Surveillance and monitoring for endemic and exotic virus diseases of cotton

The aims of this project will provide capacity in virology expertise to help protect Australian cotton from virus diseases including both existing and those that pose significant biosecurity threats. This project will also provide continued capacity in virology to support the cotton industry

Tobacco Streak Virus (TSV) in Cotton - scoping study

This project aims to examine the possible impact of Tobacco Streak Virus (TSV) on the Australian cotton industry. TSV is transmitted by thrips, causes a disease which has had a significant impact on grain crops in Central Queensland and a preliminary study in 2007 has shown that cotton is also susceptible to field infection in this region, but many questions remain unanswered. This project aims to: • Determine the impact of TSV in “normal” seasons. • Survey New South Wales and Queensland crops and determine alternative weed and crop hosts. • Assess yield-loss in cotton due to TSV, and factors that lead to systemic infection. • Assess thrips vector species present in cotton • Provide extension material on the impact and management of TSV in cotto

Tobacco Streak Virus in cotton-scoping study

In 2006, Tobacco streak virus (TSV) was identified as the causal agent of the devastating sunflower necrosis disease in central Queensland (CQ), and subsequently in 2007 as the cause of major losses in mungbeans in the same area. It has been a major factor in the recent downturn in the sunflower industry in CQ. Surveys in 2007/2008 as part of a one year scoping study (project 03DAQ005) found TSV in cotton in CQ. The symptoms were mostly confined to the feeding sites of the thrips and appeared as reddish spots and rings, but only occasionally the plants were systemically infected and showed a chlorotic mosaic and leaf deformation. The major objectives of this project (DAQ0002) were to determine: the incidence and distribution of TSV in cotton and its likely effect on yield; the thrips vector species associated with TSV infections in cotton; and the factors that may lead to systemic infections. In contrast to the extensive damage observed in sunflower and mungbean crops from the same region, TSV has caused no measurable damage in commercial cotton crops surveyed in CQ over the seasons 2008/9 to 2010/11. No TSV infected cotton was found in regions outside of CQ and the geographical distribution of TSV disease in cotton (and other susceptible hosts) appears to be closely related to the distribution of the major alternative host, parthenium weed. The most likely thrips species responsible for transmission of TSV into cotton is the tomato thrips (Frankliniella schultzei) and onion thrips (Thrips tabaci). Systemically infected plants are rarely seen in commercial crops and have also been rarely produced in controlled tests. It appears that systemic infection may be transient with only mild symptoms being produced intermittently. With current cultivars and conditions, it appears likely that TSV will continue to cause only minor levels of mild local lesions with no impact on yield in cotton crops. It appears that no specific control strategies are required to limit the impact of TSV in cotton. However, general farm hygiene to minimise the presence of the major alternative host of TSV, parthenium weed, is advised and may be of vital importance if TSV susceptible rotational crops such as mung beans are grown

Epidemiology and genetic diversity of Tobacco streak virus and related subgroup 1 ilarviruses

A quarter of Australia’s sunflower production is from the central highlands region of Queensland and is currently worth six million dollars ($AUD) annually. From the early 2000s a severe necrosis disorder of unknown aetiology was affecting large areas of sunflower crops in central Queensland, leading to annual losses of up to 20%. Other crops such as mung bean and cotton were also affected. This PhD study was undertaken to determine if the causal agent of the necrosis disorder was of viral origin and, if so, to characterise its genetic diversity, biology and disease cycle, and to develop effective control strategies. The research described in this thesis identified Tobacco streak virus (TSV; genus Ilarvirus, family Bromoviridae) as the causal agent of the previously unidentified necrosis disorder of sunflower in central Queensland. TSV was also the cause of commonly found diseases in a range of other crops in the same region including cotton, chickpea and mung bean. This was the first report from Australia of natural field infections of TSV from these four crops. TSV strains have previously been reported from other regions of Australia in several hosts based on serological and host range studies. In order to determine the relatedness of previously reported TSV strains with TSV from central Queensland, we characterised the genetic diversity of the known TSV strains from Australia. We identified two genetically distinct TSV strains from central Queensland and named them based on their major alternative hosts, TSV-parthenium from Parthenium hysterophorus and TSV-crownbeard from Verbesina encelioides. They share only 81 % total-genome nucleotide sequence identity. In addition to TSV-parthenium and TSV-crownbeard from central Queensland, we also described the complete genomes of two other ilarvirus species. This proved that previously reported TSV strains, TSV-S isolated from strawberry and TSV-Ag from Ageratum houstonianum, were actually the first record of Strawberry necrotic shock virus from Australia, and a new subgroup 1 ilarvirus, Ageratum latent virus. Our results confirmed that the TSV strains found in central Queensland were not related to previously described strains from Australia and may represent new incursions. This is the first report of the genetic diversity within subgroup 1 ilarviruses from Australia. Based on field observations we hypothesised that parthenium and crownbeard were acting as symptomless hosts of TSV-parthenium and TSV-crownbeard, respectively. We developed strain-specific multiplex PCRs for the three RNA segments to accurately characterise the range of naturally infected hosts across central Queensland. Results described in this thesis show compelling evidence that parthenium and crownbeard are the major (symptomless) alternative hosts of TSV-parthenium and TSV-crownbeard. While both TSV strains had wide natural host ranges, the geographical distribution of each strain was closely associated with the respective distribution of their major alternative hosts. Both TSV strains were commonly found across large areas of central Queensland, but we only found strong evidence for the TSV-parthenium strain being associated with major disease outbreaks in nearby crops. The findings from this study demonstrate that both TSV-parthenium and TSV-crownbeard have similar life cycles but some critical differences. We found both TSV strains to be highly seed transmitted from their respective major alternative hosts from naturally infected mother plants and survived in seed for more than 2 years. We conclusively demonstrated that both TSV strains were readily transmitted via virus-infected pollen taken from the major alternative hosts. This transmission was facilitated by the most commonly collected thrips species, Frankliniella schultzei and Microcephalothrips abdominalis. These results illustrate the importance of seed transmission and efficient thrips vector species for the effective survival of these TSV strains in an often harsh environment and enables the rapid development of TSV disease epidemics in surrounding crops. Results from field surveys and inoculation tests indicate that parthenium is a poor host of TSV-crownbeard. By contrast, crownbeard was naturally infected by, and an experimental host of TSV-parthenium. However, this infection combination resulted in non-viable crownbeard seed. These differences appear to be an effective biological barrier that largely restricts these two TSV strains to their respective major alternative hosts. Based on our field observations we hypothesised that there were differences in relative tolerance to TSV infection between different sunflower hybrids and that seasonal variation in disease levels was related to rainfall in the critical early crop stage. Results from our field trials conducted over multiple years conclusively demonstrated significant differences in tolerance to natural infections of TSV-parthenium in a wide range of sunflower hybrids. Glasshouse tests indicate the resistance to TSV-parthenium identified in the sunflower hybrids is also likely to be effective against TSV-crownbeard. We found a significant negative association between TSV disease incidence in sunflowers and accumulated rainfall in the months of March and April with increasing rainfall resulting in reduced levels of disease. Our results indicate that the use of tolerant sunflower germplasm will be a critical strategy to minimise the risk of TSV epidemics in sunflower

Distribution in Australia and seed transmission of tobacco streak virus in parthenium hysterophorus

Distribution in Australia and seed transmission of Tobacco streak virus in Parthenium hysterophorus. Plant Dis. 93:708-712. Tobacco streak virus (TSV) was found to commonly occur in Parthenium hysterophorus, as symptomless infections, in central Queensland, Australia across a large area infested with this weed. Several isolates of TSV collected across the geographic range of P. hysterophorus were found to share identical coat protein sequence with each other and with TSV from crop plants in the same area. Seed transmission of TSV in P. hysterophorus was found to occur at rates of 6.8 to 48%. There was almost no change in the rate of TSV seed transmission when P. hysterophorus seed was stored for up to 241/2 months. Implications of this relationship between TSV and P. hysterophorus for the development of virus disease epidemics in surrounding crops are discussed. © 2009 The American Phytopathological Society

Natural host range, thrips and seed transmission of distinct Tobacco streak virus strains in Queensland, Australia

Diseases caused by Tobacco streak virus (TSV) have resulted in significant crop losses in sunflower and mung bean crops in Australia. Two genetically distinct strains from central Queensland, TSV-parthenium and TSV-crownbeard, have been previously described. They share only 81% total-genome nucleotide sequence identity and have distinct major alternative hosts, Parthenium hysterophorus (parthenium) and Verbesina encelioides (crownbeard). We developed and used strain-specific multiplex Polymerase chain reactions (PCRs) for the three RNA segments of TSV-parthenium and TSV-crownbeard to accurately characterise the strains naturally infecting 41 hosts species. Hosts included species from 11 plant families, including 12 species endemic to Australia. Results from field surveys and inoculation tests indicate that parthenium is a poor host of TSV-crownbeard. By contrast, crownbeard was both a natural host of, and experimentally infected by TSV-parthenium but this infection combination resulted in non-viable seed. These differences appear to be an effective biological barrier that largely restricts these two TSV strains to their respective major alternative hosts. TSV-crownbeard was seed transmitted from naturally infected crownbeard at a rate of between 5% and 50% and was closely associated with the geographical distribution of crownbeard in central Queensland. TSV-parthenium and TSV-crownbeard were also seed transmitted in experimentally infected ageratum (Ageratum houstonianum) at rates of up to 40% and 27%, respectively. The related subgroup 1 ilarvirus, Ageratum latent virus, was also seed transmitted at a rate of 18% in ageratum which is its major alternative host. Thrips species Frankliniella schultzei and Microcephalothrips abdominalis were commonly found in flowers of TSV-affected crops and nearby weed hosts. Both species readily transmitted TSV-parthenium and TSV-crownbeard. The results are discussed in terms of how two genetically and biologically distinct TSV strains have similar life cycle strategies in the same environment

First report ofTobacco streak virus in sunflower (Helianthus annuus), cotton (Gossypium hirsutum), chickpea (Cicer arietinum) and mung bean (Vigna radiata) in Australia

Tobacco streak virus (genusIlarvirus) is recorded on sunflower (Helianthus annuus), cotton (Gossypium hirsutum), chickpea (Cicer arietinum) and mung bean (Vigna radiata) in Australia for the first time

Distribution and identification of luteovirids affecting chickpea in Sudan

In Sudan yellowing viruses are key production constraints in pulse crops. Field surveys were carried out to identify luteovirids affecting chickpea crops in the major production regions (Gezira Scheme and River Nile State). A total of 415 chickpea plant samples with yellowing and stunting symptoms were collected during the 2013, 2015 and 2018 growing seasons. Serological results (Tissue-blot immunoassays) showed that Luteoviridae and Chickpea chlorotic dwarf virus (CpCDV, genus Mastrevirus, family Geminiviridae) were the most common viruses, with rare infections with Faba bean necrotic yellows virus (FBNYV, genus Nanovirus, family Nanoviridae). Some samples reacted only with a broad-spectrum luteovirid monoclonal antibody (5G4-MAb), and others showed cross reactions between the specific monoclonal antibodies, suggesting the occurrence of new luteovirid variants. Serological results were confirmed by amplification with reverse transcription-polymerase chain reaction (RT-PCR) and sequencing of the partial coat protein gene. Molecular analyses provided a basic, sufficient and reliable characterization for four viruses affecting chickpea that belong to Polerovirus (family Luteoviridae). These were Cucurbit aphid-borne yellows virus (CABYV), Pepper vein yellows virus (PeVYV), Pepo aphid-borne yellows virus (PABYV) and Cotton leafroll dwarf virus (CLRDV), that shared high similarity with the type sequences. Phylogenetic analyses also revealed high similarity to luteovirid species. This study has established reliable, rapid and sensitive molecular tools for the detection of luteovirid species

Distribution and identification of luteovirids affecting chickpea in Sudan

In Sudan yellowing viruses are key production constraints in pulse crops. Field surveys were carried out to identify luteovirids affecting chickpea crops in the major production regions (Gezira Scheme and River Nile State). A total of 415 chickpea plant samples with yellowing and stunting symptoms were collected during the 2013, 2015 and 2018 growing seasons. Serological results (Tissue-blot immunoassays) showed that Luteoviridae and Chickpea chlorotic dwarf virus (CpCDV, genus Mastrevirus, family Geminiviridae) were the most common viruses, with rare infections with Faba bean necrotic yellows virus (FBNYV, genus Nanovirus, family Nanoviridae). Some samples reacted only with a broad-spectrum luteovirid monoclonal antibody (5G4-MAb), and others showed cross reactions between the specific monoclonal antibodies, suggesting the occurrence of new luteovirid variants. Serological results were confirmed by amplification with reverse transcription-polymerase chain reaction (RT-PCR) and sequencing of the partial coat protein gene. Molecular analyses provided a basic, sufficient and reliable characterization for four viruses affecting chickpea that belong to Polerovirus (family Luteoviridae). These were Cucurbit aphid-borne yellows virus (CABYV), Pepper vein yellows virus (PeVYV), Pepo aphid-borne yellows virus (PABYV) and Cotton leafroll dwarf virus (CLRDV), that shared high similarity with the type sequences. Phylogenetic analyses also revealed high similarity to luteovirid species. This study has established reliable, rapid and sensitive molecular tools for the detection of luteovirid species

Complete Genome Sequence of a New Mastrevirus, Chickpea Redleaf Virus 2, from Australia

We present here the complete genome sequence of a novel mastrevirus isolated from Cicer arietinum (chickpea) from Australia. We propose the name chickpea redleaf virus 2