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.

Chromosome-level genome assembly of the spotted alfalfa aphid Therioaphis trifolii

The spotted alfalfa aphid (SAA, Therioaphis trifolii) (Hemiptera: Aphididae) is a destructive pest of cultivated alfalfa (Medicago sativa L.) that leads to large financial losses in the livestock industry around the world. Here, we present a chromosome-scale genome assembly of T. trifolii, the first genome assembly for the aphid subfamily Calaphidinae. Using PacBio long-read sequencing, Illumina sequencing, and Hi-C scaffolding techniques, a 541.26 Mb genome was generated, with 90.01% of the assembly anchored into eight scaffolds, and the contig and scaffold N50 are 2.54 Mb and 44.77 Mb, respectively. BUSCO assessment showed a completeness score of 96.6%. A total of 13,684 protein-coding genes were predicted. The high-quality genome assembly of T. trifolii not only provides a genomic resource for the more complete analysis of aphid evolution, but also provides insights into the ecological adaptation and insecticide resistance of T. trifolii.

Vector species, pasture legume host range, and impact on grain legumes of an Australian soybean dwarf virus isolate

Soybean dwarf virus (SbDV; family Tombusviridae, genus Luteovirus, species Soybean dwarf virus) can cause damaging disease epidemics in cultivated plants of the family Fabaceae. The biological characteristics of SbDV isolate WA-8, including its vector species, host range, and impact on Australian grain legume cultivars, were investigated in a series of glasshouse experiments. Isolate WA-8 was classified as the YP strain, as it was transmitted by Acyrthosiphon pisum (pea aphid) and Myzus persicae (green peach aphid) and infected known strain indicator species. Of the 18 pasture legume species inoculated with SbDV, 12 were SbDV hosts, including eight that had not been identified previously as hosts. When inoculated with SbDV, field pea (Pisum sativum), faba bean (Vicia faba), lentil (Lens culinaris), and narrow-leafed lupin cv. Jurien were the most susceptible (70 to 100% plant infection rates), and albus lupin (Lupinus albus), chickpea (Cicer arietinum), and narrow-leafed lupin cv. Mandelup were less susceptible (20 to 70%). Over the course of three experiments, chickpea was the most sensitive to infection, with a > 97% reduction in dry above-ground biomass (AGB) and a 100% reduction in seed yield. Field pea cv. Gunyah, faba bean, and lentil were also sensitive, with a 36 to 61% reduction in AGB. Field pea cv. Kaspa was relatively tolerant, with no significant reduction in AGB or seed yield. The information generated under glasshouse conditions in this study provides important clues for understanding SbDV epidemiology and suggests that it has the potential to cause damage to Australian grain legume crops in the field, especially if climate change facilitates its spread.

A functional genomics approach to dissect spotted alfalfa aphid resistance in Medicago truncatula

Aphids are virus-spreading insect pests affecting crops worldwide and their fast population build-up and insecticide resistance make them problematic to control. Here, we aim to understand the molecular basis of spotted alfalfa aphid (SAA) or Therioaphis trifolii f. maculata resistance in Medicago truncatula, a model organism for legume species. We compared susceptible and resistant near isogenic Medicago lines upon SAA feeding via transcriptome sequencing. Expression of genes involved in defense and stress responses, protein kinase activity and DNA binding were enriched in the resistant line. Potentially underlying some of these changes in gene expression was the finding that members of the MYB, NAC, AP2 domain and ERF transcription factor gene families were differentially expressed in the resistant versus susceptible lines. A TILLING population created in the resistant cultivar was screened using exome capture sequencing and served as a reverse genetics tool to functionally characterise genes involved in the aphid resistance response. This screening revealed three transcription factors (a NAC, AP2 domain and ERF) as important regulators in the defence response, as a premature stop-codon in the resistant background led to a delay in aphid mortality and enhanced plant susceptibility. This combined functional genomics approach will facilitate the future development of pest resistant crops by uncovering candidate target genes that can convey enhanced aphid resistance.

Viromes of Ten Alfalfa Plants in Australia Reveal Diverse Known Viruses and a Novel RNA Virus

Alfalfa plants in the field can display a range of virus-like symptoms, especially when grown over many years for seed production. Most known alfalfa viruses have RNA genomes, some of which can be detected using diagnostic assays, but many viruses of alfalfa are not well characterized. This study aims to identify the RNA and DNA virus complexes associated with alfalfa plants in Australia. To maximize the detection of RNA viruses, we purified double-stranded RNA (dsRNA) for high throughput sequencing and characterized the viromes of ten alfalfa samples that showed diverse virus-like symptoms. Using Illumina sequencing of tagged cDNA libraries from immune-captured dsRNA, we identified sequences of the single-stranded RNA viruses, alfalfa mosaic virus (AMV), bean leafroll virus, a new emaravirus tentatively named alfalfa ringspot-associated virus, and persistent dsRNA viruses belonging to the families Amalgaviridae and Partitiviridae. Furthermore, rolling circle amplification and restriction enzyme digestion revealed the complete genome of chickpea chlorosis Australia virus, a mastrevirus (family Geminiviridae) previously reported only from chickpea and French bean that was 97% identical to the chickpea isolate. The sequence data also enabled the assembly of the first complete genome (RNAs 1–3) of an Australian AMV isolate from alfalfa.

Detection of new viruses in alfalfa, weeds and cultivated plants growing adjacent to alfalfa fields in Saudi Arabia

A total of 1368 symptomatic plant samples showing different virus-like symptoms such as mottling, chlorosis, mosaic, yellow mosaic, vein clearing and stunting were collected from alfalfa, weed and cultivated plant species growing in vicinity of alfalfa fields in five principal regions of alfalfa production in Saudi Arabia. DAS-ELISA test indicated occurrence of 11 different viruses in these samples, 10 of which were detected for the first time in Saudi Arabia. Eighty percent of the alfalfa samples and 97.5% of the weed and cultivated plants samples were found to be infected with one or more of these viruses. Nine weed plant species were found to harbor these viruses namely, Sonchus oleraceus, Chenopodium spp., Hibiscus spp., Cichorium intybus, Convolvulus arvensis, Malva parviflora, Rubus fruticosus, Hippuris vulgaris, and Flaveria trinervia. These viruses were also detected in seven cultivated crop plants growing adjacent to the alfalfa fields including Vigna unguiculata, Solanum tuberosum, Solanum melongena, Phaseolus vulgaris, Cucurbita maxima, Capsicum annuum, and Vicia faba. The newly reported viruses together with their respective percent of detection in alfalfa, and in both weeds and cultivated crop plant species together were as follows: Bean leaf roll virus (BLRV) {12.5 and 4.5%}, Lucerne transient streak virus (LTSV) {2.9 and 3.5%}, Bean yellow mosaic virus (BYMV) {1.4 and 4.5%}, Bean common mosaic virus (BCMV) {1.2 and 4.5%}, Red clover vein mosaic virus (RCVMV) {1.2 and 4%}, White clover mosaic virus (WCIMV) {1.0 and 5%}, Cucumber mosaic virus (CMV) {0.8 and 3%}, Pea streak virus (PeSV) {0.4 and 4.5%} and Tobacco streak virus (TSV) {0.3 and 2.5%}. Alfalfa mosaic virus (AMV), the previously reported virus in alfalfa, had the highest percentage of detection in alfalfa accounting for 58.4% and 62.8% in the weeds and cultivated plants. Peanut stunt virus (PSV) was also detected for the first time in Saudi Arabia with a 66.7% of infection in 90 alfalfa samples collected from the surveyed regions during the last visit that tested negative to all the previously detected viruses.

Effects of introduced and indigenous viruses on native plants: exploring their disease causing potential at the agro-ecological interface

The ever increasing movement of viruses around the world poses a major threat to plants growing in cultivated and natural ecosystems. Both generalist and specialist viruses move via trade in plants and plant products. Their potential to damage cultivated plants is well understood, but little attention has been given to the threat such viruses pose to plant biodiversity. To address this, we studied their impact, and that of indigenous viruses, on native plants from a global biodiversity hot spot in an isolated region where agriculture is very recent (<185 years), making it possible to distinguish between introduced and indigenous viruses readily. To establish their potential to cause severe or mild systemic symptoms in different native plant species, we used introduced generalist and specialist viruses, and indigenous viruses, to inoculate plants of 15 native species belonging to eight families. We also measured resulting losses in biomass and reproductive ability for some host-virus combinations. In addition, we sampled native plants growing over a wide area to increase knowledge of natural infection with introduced viruses. The results suggest that generalist introduced viruses and indigenous viruses from other hosts pose a greater potential threat than introduced specialist viruses to populations of native plants encountered for the first time. Some introduced generalist viruses infected plants in more families than others and so pose a greater potential threat to biodiversity. The indigenous viruses tested were often surprisingly virulent when they infected native plant species they were not adapted to. These results are relevant to managing virus disease in new encounter scenarios at the agro-ecological interface between managed and natural vegetation, and within other disturbed natural vegetation situations. They are also relevant for establishing conservation policies for endangered plant species and avoiding spread of damaging viruses to undisturbed natural vegetation beyond the agro-ecological interface.

Cucumber mosaic virus

Cucumber mosaic virus (CMV) is an important virus because of its agricultural impact in the Mediterranean Basin and worldwide, and also as a model for understanding plant-virus interactions. This review focuses on those areas where most progress has been made over the past decade in our understanding of CMV. Clearly, a deep understanding of the role of the recently described CMV 2b gene in suppression of host RNA silencing and viral virulence is the most important discovery. These findings have had an impact well beyond the virus itself, as the 2b gene is an important tool in the studies of eukaryotic gene regulation. Protein 2b was shown to be involved in most of the steps of the virus cycle and to interfere with several basal host defenses. Progress has also been made concerning the mechanisms of virus replication and movement. However, only a few host proteins that interact with viral proteins have been identified, making this an area of research where major efforts are still needed. Another area where major advances have been made is CMV population genetics, where contrasting results were obtained. On the one hand, CMV was shown to be prone to recombination and to show high genetic diversity based on sequence data of different isolates. On the other hand, populations did not exhibit high genetic variability either within plants, or even in a field and the nearby wild plants. The situation was partially clarified with the finding that severe bottlenecks occur during both virus movement within a plant and transmission between plants. Finally, novel studies were undertaken to elucidate mechanisms leading to selection in virus population, according to the host or its environment, opening a new research area in plant-virus coevolution.

Co-infection patterns and geographic distribution of a complex pathosystem targeted by pathogen-resistant plants

Increasingly, pathogen-resistant (PR) plants are being developed to reduce the agricultural impacts of disease. However PR plants also have the potential to result in increased invasiveness of nontarget host populations and so pose a potential threat to nontarget ecosystems. In this paper we use a new framework to investigate geographical variation in the potential risk associated with unintended release of genetically modified alfalfa mosaic virus (AMV)-resistant Trifolium repens (white clover) into nontarget host populations containing AMV, clover yellow vein virus (ClYVV), and white clover mosaic virus (WCIMV) in southeastern Australia. Surveys of 213 sites in 37 habitat types over a 300 000-km2 study region showed that T. repens is a significant weed of many high-conservation-value habitats in southeastern Australia and that AMV, ClYVV, and WClMV occur in 15-97% of nontarget host populations. However, T. repens abundance varied with site disturbance, habitat conservation value, and proximity to cropping, and all viral pathogens had distinct geographic distributions and infection patterns. Virus species frequently co-infected host plants and displayed nonindependent distributions within host populations, although co-infection patterns varied across the study region. Our results clearly illustrate the complexity of conducting environmental risk assessments that involve geographically widespread, invasive pasture species and demonstrate the general need for targeted, habitat- and pathosystem-specific studies prior to the process of tiered risk assessment.

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.

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.

Seed Transmission of Wheat streak mosaic virus Shown Unequivocally in Wheat

Under conditions that excluded any possibility of eriophyid mite vector activity, seed transmission of Wheat streak mosaic virus (WSMV) was shown in eight different wheat genotypes at rates of 0.5 to 1.5%. Virus identification in seedlings came from characteristic symptoms in wheat, enzyme-linked immunosorbent assay with WSMV-specific antibodies, reverse-transcription polymerase chain reaction tests with WSMV-specific primers, and cDNA sequence comparisons with published sequences. Sequence comparisons of four seedborne isolates showed ≥98.6% identity with the eight Australian isolates in GenBank, indicating a common seedborne origin of WSMV. These findings warrant reconsideration of currently accepted views on WSMV epidemiology and the likelihood of introducing it to new locations through planting untested wheat seed and the movement of germplasm.