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.

Updates on cowpea viruses in Southwest Nigeria: distribution, prevalence and coinfection

Cowpea is an important source of dietary proteins in the semi-arid regions of sub-Saharan Africa. Its productivity is constrained by several viral diseases and there are limited updates on the incidence and distribution of these diseases in Nigeria. This study assessed the distribution and prevalence of cowpea viruses in Southwest Nigeria. Field surveys were conducted in 2017 and 2018, in which a total of 600 leaf samples were randomly collected from 60 cowpea fields in four (Oyo, Ogun, Ondo and Osun) states at 15 fields per state and 10 samples per field. Disease incidence and severity were recorded while virus infections were confirmed by enzyme-linked immunosorbent assay or reverse transcription polymerase chain reaction. Viral disease symptoms of systemic mosaic, mottling, puckering, vein-banding, leaf deformation and stunted growth were observed. Highest virus incidence and severity (100% and 4.8 ± 0.4) were observed at Adeosun Avenue, Ondo state, whereas Boredun, Osun state had the least (80% and 3.8 ± 0.7), with some symptomless fields found among the states. Seven viruses, viz.: cowpea aphid-borne mosaic virus (CABMV), cowpea mild mottle virus (CPMMV), bean common mosaic virus-blackeye cowpea mosaic strain (BCMV-BlCM), cucumber mosaic virus (CMV), southern bean mosaic virus (SBMV), cowpea mottle virus (CMoV) and cowpea yellow mosaic virus (CYMV) were detected from 173 (28.8%) samples collected from 32 (53.3%) fields across the states. CPMMV was prevalent, detected from 30.0% of surveyed fields, whereas CYMV was the least prevalent (3.3%). Multiple infections of two to four viruses were observed among 12.5% of samples from 51.7% of fields. Highest incidence of single and multiple virus infections were observed in Ondo state. This updates on virus distributions in Southwest Nigeria will be useful for multiple virus resistance-breeding programs and other viral disease management strategies for improved cowpea productivity.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42360-022-00576-8.

A Review of Viruses Infecting Yam (Dioscorea spp.)

Yam is an important food staple for millions of people globally, particularly those in the developing countries of West Africa and the Pacific Islands. To sustain the growing population, yam production must be increased amidst the many biotic and abiotic stresses. Plant viruses are among the most detrimental of plant pathogens and have caused great losses of crop yield and quality, including those of yam. Knowledge and understanding of virus biology and ecology are important for the development of diagnostic tools and disease management strategies to combat the spread of yam-infecting viruses. This review aims to highlight current knowledge on key yam-infecting viruses by examining their characteristics, genetic diversity, disease symptoms, diagnostics, and elimination to provide a synopsis for consideration in developing diagnostic strategy and disease management for yam.

Genetic Structure of Cucumber Mosaic Virus From Natural Hosts in Nigeria Reveals High Diversity and Occurrence of Putative Novel Recombinant Strains

Cucumber mosaic virus (CMV, Bromoviridae: Cucummovirus), one of the most widespread plant viruses with several hosts, causes huge losses in yield quality and quantity. The occurrence of various CMV strains and high genetic diversity within the virus complicate its management. We describe the population structure of CMV in Nigeria using partial RNA1 and RNA3 gene sequences from three natural hosts: pepper (Capsicum annuum), tomato (Solanum lycopersicum), and watermelon (Citrullus lanatus). One hundred and six leaf samples were obtained from 16 locations across Nigeria, and specific primers were used to amplify the two gene fragments using PCR. Twenty-four samples tested positive for CMV using RNA1 primers, and amplicons were sequenced from 12 isolates, revealing 82.94–99.80% nucleotide and 85.42–100% amino acid sequence similarities within the population. The partial RNA3 fragment, corresponding to the complete coat protein (CP) gene, was sequenced from seven isolates, with 95.79–97.90% and 98.62–100% nucleotide and amino acid intrapopulation similarities, respectively. The isolates belonged to subgroup IB and formed distinct phylogenetic clusters in both gene sets, indicating putative novel strains. Recombination signals, supported by phylogenetic inferences, were detected within the RNA1 dataset (P ≤ 0.05) and identified a recombinant isolate within the Nigerian sequences. No recombination was detected within the CP genes. Population genetics parameters established high diversity within the Nigerian population compared to other isolates worldwide, while selection pressure estimates revealed the existence of negative selection in both gene sets. Although CMV subgroup IB strains were postulated to originate from Asia, this study reveals their prevalence across several hosts from different locations in Nigeria. To our knowledge, this is the first comprehensive description of a recombinant CMV subgroup IB isolate from West Africa, which has implications for its robust detection and overall management.

First report of Cucumber mosaic virus infecting Ocimum gratissimum (L.) in Calabar, Cross River State, Nigeria

Leaf samples of Ocimum gratissimum (L.) exhibiting vein banding, mosaic and chlorotic spots were collected randomly from the field. The symptomatic samples reacted positively to specific CMV antibody in antigen coated plate enzyme linked immunosorbent assay and to confirm the presence of CMV, RT-PCR was performed using CMV-specific primers that amplify a 519 bp region from the viral coat protein gene. The expected amplicon shared homology of 97.06% with a Nigerian isolate MH178110. Phylogenetic tree constructed revealed the isolate in close association with CMV strains belonging to subgroup II. This is the first molecular evidence of CMV in O. gratissimum in Nigeria and adds to the list of natural host for the virus.

Biology and genetic diversity of phasey bean mild yellows virus, a common virus in legumes in Australia

This study examined the natural and experimental host range and aphid and graft transmission of the tentative polerovirus phasey bean mild yellows virus (PBMYV). Eleven complete coding sequences from PBMYV isolates were determined from a range of hosts and locations. We found two genetically distinct variants of PBMYV. PBMYV-1 was the originally described variant, and PBMYV-2 had a large putative recombination in open reading frame 5 such that PBMYV-1 and PBMYV-2 shared only 65-66% amino acid sequence identity in the P5 protein. The virus was transmitted by a clonal colony of cowpea aphids (Aphis craccivora) and by grafting with infected scions but was not transmitted by a clonal colony of green peach aphids (Myzus persicae). PBMYV was found in natural infections in 11 host species with a range of symptoms and severity, including seven important grain legume crops from across a wide geographic area in Australia. PBMYV was common and widespread in the tropical weed phasey bean (Macroptilium lathyroides), but it is likely that there are other major alternative hosts for the virus in temperate regions of Australia. The experimental host range of PBMYV included the Fabaceae hosts chickpea (Cicer arietinum), faba bean (Vicia faba), pea (Pisum sativum), and phasey bean, but transmissions failed to infect several other members of the families Asteraceae, Cucurbitaceae, Fabaceae and Solanaceae. PBMYV was commonly found in grain legume crops in eastern and western Australia, sometimes at greater than 90% incidence. This new knowledge about PBMYV warrants further assessments of its economic impact on important grain legume crops.

Molecular Viral Diagnosis and Sanitation of Yam Genetic Resources: Implications for Safe Yam Germplasm Exchange

Yam (Dioscorea spp.) is an important crop in tropical and subtropical regions. Many viruses have been recently identified in yam, hampering genetic conservation and safe international exchanges of yam germplasm. We report on the implementation of reliable and cost-effective PCR-based detection tools targeting eight different yam-infecting viruses. Viral indexing of the in vitro yam collection maintained by the Biological Resources Center for Tropical Plants (BRC-TP) in Guadeloupe (French West Indies) unveiled a high prevalence of potyviruses, badnaviruses, Dioscorea mosaic associated virus (DMaV) and yam asymptomatic virus 1 (YaV1) and a high level of coinfections. Infected yam accessions were subjected to a combination of thermotherapy and meristem culture. Sanitation levels were monitored using PCR-based and high-throughput sequencing-based diagnosis, confirming the efficacy and reliability of PCR-based detection tools. Sanitation rates were highly variable depending on viruses. Sixteen accessions were successfully sanitized, paving the way to safe yam germplasm exchanges and the implementation of clean seed production programs worldwide.

De novo Genome Assembly and Single Nucleotide Variations for Soybean Mosaic Virus Using Soybean Seed Transcriptome Data

Soybean is the most important legume crop in the world. Several diseases in soybean lead to serious yield losses in major soybean-producing countries. Moreover, soybean can be infected by diverse viruses. Recently, we carried out a large-scale screening to identify viruses infecting soybean using available soybean transcriptome data. Of the screened transcriptomes, a soybean transcriptome for soybean seed development analysis contains several virus-associated sequences. In this study, we identified five viruses, including soybean mosaic virus (SMV), infecting soybean by de novo transcriptome assembly followed by blast search. We assembled a nearly complete consensus genome sequence of SMV China using transcriptome data. Based on phylogenetic analysis, the consensus genome sequence of SMV China was closely related to SMV isolates from South Korea. We examined single nucleotide variations (SNVs) for SMVs in the soybean seed transcriptome revealing 780 SNVs, which were evenly distributed on the SMV genome. Four SNVs, C-U, U-C, A-G, and G-A, were frequently identified. This result demonstrated the quasispecies variation of the SMV genome. Taken together, this study carried out bioinformatics analyses to identify viruses using soybean transcriptome data. In addition, we demonstrated the application of soybean transcriptome data for virus genome assembly and SNV analysis.

Differential responses to virus challenge of laboratory and wild accessions of australian species of nicotiana, and comparative analysis of RDR1 gene sequences

Nicotiana benthamiana is a model plant utilised internationally in plant virology because of its apparent hyper-susceptibility to virus infection. Previously, others showed that all laboratory accessions of N. benthamiana have a very narrow genetic basis, probably originating from a single source. It is unknown if responses to virus infection exhibited by the laboratory accession are typical of the species as a whole. To test this, 23 accessions of N. benthamiana were collected from wild populations and challenged with one to four viruses. Additionally, accessions of 21 other Nicotiana species and subspecies from Australia, one from Peru and one from Namibia were tested for susceptibility to the viruses, and for the presence of a mutated RNA-dependent RNA polymerase I allele (Nb-RDR1m) described previously from a laboratory accession of N. benthamiana. All Australian Nicotiana accessions tested were susceptible to virus infections, although there was symptom variability within and between species. The most striking difference was that plants of a laboratory accession of N. benthamiana (RA-4) exhibited hypersensitivity to Yellow tailflower mild mottle tobamovirus infection and died, whereas plants of wild N. benthamiana accessions responded with non-necrotic symptoms. Plants of certain N. occidentalis accessions also exhibited initial hypersensitivity to Yellow tailflower mild mottle virus resembling that of N. benthamiana RA-4 plants, but later recovered. The mutant Nb-RDR1m allele was identified from N. benthamiana RA-4 but not from any of 51 other Nicotiana accessions, including wild accessions of N. benthamiana, demonstrating that the accession of N. benthamiana used widely in laboratories is unusual.

The prevalence of badnaviruses in West African yams (Dioscorea cayenensis-rotundata) and evidence of endogenous pararetrovirus sequences in their genomes

Yam (Dioscorea spp.) is an important vegetatively-propagated staple crop in West Africa. Viruses are pervasive in yam worldwide, decreasing growth and yield, as well as hindering the international movement of germplasm. Badnaviruses have been reported to be the most prevalent in yam, and genomes of some other badnaviruses are known to be integrated in their host plant species. However, it was not clear if a similar scenario occurs in Dioscorea yam. This study was conducted to verify the prevalence of badnaviruses, and determine if badnavirus genomes are integrated in the yam genome. Leaf samples (n=58) representing eight species of yam from global yam collections kept at CIRAD, France, and 127 samples of D. rotundata breeding lines (n=112) and landraces (n=15) at IITA, Nigeria, were screened using generic badnavirus PCR primers. Positive amplification of an expected ca. 579bp fragment, corresponding to a partial RT-RNaseH region, was detected in 47 (81%) of 58 samples analysed from CIRAD collections, and 100% of the 127 IITA D. rotundata samples. All the D. cayenensis and D. rotundata samples from the CIRAD and IITA collections tested PCR-positive, and sequencing of a selection of the PCR products confirmed they were typical of the genus Badnavirus. A comparison of serological and nucleic acid techniques was used to investigate whether the PCR-positives were sequences amplified from badnavirus particles or putative endogenous badnavirus sequences in the yam genome. Protein A sandwich-enzyme-linked immunosorbent assay (PAS-ELISA) with badnavirus polyclonal antisera detected cross-reacting viral particles in only 60% (92 of 153) of the CIRAD collection samples analysed, in contrast to the aforementioned 81% by PCR. Immunosorbent electron microscopy (ISEM) of virus preparations of a select set of 16 samples, representing different combinations of positive and negative PCR and PAS-ELISA results, identified bacilliform particles in 11 of these samples. Three PCR-positive yam samples from Burkina Faso (cv. Pilimpikou) were identified in which no viral particles were detected by either PAS-ELISA or ISEM. Southern hybridisation results using a yam badnavirus RT-RNaseH sequence (Gn155Dr) as probe, supported a lack of badnavirus particles in the cv. Pilimpikou and identified their equivalent sequences to be of plant genome origin. Probe Gn155Dr, however, hybridised to viral particles and plant genomic DNA in three D. rotundata samples from Guinea. These results represent the first data demonstrating the presence of integrated sequences of badnaviruses in yam. The implications of this for virus-indexing, breeding and multiplication of seed yams are discussed.

Virus diseases of peas, beans, and faba bean in the Mediterranean region

In the Mediterranean region, pea, bean, and faba bean production is affected by around 17 major viruses. These viruses do not have the same ecology and consequently require a variety of different preventive measures to control them. Some of these viruses have a narrow host range, such as Faba bean necrotic yellows virus (FBNYV), and others, such as Alfalfa mosaic virus (AMV) and Cucumber mosaic virus (CMV), a very wide host range. Such features are important when identifying sources of virus inoculum in a region, and the vectors can transmit viruses from natural reservoirs to the crop plants. Some of these viruses are seed borne and, consequently, can be disseminated long distances through infected seeds. Crop losses caused by these viruses are variable, depending on the sensitivity and susceptibility of the crop to infection. Host resistance genes have been identified for some of these viruses, but in others, such as FBNYV, no resistance genes in faba bean have been identified yet. Significant progress was made in developing precise methods for the identification of these viruses, and new virus problems are being identified every year. This chapter is not intended to be a review for pea, bean, and faba bean viruses, but rather focuses on the major viruses which affect these crops in the Mediterranean basin with focus on the progress made over the past two decades.

Lack of Seed Coat Contamination with Cucumber mosaic virus in Lupin Permits Reliable, Large-Scale Detection of Seed Transmission in Seed Samples

Sowing seed stocks with minimal virus content provides a key control measure in preventing damaging epidemics of Cucumber mosaic virus (CMV) in crops of narrow-leafed lupin (Lupinus angustifolius). A seed testing service provides an estimate of percent CMV infection based on a dry seed test in which bulked subsamples of ungerminated seed are ground to a fine powder for testing. When enzyme-linked immunosorbent assay (ELISA) was used, CMV antiserum that gave low background optical density (A₄₀₅) values with extracts of powder from subsamples of healthy seed provided greatest accuracy, readily detecting one infected seed in subsamples of 100 seeds. In comparative ELISAs on duplicate subsamples from eight different seed stocks, germination and dry seed tests always gave similar percent infection values. When seed coats were separated from the embryos of CMV-infected and healthy lupin seeds before testing by ELISA, the virus was only detected in embryos from infected seeds and never in their seed coats. Treatment with trisodium phosphate did not alter the low ELISA optical density (A₄₀₅) values obtained with seed coats separated from infected seeds. Therefore, seed coat contamination with CMV is lacking in lupin, justifying large-scale routine use of a dry seed test to estimate percent virus infection in commercial seed samples.

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.

Carrot virus Y: symptoms, losses, incidence, epidemiology and control

Carrot virus Y (CarVY) is a newly described potyvirus that causes a foliar and root disease in carrots which seriously diminishes yield and quality. It infects crops in most commercial carrot producing areas of Australia. Infection sometimes reaches very high incidences within individual crops resulting in their being abandoned due to unmarketability of the roots. A range of commonly grown carrot cultivars were all susceptible. CarVY symptoms in carrot foliage are chlorotic mottle, marginal necrosis or reddening and generalised chlorosis of leaves, increased subdivision of leaflets giving a 'feathery' appearance and plant stunting. Roots from plants infected early are stubby showing severe distortion and knobliness, while those from plants infected late are thin with little distortion. The known host range of CarVY is narrow and the key infection sources for spread by aphid vectors to newly sown crops are infected 'volunteer' carrots and adjacent infected carrot crops. Continuous irrigated carrot production in sequential plantings on the same farm all-year-round results in massive infection with the virus, while discontinuous production results in low incidences. Exposure of young carrot plants to peak aphid populations initiates early epidemics. Case histories showing how control measures affected CarVY incidence are described for one farm that deployed them compared with one that did not. An integrated control strategy devised for sustainable management of CarVY in carrot crops is described. Preliminary tests indicate that seed transmission of CarVY may occur at low levels in carrot, so introduction of the virus to isolated sites may be from inadvertent sowings of contaminated carrot seed.

Determining 'threshold' levels for seed-borne virus infection in seed stocks

There have been many advances in testing procedures to detect seed-borne virus infection in seed samples. However, scant attention has been given to the implications of improved test results in terms of the economic losses resulting from sowing seed stocks with different amounts of infection. For agricultural and horticultural industries to use the results of tests on representative samples, defined 'threshold' values for percentage seed infection are required that identify acceptable levels of risk of economic losses resulting from sowing the virus-infected seed stocks. Such information is provided by field experiments in which infected seed is sown and the consequences are followed in terms of virus spread, yield losses and infection of newly produced seed. These field experiments need to continue over several years at diverse sites so that they represent a wide range of infection scenarios. Extensive surveys to determine seed-borne virus occurrence in different regions are also required to define areas of greater or lesser risk of economic losses. In this paper, an example is described of how field experiments and surveys were used to define 'threshold' values of seed-borne Cucumber mosaic virus infection in an annual crop (lupin: Lupinus angustifolius) and two such examples are given for pasture species: Cucumber mosaic virus in subterranean clover (Trifolium subterraneum), and Alfalfa mosaic virus in annual burr medic (Medicago polymorpha). The aim of this paper is to encourage others to address the urgent need for similar 'threshold' information with other economically important combinations of seed-borne viruses and host plant.

Seed transmission of cucumber mosaic virus in spinach

ABSTRACT Spinach (Spinacia oleracea) seed from a commercial breeding line suspected of harboring cucumber mosaic virus (CMV) was analyzed for seed transmission of the virus. Initial seed grow-out tests and enzymelinked immunosorbent assay studies indicated that CMV was present in this seed lot at a level of nearly 15%. To verify these results and gain insight into the mechanism of seed transmission, four combinations of crosses between healthy and/or infected parent plants were conducted. None of the spinach seedlings derived from crossing healthy male and healthy female plants contained CMV, whereas a portion of seedlings derived from all of the other three crosses, i.e., healthy male and infected female, infected male and healthy female, and infected male and infected female plants, were infected with CMV. The results demonstrate that CMV is seed transmitted in spinach and indicate that both male and female parent plants can serve as infection sources. Ultrastructural studies, including immunogold labeling, revealed the presence of virus particles in the cytoplasm of ovary wall cells, ovule integuments and nucellus, anther, and seed-coat cells, as well as fine fibril-containing vesicles and electron-dense inclusions of amorphous aggregates in the central vacuoles of these cells. In addition, reverse transcription-polymerase chain reaction (RT-PCR) was used to amplify 860-bp cDNA fragments containing the CMV coat protein (CP) gene from the embryo, endosperm, and pollen tissues of CMV-infected plants. Taken together, these studies indicate that CMV occurs in virtually all spinach reproductive tissues. Analysis of several RT-PCR amplified and cloned CP genes and flanking sequences from parent and progeny plants revealed that the spinachinfecting CMV was a member of subgroup II. Furthermore, cDNA sequencing and restriction endonuclease mapping consistently revealed two sequence variants, designated SP103 and SP104, in most plants analyzed. These data suggest that there may have been mixed infections of two distinct, seed-transmitted CMV variants in spinach.

Nucleotide and deduced amino acid sequence of the 3' end of the BYMV-MI genome

We have cloned and sequenced cDNA transcribed from the 3' 1,239 nucleotides of the genomic RNA of a Western Australian isolate (MI) of bean yellow mosaic potyvirus (BYMV). This sequence contains 246 nucleotides of the NIb (replicase) gene and 819 nucleotides representing the entire coding region of the viral coat protein gene, followed by a 3' non-coding region of 174 nucleotides. The coding region of the coat protein gene is identical in length (273 amino acids) to that already reported for other isolates of this virus. The sequence identities obtained for BYMV-MI and published sequences of BYMV isolates range between 85% and 92% for the coding region of the coat protein and 90% to 98% for the 3' non-coding region. Likewise, the region of the NIb gene sequenced shows 99% and 97% sequence identity in the deduced amino acid and the nucleotide sequences, respectively.

RNA 4 sequences from cucumber mosaic virus subgroups I and II

The complete sequences of RNA 4 from cucumber mosaic virus (CMV) strains Ny (subgroup I) and Sn (subgroup II) have been determined and compared to all other known complete CMV RNA 4 sequences. The identification of a unique EcoRI site, present only in subgroup-II RNA 4 sequences, provides the basis for a simple method of classifying CMV isolates.