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

Australian Cool-Season Pulse Seed-Borne Virus Research: 1. Alfalfa and Cucumber Mosaic Viruses and Less Important Viruses

Here, we review the research undertaken since the 1950s in Australia's grain cropping regions on seed-borne virus diseases of cool-season pulses caused by alfalfa mosaic virus (AMV) and cucumber mosaic virus (CMV). We present brief background information about the continent's pulse industry, virus epidemiology, management principles and future threats to virus disease management. We then take a historical approach towards all past investigations with these two seed-borne pulse viruses in the principal cool-season pulse crops grown: chickpea, faba bean, field pea, lentil, narrow-leafed lupin and white lupin. With each pathosystem, the main focus is on its biology, epidemiology and management, placing particular emphasis on describing field and glasshouse experimentation that enabled the development of effective phytosanitary, cultural and host resistance control strategies. Past Australian cool-season pulse investigations with AMV and CMV in the less commonly grown species (vetches, narbon bean, fenugreek, yellow and pearl lupin, grass pea and other Lathyrus species) and those with the five less important seed-borne pulse viruses also present (broad bean stain virus, broad bean true mosaic virus, broad bean wilt virus, cowpea mild mottle virus and peanut mottle virus) are also summarized. The need for future research is emphasized, and recommendations are made regarding what is required.

Host Resistance to Virus Diseases Provides a Key Enabler towards Fast Tracking Gains in Grain Lupin Breeding

Four lupin species, Lupinus angustifolius, L. albus, L. luteus, and L. mutabilis, are grown as cool-season grain legume crops. Fifteen viruses infect them. Two of these, bean yellow mosaic virus (BYMV) and cucumber mosaic virus (CMV), cause diseases that threaten grain lupin production. Phytosanitary and cultural control measures are mainly used to manage them. However, breeding virus-resistant lupin cultivars provides an additional management approach. The need to develop this approach stimulated a search for virus resistance sources amongst cultivated lupin species and their wild relatives. This review focuses on the progress made in optimizing virus resistance screening procedures, identifying host resistances to BYMV, CMV, and additional viral pathogen alfalfa mosaic virus (AMV), and the inclusion of BYMV and CMV resistance within lupin breeding programs. The resistance types found in different combinations of virus and grain lupin species include localized hypersensitivity, systemic hypersensitivity, extreme resistance, and partial resistance to aphid or seed transmission. These resistances provide a key enabler towards fast tracking gains in grain lupin breeding. Where studied, their inheritance depended upon single dominant genes or was polygenic. Although transgenic virus resistance was incorporated into L. angustifolius and L. luteus successfully, it proved unstable. Priorities for future research are discussed.

Host plant affiliations of aphid vector species found in a remote tropical environment

The Ord River Irrigation Area (ORIA) produces annual crops during the dry season (April to October), and perennial crops all-year-round, and is located in tropical northwestern Australia. Sandalwood plantations cover 50 % of the ORIA's cropping area. Aphids cause major crop losses through transmission of viruses causing debilitating diseases and direct feeding damage. During 2016-2017, in both dry and wet seasons a total of 3320 leaf samples were collected from diverse types of sites on cultivated and uncultivated land and 1248 (38 %) of them were from aphid-colonized plants. In addition, aphids were found at 236 of 355 sampling sites. The 62 plant species sampled came from 23 families 19 of which contained aphid-colonized species. Aphid hosts included introduced weeds, Australian native plants, and volunteer or planted crop plants. Six aphid species were identified by light microscopy and CO1 gene sequencing, but there was no within species nucleotide sequence diversity. Aphis nerii, Hysteroneura setariae, Rhopalosiphum maidis and Schoutedenia ralumensis each colonized 1-3 plant species from a single plant family. A. craccivora colonized 14 species in five plant families. A. gossypii was the most polyphagous species colonizing 19 species in 11 plant families. A. gossypii, A. craccivora, A. nerii and S. ralumensis were found in both wet and dry seasons. Because of A. craccivora's prevalence and high incidences on understory weeds and host trees, sandalwood plantations were important reservoirs for aphid spread to wild and crop plant hosts growing in cultivated and uncultivated land. Alternative hosts growing in rural bushland, irrigation channel banks, vacant or fallow land, and orchard plantation understories also constituted significant aphid reservoirs. This study provides new knowledge of the ecology of aphid vector species not only in the ORIA but also in tropical northern Australia generally. It represents one of relatively few investigations on aphid ecology in tropical environments worldwide.

Application of Loop-Mediated Isothermal Amplification in an Early Warning System for Epidemics of an Externally Sourced Plant Virus

Restricting Turnip yellows virus (TuYV) spread in canola (Brassica napus) crops often relies upon the application of systemic insecticides to protect young vulnerable plants from wide-scale green-peach aphid (GPA; Myzus persicae) colonization and subsequent virus infection. For these to be applied at the optimal time to ensure they prevent epidemics, growers would need to be forewarned of incoming viruliferous aphid migration and colonization. This study was conducted to field validate a loop-mediated isothermal amplification (LAMP) protocol designed to detect TuYV in aphids caught on traps and develop an early warning system for TuYV epidemics. Double-sided yellow sticky traps were deployed at 30 sites sown with canola over a two-year period in the south-west Australian grainbelt. Using LAMP, the percentage (%) of trap sides with TuYV-carrying aphids was measured and related to TuYV infection incidence in the adjacent crop. When TuYV was detected in aphids on >30% trap sides in a six-week period from pre-emergence to GS15 (five-leaf stage), TuYV reached >60% crop incidence by GS30 (beginning of stem elongation). Whereas, TuYV detection in aphids on ≤15% trap sides during this period was associated with ≤6% TuYV incidence by GS30. Furthermore, when large numbers of aphids, including GPA, were caught during this period but no TuYV was detected in them, minimal TuYV spread (≤5%) occurred in the crop by GS30. Therefore, the LAMP TuYV protocol can be used in an early warning system for TuYV epidemics by providing detection of initial viruliferous aphid migration into a canola crop before they establish colonies throughout the crop and spread virus. This would enable proactive, non-prophylactic, and thereby more effective systemic insecticide applications to minimize seed yield and quality losses due to early season TuYV infection.

Forecasting model for Pea seed-borne mosaic virus epidemics in field pea crops in a Mediterranean-type environment

An empirical model was developed to forecast Pea seed-borne mosaic virus (PSbMV) incidence at a critical phase of the annual growing season to predict yield loss in field pea crops sown under Mediterranean-type conditions. The model uses pre-growing season rainfall to calculate an index of aphid abundance in early-August which, in combination with PSbMV infection level in seed sown, is used to forecast virus crop incidence. Using predicted PSbMV crop incidence in early-August and day of sowing, PSbMV transmission from harvested seed was also predicted, albeit less accurately. The model was developed so it provides forecasts before sowing to allow sufficient time to implement control recommendations, such as having representative seed samples tested for PSbMV transmission rate to seedlings, obtaining seed with minimal PSbMV infection or of a PSbMV-resistant cultivar, and implementation of cultural management strategies. The model provides a disease forecast risk indication, taking into account predicted percentage yield loss to PSbMV infection and economic factors involved in field pea production. This disease risk forecast delivers location-specific recommendations regarding PSbMV management to end-users. These recommendations will be delivered directly to end-users via SMS alerts with links to web support that provide information on PSbMV management options. This modelling and decision support system approach would likely be suitable for use in other world regions where field pea is grown in similar Mediterranean-type environments.

Pea seed-borne mosaic virus Pathosystem Drivers under Mediterranean-Type Climatic Conditions: Deductions from 23 Epidemic Scenarios

Drivers of Pea seed-borne mosaic virus (PSbMV) epidemics in rainfed field pea crops were examined under autumn to spring growing conditions in a Mediterranean-type environment. To collect aphid occurrence and PSbMV epidemic data under a diverse range of conditions, 23 field pea data collection blocks were set up over a 6-year period (2010 to 2015) at five locations in the southwest Australian grain-growing region. PSbMV infection levels in seed sown (0.1 to 13%), time of sowing (22 May to 22 June), and cultivar (Kaspa or PBA Twilight) varied with location and year. Throughout each growing season, rainfall data were collected, leaf and seed samples were tested to monitor PSbMV incidence in the crop and transmission from harvested seed, and sticky traps were used to monitor flying aphid numbers. Winged migrant Acyrthosiphon kondoi, Lipaphis erysimi, Myzus persicae, and Rhopalosiphum padi were identified in green tile traps in 2014 and 2015. However, no aphid colonization of field pea plants ever occurred in the blocks. The deductions made from collection block data illustrated how the magnitude of PSbMV spread prior to flowering is determined by two primary epidemic drivers: (i) PSbMV infection incidence in the seed sown, which defines the magnitude of virus inoculum source for within-crop spread by aphids, and (ii) presowing rainfall that promotes background vegetation growth which, in turn, drives early-season aphid populations and the time of first arrival of their winged migrants to field pea crops. Likely secondary epidemic drivers included wind-mediated PSbMV plant-to-plant contact transmission and time of sowing. PSbMV incidence at flowering time strongly influenced transmission rate from harvested seed to seedlings. The data collected are well suited for development and validation of a forecasting model that informs a Decision Support System for PSbMV control in field pea crops.

Control of plant virus diseases in cool-season grain legume crops

Cool-season grain legume crops become infected with a wide range of viruses, many of which cause serious diseases and major yield losses. This review starts by discussing which viruses are important in the principal cool-season grain legume crops in different parts of the world, the losses they cause and their economic impacts in relation to control. It then describes the main types of control measures available: host resistance, phytosanitary measures, cultural measures, chemical control, and biological control. Examples are provided of successful deployment of the different types of measures to control virus epidemics in cool-season grain legume crops. Next it emphasizes the need for integrated approaches to control because single control measures used alone rarely suffice to adequately reduce virus-induced yield losses in these crops. Development of effective integrated disease management (IDM) strategies depends on an interdisciplinary team approach to (i) understand the ecological and climatic factors which lead to damaging virus epidemics and (ii) evaluate the effectiveness of individual control measures. In addition to using virus-resistant cultivars, other IDM components include sowing virus-tested seed stocks, selecting cultivars with low seed transmission rates, using diverse phytosanitary or cultural practices that minimize the virus source or reduce its spread, and using selective pesticides in an environmentally responsible way. The review finishes by briefly discussing the implications of climate change in increasing problems associated with control and the opportunities to control virus diseases more effectively through new technologies.

Biological Properties of Potato virus X in Potato: Effects of Mixed Infection with Potato virus S and Resistance Phenotypes in Cultivars from Three Continents

Interactions between Potato virus X (PVX) and Potato virus S (PVS) were studied in potato plants, and isolates of PVX were inoculated to potato cultivars from four continents to identify occurrence of PVX resistance genes. Mixed infection with PVX and PVS increased the titer of PVS and enhanced expression of foliar symptoms in primarily and secondarily infected plants of 'Royal Blue'. PVX isolates belonging to strain groups 1 and 3 (WA1+3) or 3 (XK3 and TAS3) were sap and graft inoculated (1 to 3 isolates each) to 38 cultivars and one breeding line. Presence of extreme PVX resistance gene Rx was identified in four Australian ('Auski', 'Billabong', 'Flame', and 'Ruby Lou') and two European ('Mondial' and 'Rodeo') cultivars, and in a clone of North American 'Atlantic'. PVX hypersensitivity gene Nx was identified for the first time in two Australian ('Bliss' and 'MacRusset'), four European ('Almera', 'Harmony', 'Maxine', and 'Nadine'), and one North American ('Ranger Russet') cultivars, and in Australian breeding line 98-10713. PVX hypersensitivity gene Nb was identified for the first time in one Australian ('White Star'), five European ('Innovator', 'Kestrel', 'Kipfler', 'Laurine', and 'Royal Blue'), and one North American ('Shepody') cultivars. Probable ancestral sources of the resistance genes found in different cultivars were identified. Thus, although PVX resistance genes often occur in parents used in crosses, knowledge of their occurrence in parents and cultivars is often lacking. On sap inoculation, systemic hypersensitive phenotypes that caused shoot death often developed in cultivars with Nx but not necessarily in all shoots. This phenotype caused severe necrotic symptoms in infected tubers. In some instances, passage through cultivars with Nb separated strain group 3 from mixed isolate WA1+3.

Resistance Phenotypes in Diverse Accessions, Breeding Lines, and Cultivars of Three Mustard Species Inoculated with Turnip mosaic virus

The responses of 44 accessions, breeding lines, or cultivars of Brassica juncea (Indian mustard), 9 of B. carinata (Ethiopian mustard), 5 of B. nigra (black mustard), and 6 crosses between B. juncea and B. napus (canola) to sap inoculation with Turnip mosaic virus (TuMV) were investigated. Eleven different phenotypes were obtained, including six previously recognized in B. napus (+, O, R, R_N, R_N/+, and +_N) and five not recorded before (+_St, R_N/St, R_N/St/+, +_N¹, and +_ND). All but two (+ and +_St) were resistance phenotypes. The resistance phenotypes in B. carinata and B. juncea × B. napus crosses prevented systemic infection but those in B. juncea and B. nigra included systemic necrosis. Absence of systemic invasion associated with resistance phenotypes in B. carinata was confirmed by graft inoculations. The resistance phenotypes may reflect the presence of known TuMV resistance genes located in the A genome or unknown genes in the B genome in B. juncea, unknown resistance genes in the B or C genomes in B. carinata, and unknown resistance genes in the B genome in B. nigra. Further research to identify the resistance genes involved would establish the potential usefulness of these resistance phenotypes in breeding TuMV-resistant mustard cultivars for biofuel production.

Principles of predicting plant virus disease epidemics

Predicting epidemics of plant virus disease constitutes a challenging undertaking due to the complexity of the three-cornered pathosystems (virus, vector, and host) involved and their interactions with the environment. A complicated nomenclature is used to describe virus epidemiological models. This review explains how the nomenclature evolved and provides a historical account of the development of such models. The process and steps involved in devising models that incorporate weather variables and data retrieval and are able to forecast plant virus epidemics effectively are explained. Their application to provide user-friendly, Internet-based decision support systems (DSSs) that determine when and where control measures are needed is described. Finally, case studies are provided of eight pathosystems representing different scenarios in which modeling approaches have been used with varying degrees of effectiveness to forecast virus epidemics in parts of the world with temperate, Mediterranean, subtropical, and tropical climates.

Quantifying effects of seedborne inoculum on virus spread, yield losses, and seed infection in the pea seed-borne mosaic virus-field pea pathosystem

Field experiments examined the effects of sowing field pea seed with different amounts of infection with Pea seed-borne mosaic virus (PSbMV) on virus spread, seed yield, and infection levels in harvested seed. Plots were sown with seed with actual or simulated seed transmission rates of 0.3 to 6.5% (2005) or 0.1 to 8% (2006), and spread was by naturally occurring migrant aphids. Plants with symptoms and incidence increased with the amount of primary inoculum present. When final incidence reached 97 to 98% (2005) and 36% (2006) in plots sown with 6.5 to 8% infected seed, yield losses of 18 to 25% (2005) and 13% (2006) resulted. When incidence reached 48 to 76% in plots sown with 1.1-2 to 2% initial infection, seed yield losses were 15 to 21% (2005). Diminished seed weight and seed number both contributed to the yield losses. When the 2005 data for the relationships between percent incidence and yield or yield gaps were plotted, 81 to 84% of the variation was explained by final incidence and, for each 1% increase, there was a yield decline of 7.7 to 8.2 kg/ha. Seed transmission rates in harvested seed were mostly greater than those in the seed sown when climatic conditions favored early virus spread (1 to 17% in 2005) but smaller when they did not (0.2 to 2% in 2006). In 2007, sowing infected seed at high seeding rate with straw mulch and regular insecticide application resulted in slower spread and smaller seed infection than sowing at standard seeding rate without straw mulch or insecticide. When data for the relationship between final percent incidence and seed transmission in harvested seed were plotted (all experiments), 95 to 99% of the variation was explained by PSbMV incidence. A threshold value of <0.5% seed infection was established for sowing in high-risk zones.