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

Abstract

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 % totalgenome 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 strainspecific 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-4 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 ...

Virus Diseases of Cereal and Oilseed Crops in Australia: Current Position and Future Challenges

“…In a glasshouse experiment in NSW, infecting a mixture of mustard and canola plants, with TuYV or TuMV diminished their seed yields by 12% or 84% overall, respectively [205]. The most significant virus diseases of sunflower and cotton are caused by tobacco streak virus in sunflower (TSV; genus Ilarvirus, family Bromoviridae) [216][217][218][219][220], and cotton bunchy top virus in cotton (CBTV; genus, Polerovirus, family Solemoviridae) [147,[221][222][223][224]. They are important in Australia's subtropics and are present in its tropical regions (Figure 1; Table 2).…”

Field evaluation of tolerance toTobacco streak virusin sunflower germplasm, and observations of seasonal disease spread

“…TSV has also been associated with disease epidemics in sunflower and a range of legume and vegetable crops in India, Brazil and the United States of America (Almeida et al, 2005;Rabedeaux et al, 2005;Kumar et al, 2008). Symptoms in sunflower typically include chlorosis and distortion of leaves, severe stem and terminal necrosis, often progressing to complete collapse and death of affected plants (Kumar et al, 2008;Sharman, 2015;Sharman et al, 2015). The region affected by TSV spans more than 200 km from south of the town of Springsure to north of Clermont.…”