should be described within the context of the original strain groups based on the original methods of distinguishing strains (i.e., tobacco and potato assays involving use of 'differential' potato cultivars). Additionally, sequence characterization of the complete genomes of isolates is highly recommended. However, it is acceptable to amend the names of PVY isolates with additional, specific codes to show that the isolate differs at the molecular, serological or phenotypic level from the typical strains within a strain group. The new isolates should preferably not be named using geographical, cultivar, or place-association designations. Since many new variants of PVY are being discovered, any new static classification system will be meaningless for the time being. A more systematic investigation and characterization of PVY from potato at the biological and molecular levels should eventually result in a biologically meaningful genetic strain concept.

Yield-limiting potential of Beet western yellows virus in Brassica napus

Losses in seed yield and quality caused by infection with Beet western yellows virus (BWYV) alone or in combination with direct feeding damage by Myzus persicae (green peach aphid) were quantified in field experiments with Brassica napus (canola, oilseed rape) in the ‘grainbelt’ region of south-western Australia. Plants infected with BWYV and infested with M. persicae were introduced into plots early to provide infection sources and spread BWYV to B. napus plants. Insecticides were applied as seed dressings and/or foliar applications to generate a wide range of BWYV incidences in plots. Colonisation by vector aphids and spread of BWYV infection were recorded in the plots of the different treatments. At sites A (Medina) and B (Badgingarra) in 2001, foliar insecticide applications were applied differentially at first, but, later, ‘blanket’ insecticide sprays were applied to all plots to exclude any direct feeding damage by aphids. When BWYV infection at sites A and B reached 96% and 100% of plants, it decreased seed yield by up to 46% and 37%, respectively. Also, variation in BWYV incidence explained 95% (site A) and 96% (site B) of the variation in yield gaps, where for each 1% increase in virus incidence there was a yield decrease of 12 (site A) and 6 (site B) kg/ha. At both sites, this yield decline was entirely because fewer seeds formed on infected plants. At site B, BWYV infection significantly diminished oil content of seeds (up to 3%), but significantly increased individual seed weight (up to 11%) and erucic acid content (up to 44%); significant increases in seed protein content (up to 6–11%) were recorded at both sites. In field experiments at sites B and C (Avondale) in 2002, insecticides were applied as seed dressings or foliar sprays. At site B, when BWYV incidence reached 98%, the overall yield loss caused by BWYV and direct M. persicae feeding damage combined was 50%. At site C, when BWYV incidence reached 97%, the overall combined yield decline caused by BWYV and direct feeding damage was 46%. This research under Australian conditions shows that, when aphids spread it to B. napus plantings such that many plants become infected at an early growth stage, BWYV has substantial yield-limiting potential in B. napus crops. Although the results represent a worst case scenario, the losses were greater than those reported previously in Europe and are cause for concern for the Australian B. napus industry. When applied at 525 g a.i./100 kg of seed, imidacloprid seed dressing controlled insecticide-resistant M. persicae and effectively suppressed spread of BWYV for 2.5 months and increased seed yield by 84% at site B and 88% at site C. Therefore, provided that mixing the insecticide with seed is sufficiently thorough, dressing seed with imidacloprid before sowing provides good prospects for control of BWYV and M. persicae in B. napus crops.

Occurrence of Beet western yellows virus and its aphid vectors in over-summering broad-leafed weeds and volunteer crop plants in the grainbelt region of south-western Australia

During the summer periods of 2000, 2001, and 2002, presence of Beet western yellows virus (BWYV) was assessed in tests on samples from at least 12 broad-leafed weed species and 5 types of volunteer crop plants growing in the grainbelt region of south-western Australia. In 2000, BWYV was detected in 2 of 35 sites in 2% of 1437 samples, whereas in 2001 and 2002 the corresponding figures were 3 of 108 sites in 0.04% of 8782 samples, and 1 of 30 sites in 0.08% of 2524 samples, respectively. The sites with infection were in northern, central, and southern grainbelt districts, and in high and medium rainfall zones. The hosts in which BWYV was detected were the weeds Citrullus lanatus (Afghan or wild melon), Conzya spp. (fleabane), Navarretia squarrosa (stinkweed), and Solanum nigrum (blackberry nightshade), and the volunteer crop plant Brassica napus (canola). Small populations of aphids were found over-summering at 28% (2000), 4% (2001), and 17% (2002) of sites, mostly infesting volunteer canola and Raphanus raphanistrum (wild radish). They occurred in high, medium, and low rainfall zones, but were only found in central and southern grainbelt districts. The predominant aphid species found was Brevicoryne brassicae, with Acyrthosiphon pisum, Brachycaudus helichrysi, Hyperomyzus lactucae, Lipaphis erysimi, Myzus persicae, and Uroleucon sonchi present occasionally. The importance of these findings in relation to the epidemiology and control of BWYV in the grainbelt is discussed.

Incidence and distribution of viruses infecting cucurbit crops in the Northern Territory and Western Australia

During 2003–04, a survey was done to determine the incidence and distribution of virus diseases infecting cucurbit crops growing in the field at Kununurra, Broome, and Carnarvon in north-western Australia, Perth in south-western Australia, and Darwin and Katherine in the Northern Territory. Overall, 43 cucurbit-growing farms and 172 crops of susceptible cultivars were sampled. From each crop, shoot samples were collected from plants chosen at random and from symptomatic plants. Shoot samples were sometimes also collected from potential alternative virus hosts (cucurbit volunteer plants and weeds). All samples were tested by enzyme-linked immunosorbent assay (ELISA) using antibodies to Cucumber mosaic virus (CMV), Papaya ringspot virus-cucurbit strain (PRSV), Squash mosaic virus (SqMV), Watermelon mosaic virus (WMV), and Zucchini yellow mosaic virus (ZYMV). Samples from one-third of the crops were also tested by tissue blot immunosorbent assay (TBIA) using generic luteovirus antibodies. Overall, 72% of farms and 56% of crops sampled were virus-infected. The growing areas with the highest incidences of virus infection were Darwin and Carnarvon, and those with the lowest incidences were Katherine and Perth. For WA, overall 78% of farms and 56% of crops were virus-infected, and in the NT the corresponding figures were 55% of farms and 54% of crops. Overall virus incidences in individual crops sometimes reached 100% infection. Crops of cucumber, melon, pumpkin, squash, and zucchini were all infected, with squash and zucchini being the most severely affected. The most prevalent viruses were ZYMV and PRSV, each being detected in 5 and 4 of 6 cucurbit-growing areas, respectively, with infected crop incidences of <1–100%. SqMV was detected in 2 cucurbit-growing areas, sometimes reaching high incidences (<1–60%). WMV and CMV were found in 3 and 4 of 6 cucurbit-growing areas, respectively, but generally at low incidences in infected crops (<1–8%). Infection with luteovirus was found in 3 growing areas but only occurred in 16% of crops. Beet western yellows virus was detected once but at least one other luteovirus was also present. Infection of individual crops by more than 1 virus was common, with up to 4 viruses found within the same crop. Virus-resistant pumpkin cultivars (6 crops) had little infection when adjacent virus-susceptible cucurbit crops had high virus incidences. Viruses were detected in cucurbit volunteer plants and weeds, suggesting that they may act as important reservoirs for spread to nearby cucurbit crops. In general, established cucurbit-growing farms in close proximity to others and with poor crop hygiene suffered most from virus epidemics, whereas isolated farms with large-sized crops or that had only recently started growing cucurbits had less infection. The extent of infection revealed in this survey, and the financial losses to growers resulting from virus-induced yield losses and high fruit rejection rates, are cause for concern for the Australian cucurbit industry.

Incidence and distribution of Barley yellow dwarf virus and Cereal yellow dwarf virus in over-summering grasses in a Mediterranean-type environment

During the summer periods of 2000 and 2001, incidences of infection with Barley yellow dwarf virus (BYDV) and Cereal yellow dwarf virus (CYDV) were determined in grass weeds and volunteer cereals surviving at isolated sites throughout the grainbelt of south-western Australia, which has a Mediterranean-type climate. Samples of Cynodon dactylon, Eragrostis curvula, Erharta calycina, Pennisetum clandestinum, and volunteer cereals (mostly wheat) were tested for BYDV (serotypes MAV, PAV and RMV) and CYDV (serotype RPV), and those of at least 19 other grass species were tested for BYDV only (serotypes PAV and MAV). In 2000, BYDV and/or CYDV were detected in 33% of 192 sites in 0.7% of 26 700 samples, and in 2001 the corresponding values were 19% of 176 sites and 0.5% of 21 953 samples. Infection was distributed relatively evenly throughout the different annual average rainfall zones of the grainbelt, but when sites were categorised according to actual rainfall for late spring to early autumn, the proportion of sites and samples infected increased where such rainfall exceeded 300 mm. In both summer sampling periods, the most abundant grass species were C. dactylon and E. curvula, with BYDV and/or CYDV being detected in 0.1–0.6% and 0.1–0.5% of samples, respectively. The corresponding incidences were 0–1% for Erharta calycina, 7–8% for P. clandestinum, and 0.2–2% for volunteer wheat. The most abundant species tested for BYDV only were Chloris truncata and Digitaria sanguinalis, with infection incidences of 0.2–0.7 and 0.2–0.3%, respectively. Chloris virgata (2–3%) and Urochloa panicoides (0.3–0.6%) were the only other infected species. Within individual sites and host species, the greatest incidences of CYDV were in P. clandestinum (23% in 2000 and 18% in 2001) and of BYDV in Chloris virgata (14% with PAV and 12% with MAV in 2000). Small populations of grass-infesting aphids were found over-summering at 26% (2000) and 3% (2001) of sites and occurred in all 3 annual rainfall zones. The predominant species was Hysteroneura setariae, but Rhopalosiphum maidis, R. padi, and Sitobion miscanthi occurred occasionally. Presence of over-summering BYDV, CYDV, and aphids in all rainfall zones has important implications for virus spread to cereal crops throughout the grainbelt.

Further studies on Carrot virus Y: hosts, symptomatology, search for resistance, and tests for seed transmissibility

Carrot virus Y (CarVY) was studied to provide information on its host range and symptoms, identify any alternative natural hosts and sources of host resistance in carrot germplasm, and determine whether it is seed-borne. Twenty-two species belonging to the Apiaceae were inoculated with CarVY by viruliferous aphids in the glasshouse. Systemic infection with CarVY developed in carrot itself, 4 other Daucus species, 5 herbs, 1 naturalised weed, and 2 Australian native plants. When 7 of these host species were exposed to infection in the field, all became infected systemically. In both glasshouse and field, the types of symptoms that developed in infected plants and their severity varied widely from host to host. Following inoculation with infective sap, the virus was detected in inoculated leaves of 1 additional species in the Apiacaeae, and 2 species of Chenopodiaceae. A field survey did not reveal any alternative hosts likely to be important as CarVY infection reservoirs. When 34 accessions of wild carrot germplasm and 16 of other Daucus spp. were inoculated with infective aphids, symptom severity varied widely among accessions but no source of extreme resistance to CarVY was found. Tests on seedlings grown from seed collected from individual infected plants or field plantings (most with CarVY incidences of >92%) of cultivated carrot (34 135 seeds), wild carrot (20 978 seeds), Anethum graveolens (22 921 seeds), and 3 other host species (3304 seeds) did not detect any seed transmission of CarVY. The implications of these results for control of the virus in carrot crops, minimising the losses it causes, and avoiding its introduction to new locations are discussed.

Occurrence of virus infection in seed stocks and 3-year-old pastures of lucerne (Medicago sativa)

In tests on seed samples from 26 commercial seed stocks of lucerne (Medicago sativa) to be sown in south-western Australia in 2001, infection with Alfalfa mosaic virus (AMV) was found in 21 and Cucumber mosaic virus (CMV) in 3 of them. Bean yellow mosaic virus (BYMV) and Pea seed-borne mosaic virus (PSbMV) were not detected in any. Incidences of infection within individual affected seed samples were 0.1–4% (AMV) and 0.1–0.3% (CMV), and the infected seed stocks were from 3 (CMV) and at least 11 (AMV) different lucerne cultivars. In a survey of 31 three-year-old lucerne pastures in the same region in 2001, in randomly collected samples, AMV was found in 30 and luteovirus infection in 11 pastures. Pastures in high, medium, and low rainfall zones were all infected. Incidences of AMV within individual infected pastures were high, with 50–98% of plants infected in 20 of them and only 3 having <10% infection, but luteovirus incidences were only 1–5%. In addition to various cultivar mixtures, at least 8 (AMV) and 3 (luteoviruses) different individual lucerne cultivars were infected. When the species of luteovirus present were identified, they were Bean leaf roll virus, Beet western yellows virus ( = Turnip yellows virus), or Subterranean clover red leaf virus ( = Soybean dwarf virus). CMV and legume-infecting potyviruses (BYMV, PSbMV, and Clover yellow vein virus) were not detected in any of the lucerne samples. Acyrthosiphon kondoi infestation was common in the samples collected, and A. pisum and Aphis craccivora were also found. Widespread infection in lucerne stands, and their frequent colonisation by aphid vectors, are cause for concern not only because of virus-induced production losses in lucerne itself but also because they provide virus infection reservoirs for spread to nearby grain legume crops and annual legume pastures.

Lettuce big-vein disease: sources, patterns of spread, and losses

Most batches of lettuce seedlings taken over an 18-month period from a vegetable nursery were infested with lettuce big-vein disease (LBVD) with an up to 31% incidence. Using lettuce seedlings in bait tests, contamination was detected at the nursery in potting mix composted for different periods and in dirt from under the benches, and at the bark supplier's site in this ingredient of the potting mix and waste 'bark' from the ground. In a field experiment in which lettuce seedlings from the infested nursery were inoculated with infested roots or left uninoculated before transplanting into subplots on land with no history of lettuce planting, disease progress followed a sigmoid curve with the former but an almost straight line with the latter. However, significant clustering of symptomatic plants was found only in the subplot with the uninoculated plants. Leaf symptoms of LBVD were more severe in lettuces infested later, whereas symptoms in those infested earlier were obvious initially but then became milder. The disease impaired formation of hearts: the proportion of symptomatic plants that lacked hearts was 24–36% when leaf symptoms first appeared 5–7 weeks after transplanting, but 14–16% after 8–9 weeks. When leaf symptoms first appeared at 5–6 weeks, there was a fresh weight loss of 14–15% for heads (all plants) and 39% for hearts (excluding plants without hearts). When leaf symptoms first appeared 7 weeks after transplanting, there was no significant yield loss for heads and only a 14% loss for hearts. At 8–9 weeks, there were no significant yield losses for heads or hearts.

Yield losses caused by virus infection in four combinations of non-persistently aphid-transmitted virus and cool-season crop legume

Field experiments provided quantitative information on the yield losses caused by virus infection within 4 different combinations of non-persistently aphid-transmitted virus and cool-season crop legume: Alfalfa mosaic virus (AMV) in chickpea, faba bean and lentil, and Cucumber mosaic virus (CMV) in lentil. Virus infection foci were introduced into plots and naturally occurring aphids spread infection from these to the other plants. Plants were tagged individually when typical virus symptoms first appeared during the growing period. Paired plant comparisons between symptomatic and asymptomatic plants were made to measure different yield loss parameters. Late infection with AMV in faba bean cv. Fiord diminished shoot dry weight by 41% and seed yield by 45%, but plants infected earlier recovered sufficiently from their initial shock reaction not to produce significant yield losses. In plants of lentil cv. Matilda first showing symptoms at different times, infection with AMV decreased shoot dry weight by 74–76%, seed yield by 81–87% and individual seed weight by 10–21%, while CMV diminished shoot dry weight by 72–81%, seed yield by 80–90% and individual seed yield by 17–25%. Early infection with AMV killed plants of chickpea cv. Tyson while later infection decreased shoot dry weight by 50%, seed yield by 98% and individual seed weight by 90%. The first tentative evidence for seed transmission of AMV in faba bean is reported with a transmission rate of 0.04%.

The complete nucleotide sequence of Subterranean clover mottle virus

The complete nucleotide sequence of Subterranean clover mottle virus (SCMoV) genomic RNA has been determined. The SCMoV genome is 4,258 nucleotides in length. It shares most nucleotide and amino acid sequence identity with the genome of Lucerne transient streak virus (LTSV). SCMoV RNA encodes four overlapping open reading frames and has a genome organisation similar to that of Cocksfoot mottle virus (CfMV). ORF1 and ORF4 are predicted to encode single proteins. ORF2 is predicted to encode two proteins that are derived from a -1 translational frameshift between two overlapping reading frames (ORF2a and ORF2b). A search of amino acid databases did not find a significant match for ORF1 and the function of this protein remains unclear. ORF2a contains a motif typical of chymotrypsin-like serine proteases and ORF2b has motifs characteristically present in positive-stranded RNA-dependent RNA polymerases. ORF4 is likely to be expressed from a subgenomic RNA and encodes the viral coat protein. The ORF2a/ORF2b overlapping gene expression strategy used by SCMoV and CfMV is similar to that of the poleroviruses and differ from that of other published sobemoviruses. These results suggest that the sobemoviruses could now be divided into two distinct subgroups based on those that express the RNA-dependent RNA polymerase from a single, in-frame polyprotein, and those that express it via a -1 translational frameshifting mechanism.

Yield limiting potential of necrotic and non-necrotic strains of Bean yellow mosaic virus in narrow-leafed lupin (Lupinus angustifolius)

The yield losses caused by necrotic and non-necrotic strains of Bean yellow mosaic virus (BYMV) in narrow-leafed lupin (Lupinus angustifolius) were quantified in field experiments. Clover plants infected with either were introduced into plots to provide infection sources, and aphids spread infection to the lupin plants. When the effects of virus infection were examined in individual lupin plants infected with necrotic BYMV, they were killed by early infection so there was no seed production. With late infection, shoot dry wt, seed yield, and seed number were decreased by at least 55%, 80%, and 74%, respectively. With non-necrotic BYMV, shoot dry wt, seed yield, and seed number diminished with increasing duration of plant infection, these decreases ranging over 27–88%, 48–99%, and 35–98% for late to early infection, respectively. In partially infected stands in which both necrotic and non-necrotic BYMV were spreading, an additional incidence of 28% in plots with introduced non-necrotic strain foci over that in plots without introduced foci was sufficient to decrease overall seed yield significantly. However, an additional incidence of 10% was insufficient to do so in plots with introduced necrotic strain foci. In plots into which different numbers of clover plants infected with non-necrotic BYMV were introduced, subsequent incidence of infection depended on the magnitude of the initial virus source, and yield was decreased by 21–24%, 31–43%, and 64–66% with 4, 8, or 16 foci/plot, respectively. With both types of strain, yield loss in infected plants was mainly due to failure to produce any seed or to fewer seeds being produced, but smaller seed size also contributed. These results show that non-necrotic strains of BYMV have considerable yield-limiting potential in narrow-leafed lupin crops despite causing milder symptoms than necrotic strains. No evidence was obtained of seed-transmission of non-necrotic BYMV in narrow-leafed lupin, but a 0.2% seed transmission rate was detected in yellow lupin (Lupinus luteus).

A non-aphid-transmissible isolate of bean yellow mosaic potyvirus has an altered NAG motif in its coat protein

An isolate of Bean yellow mosaic virus (BYMV) not transmitted by aphids (NAT) was compared with the aphid-transmissible isolate (MI) from which it was derived. For each isolate, the sequence of the coat protein and parts of the helper component was determined. A single nucleotide substitution caused a NAG to NAS alteration in the coat protein of the non aphid-transmissible isolate. Loss of aphid transmissibility in isolate BYMV(MI)-NAT was most likely caused by this mutation within the NAG motif. Systemic movement and accumulation of the virus in infected plants were not affected by the mutation.

Quantification of Yield Losses Caused by Barley yellow dwarf virus in Wheat and Oats

Grain yield data obtained from five field experiments in Western Australia from 1992 to 1994, in which insecticide applications suppressed the spread of Barley yellow dwarf virus (BYDV) in wheat and oats, were used to quantify the relationships between incidence of BYDV and yield gaps, 500-seed weight, and percent shriveled grain. Yield gaps ranged from 0 to 2,700 kg/ha, and the relationship between yield gap and incidence of BYDV was always linear. Single point yield loss models revealed that BYDV infection explained most of the variation in yield gaps. There was a significant linear relationship between incidence of BYDV and 500-seed weight for wheat, but not for oats. The percent shriveled grain always increased with an increase in incidence of BYDV in wheat but not in oats. Cost-benefit relationships were determined for the return on investment when deploying imidacloprid-treated seed and/or one or two foliar applications of pyrethroid insecticides to reduce incidence of BYDV and to decrease the yield gaps in wheat and oats due to BYDV.

Incidence of virus infection in experimental plots, commercial crops, and seed stocks of cool season crop legumes

Experimental plots of cool season crop legumes growing at diverse locations in Western Australia were inspected for plants with suspect virus symptoms over 4 growing seasons (1994, 1997, 1998, 1999), and plant samples were tested for infection with alfalfa mosaic (AMV), bean yellow mosaic (BYMV), cucumber mosaic (CMV), and pea seed-borne mosaic (PSbMV) viruses. All 4 viruses were detected in faba bean (Vicia faba); BYMV, CMV, and PSbMV in field pea (Pisum sativum); AMV, CMV, and PSbMV in lentil (Lens culinaris); and AMV and CMV in chickpea (Cicer arietinum). Among minor crop species, AMV, BYMV, and CMV were found in narbon bean (V. narbonensis) and grass pea (Lathyrus sativus); BYMV and CMV in dwarf chickling (L. cicera); BYMV in bitter vetch (V. e r v i l i a ) and L. clymenum; and AMV in fenugreek (Trigonella foenum-graecum). Incidences of individual viruses varied widely from site to site but plot infection sometimes reached 100%. Symptom severity varied widely with virus–crop combination. In large-scale surveys of commercial crops of field pea and faba bean over 2 (1998, 1999) and 3 (1994, 1998, 1999) growing seasons, respectively, randomly collected samples from each crop were tested for presence of AMV, BYMV, CMV, and PSbMV. In 1999 they were also tested for beet western yellows virus (BWYV). All 5 viruses were detected in both species. BWYV was found in 35% of faba bean and 56% of the field pea crops sampled in 1999, with incidences of infection in individual crops up to 40% and 49%, respectively. PSbMV was found in 42% and BYMV in 18% of field pea crops in 1999. In individual crops, highest infection incidences of BYMV and PSbMV detected were 31% for BYMV in faba bean in 1998 and 9% for PSbMV in field pea in 1999. CMV and AMV incidences in both species never exceeded 7% of crops or 4% of plants within individual crops. Infection by 2 different viruses within individual crops was common, even 3 were sometimes found. Cultivars infected with most viruses were Fiesta and Fiord for faba bean, and Dundale, Laura, and Magnet for field pea. BYMV was detected in the crop tested of dwarf chickling. In tests on seed samples from Western Australia of 30 commercial seed stocks of field pea, 11 of faba bean, and 50 of chickpea, PSbMV was detected in 11, 1, and 1, respectively; CMV in 1, 1, and 3; BYMV in 3, 1, and 0; and AMV in 0, 0, and 1. This appears to be the first record of seed transmission of CMV in pea and faba bean. Seed samples from Victoria were also found to contain viruses: PSbMV in pea and AMV in lentil. Widespread infection with viruses in evaluation plots and commercial crops of cool season crop legumes is a cause for concern, especially where individual crop incidences are high and 2 or more viruses are present. Sowing of infected seed stocks leads to introduction of randomly dispersed sources of virus infection within the crop sown, resulting in spread of infection and yield losses. Appropriate control measures are discussed.

Cucumber mosaic cucumovirus infection of cool-season crop, annual pasture, and forage legumes: susceptibility, sensitivity, and seed transmission

Seven field experiments were done in 19944—98 to determine the relative susceptibilities and sensitivities of a wide range of alternative crop, annual pasture, and forage legumes to infection with cucumber mosaic virus (CMV). Seed harvested from some species was tested for seed transmission of the virus. Most of the 24 genotypes of Cicer arietinum and 39 of Lens culinaris tested in 2 replicated field experiments were ranked as highly susceptible or susceptible; moderate resistance was recorded in 8Lens culinaris genotypes, the most resistant of which was ILL7163, and in C. arietinum cv. Amethyst Mutant. Sensitivity varied from low to high in different Lens culinaris genotypes, whereas in C. arietinum they were all sensitive or highly sensitive. In 4 other experiments, 12 species (49 genotypes) of other crop legumes were ranked as follows: Vicia narbonensis susceptible to moderately resistant, V. ervilia susceptible, Pisum sativum resistant, and V. faba resistant to potentially highly resistant; Lathyrus cicera,L. clymenum, L. ochrus, L. sativus, L. tingitanus, V. benghalensis, V. monantha, and V. s a t i v a were not infected. V. ervilia andV. faba were very sensitive to infection, but V. narbonensis had intermediate sensitivity and P. s a t i v u m was tolerant. When single genotypes of each of 16 pasture and forage species were tested in 2 replicated field experiments, 1 was highly susceptible, 3 were susceptible, 9 moderately resistant, 2 resistant, and 1 was potentially highly resistant. The 4 most susceptible were the sensitive species Trifolium incarnatum and T. isthmocarpum and the intermediately sensitive species T. michelianum and T. vesiculosum. T. squarrosum (intermediate sensitivity) and T. spumosum (very sensitive) were resistant and Ornithopus sativus was not infected. In sap inoculations, L. ochrus,L. sativus, and P. sativum occasionally became infected. In aphid inoculations,Lens culinaris ILL7163 and V. faba became infected only rarely and V. benghalensis cv. Popany developed a systemic hypersensitive reaction. The following were not infected in the field or glasshouse: L. cicera ATC80521, L. clymenum C7022, O. sativus cv. Cadiz, and V. sativa cv. Languedoc.Seed transmission of CMV was detected for the first time in one crop species, V. narbonensis(0.1mp;mdash;0.8%), and confirmed in C. arietinum (0.2–0.3%) and Lens culinaris (0.3%). It was also detected in T. cherleri (0.05%), T. clypeatum (0.05%), T. dasyurum (0.1%), T. incarnatum (5%), T. purpureum (0.04%), T. spumosum (0.5%), T. squarrosum (0.1%), and T. vesiculosum (1%), but not in 8 other pasture or forage species. The high susceptibility and sensitivity to CMV of some alternative crop, annual pasture, and forage legumes is cause for concern, especially when they are intended for sowing in CMV-prone high rainfall zones. Infection of seed stocks with CMV is also of concern as it leads to inadvertent introductions of the virus.

Alfalfa mosaic and pea seed-borne mosaic viruses in cool season crop, annual pasture, and forage legumes: susceptibility, sensitivity, and seed transmission

Field experiments determined the susceptibilities and sensitivities of a wide range of crop, annual pasture, and forage legumes to infection with alfalfa mosaic (AMV) and pea seed-borne mosaic (PSbMV) viruses. Seed harvested from most of the species was tested for virus seed transmission. With AMV, all 23 Cicer arietinum genotypes tested were ranked as highly susceptible, and 9 out of 19 Lens culinaris genotypes as highly susceptible, 8 susceptible, 1 moderately resistant, and 1 resistant. Genotypes of Vicia narbonensis (5), Lathyrus cicera (5), L. sativus (5), L. ochrus(2), V. sativa (1), and V. benghalensis (1) were highly susceptible, susceptible, or moderately resistant. Genotypes of Pisum sativum (5) and V. faba(3) were susceptible, moderately resistant, or resistant but 1 genotype of V. faba was not found infected. Sensitivities ranged from low in L. ochrus to high in some genotypes of most species tested exceptV. benghalensis. The 20 genotypes (19 species) of pasture and forage legumes ranged from ‘not found infected’ in Hedysarum coronarium to ‘highly susceptible’ in Ornithopus sativus and Trifolium resupinatum. Sensitivity varied from low in T. michelianum to very high in Biserrula pelecinusand Ornithopus sativus. With PSbMV, the genotypes ofP. s a t i v u m (17), V. narbonensis (5), and L. cicera(3) were ranked as highly susceptible, susceptible, or moderately resistant, while those of L. ochrus(3), V. faba(6), V. sativa (3), V. benghalensis (2) and V. ervilia(1) were either moderately resistant or resistant. The genotypes of C. arietinum (6) and Lens culinaris (6) were all resistant. With L. sativus, 2 genotypes were resistant and 1 was not found infected. Sensitivities ranged from low in some P. sativum genotypes to high in some ofL. ciceraand V. narbonensis. The seed coats of 9 crop legume species developed necrotic ring markings, a serious quality defect due to PSbMV infection. Of the 19 genotypes (1/species) of pasture and forage legumes, 4 were resistant with only symptomless infection developing and the remainder not found infected. In glasshouse inoculations to genotypes not found infected in the field, AMV infected V. faba cv. Ascot systemically butH. coronarium cv. Grimaldi (with AMV) and L. sativus BIO L254 (with PSbMV) only became infected in inoculated leaves, H. coronarium developing a localised hypersensitive reaction. Seed transmission of AMV was detected in L. cicera(2%), L. sativus (0.9–4%), V. benghalensis(0.9%), V. narbonensis (0.1%), and V. sativa (0.7%). It was also found in 15 pasture and forage legume species, ranging from 0.05% in T. michelianum to 7% in Trigonella balansae. Seed transmission of PSbMV was detected in L. cicera(0.4%), L. clymenum (5%), L. ochrus (0.7%), L. sativus (1%), P sativum(1–18%), V. benghalensis (0.1%), V. faba (2%), and V. sativa (0.3%). The implications of these findings and their importance to the management of these and other virus diseases are discussed.

Bean yellow mosaic potyvirus infection of alternative annual pasture, forage, and cool season crop legumes: susceptibility, sensitivity, and seed transmission

Seven field and 5 glasshouse experiments were done during 1994–98 to determine the relative susceptibilities and sensitivities of a wide range of alternative annual pasture, forage, and crop legumes to infection with isolate MI of bean yellow mosaic virus (BYMV). Seed harvested from some species was also tested for seed transmission of the virus. Seven of 18 genotypes belonging to 17 species of annual pasture and forage legumes evaluated in 2 replicated field experiments were ranked as highly susceptible to BYMV, 7 as susceptible, 2 as moderately resistant, 1 as resistant, and 1 as highly resistant. The most susceptible and sensitive were Biserrula pelecinus, Trifolium cherleri, T. incarnatum, and T. spumosum. Ornithopus sativus was resistant but sensitive, whereas Hedysarum coronarium was highly resistant. H. coronarium was not infected when manually inoculated repeatedly with 3 different BYMV isolates. Seventy-three of the 94 genotypes of 7 crop legume species tested in the same replicated field experiments were ranked as highly susceptible, including 58/68 of Lens culinaris. Of the remaining genotypes, 6 were susceptible, 5 moderately resistant, 9 resistant, and 1 highly resistant. Five other crop legumes were included in other field experiments in which these species were ranked as highly susceptible (1) or resistant (4). Overall, the most susceptible and sensitive crop legume species were Lens culinaris (most genotypes), Lathyrus cicera, L. ochrus, and Vicia narbonensis. Lathyrus sativus (3 genotypes only), V. sativa (4 genotypes), Cicer arietinum, Pisum sativum, and V. faba were resistant to isolate MI, and Lens culinaris ILL7163 was highly resistant. When infected, C. arietinum was ranked as highly sensitive but symptoms within the other resistant crop species varied in sensitivity between genotypes. Extreme resistance was confirmed in Lens culinaris ILL7163 when it was manually and aphid-inoculated repeatedly with 3 different BYMV isolates. When testing seedlings for seed transmission of BYMV, germination on moist paper towels before testing usually proved more effective than growing in soil in the glasshouse. Low rates of seed transmission of BYMV (0.03–1%) were detected in 9 alternative pasture or forage and 3 alternative crop legume species. This is the first report of seed transmission of BYMV in these species. The pasture or forage species with the highest seed transmission rates were T. clypeatum and T. spumosum (both 1%). The crop legume species in which seed transmission was found were L. cicera (0.1%), L. sativus (0.2%), and V. sativa (0.5%). The high susceptibility and sensitivity to BYMV in some alternative annual pasture, forage, and crop legumes is a cause for concern, especially when they are intended for sowing in BYMV-prone high rainfall zones. Seed transmission of BYMV also leads to inadvertent introduction of the virus to new sites.

Viruses infecting canola (Bassica napus) in south-west Australia: incidence, distribution, spread, and infection reservoir in wild radish (Raphanus raphinistrum)

Over 2 growing seasons, the incidences of infection with beet western yellows (BWYV), cauliflower mosaic (CaMV), and turnip mosaic (TuMV) viruses were determined in canola (Brassica napus) crops growing in the agricultural area of south-west Australia. Tissue blot immunoassay was used to detect BWYV and enzyme-linked immunosorbent assay to detect CaMV and TuMV. In 1998, BWYV was detected in 59% of 159 crops surveyed, whereas in 1999 it was found in 66% of 56 crops. Incidences within individual infected crops were 1–65% (1998) and 1–61% (1999). Infection occurred widely in high and medium rainfall zones, but was also readily detected in the low rainfall zone. In addition, BWYV was found in canola samples from 5 sites in New South Wales. Most cultivars tested (9 of 10) in the canola crop survey were infected with BWYV. No clear relationship was found between BWYV infection and any particular type of disease symptom. Overall, the incidence of BWYV at the crop edge was marginally greater than that inside the crop. CaMV was detected in 27% of 143 crops in 1998 but in only 2 of 47 in 1999. Incidences within individual infected crops were 1–17% in 1998 but only 1% in 1999. CaMV infected 6 of 10 cultivars and was present in high, medium, and low rainfall zones. Obvious chlorotic ringspot symptoms were associated with CaMV infection. TuMV was detected in 5% of 139 crops in 1998 but in only 1 of 47 from 1999. Incidences within the individual infected crops were 1–5% in 1998 and 1% in 1999; 3 of 10 cultivars were infected and it was found in high and medium rainfall zones. BWYV, CaMV, and TuMV were all found infecting wild radish (Raphanus raphinistrum). In general, incidences of BWYV were greater in wild radish than in canola. In 1998, BWYV was detected in wild radish at 9 of 12 sites sampled in 5 of 6 districts, with infection incidences up to 48%. In 1999, it was detected at all 10 sites sampled in 7 districts, with incidences up to 96%. Infected samples came from all rainfall zones, and from several different types of sites, some of which were distant from canola crops. Despite the presence of possible viral symptoms in wild radish, none was clearly associated with BWYV infection. In contrast, TuMV caused obvious mottle and ‘oak leaf’ patterns in wild radish plants. The finding of widespread virus infection in canola crops and a substantial virus reservoir in wild radish weeds is cause for concern to the canola industry.