Allelopathy for weed control in agricultural systems

Weeds are a hidden foe for crop plants, interfering with their functions and suppressing their growth and development. Yield losses of ∼34 are caused by weeds among the major crops, which are grown worldwide. These yield losses are higher than the losses caused by other pests in the crops. Sustainable weed management is needed in the wake of a huge decline in crop outputs due to weed pressure. A diversity in weed management tools ensures sustainable weed control and reduces chances of herbicide resistance development in weeds. Allelopathy as a tool, can be importantly used to combat the challenges of environmental pollution and herbicide resistance development. This review article provides a recent update regarding the practical application of allelopathy for weed control in agricultural systems. Several studies elaborate on the significance of allelopathy for weed management. Rye, sorghum, rice, sunflower, rape seed, and wheat have been documented as important allelopathic crops. These crops express their allelopathic potential by releasing allelochemicals which not only suppress weeds, but also promote underground microbial activities. Crop cultivars with allelopathic potentials can be grown to suppress weeds under field conditions. Further, several types of allelopathic plants can be intercropped with other crops to smother weeds. The use of allelopathic cover crops and mulches can reduce weed pressure in field crops. Rotating a routine crop with an allelopathic crop for one season is another method of allelopathic weed control. Importantly, plant breeding can be explored to improve the allelopathic potential of crop cultivars. In conclusion, allelopathy can be utilized for suppressing weeds in field crops. Allelopathy has a pertinent significance for ecological, sustainable, and integrated weed management systems.

Biodiversity, biosecurity and integrated pest management

Breaches of biosecurity, leading to incursions by invasive species, have the potential to cause substantial economic, social and environmental losses, including drastic reduction in biodiversity. It is argued that improving biosecurity reduces risk to biodiversity, while maintaining stable ecosystems through biodiversity can be a safeguard against biosecurity breaches. The global costs of invasive alien species (IAS) have been estimated at around US$350 billion, while alien invertebrate and vertebrate pests and weeds are estimated to cost Australia at least $7 billion a year. A striking, current, example is the incursion by Myrtle Rust (Puccinia psidii) an organism which can infect all members of the Myrtaceae, the most important family in the Australian flora. Myrtle rust was first detected on a property on the central coast of New South Wales in late April 2010. Two years later the disease has been detected in numerous locations in Queensland and New South Wales ranging from commercial plant nurseries and public amenities to large areas of bushland. This particular breach of biosecurity will, inevitably, diminish biodiversity of flora and fauna over large areas of the continent. Integrated pest management (IPM), an enrichment of diversity in managing invasive and other pest species, offers the best opportunity to address problems such as these. Australia's response to increasing biosecurity risk is comprehensive and includes national networking of scientists engaged in a complex program of biosecurity research and development, including studies of IPM. This network is being enhanced by the development of international linkages.

Commercial-scale Alternaria brown spot resistance screening as the first step in breeding new mandarins for Australia

Rapid screening tests and an appreciation of the simple genetic control of Alternaria brown spot (ABS) susceptibility have existed for many years, and yet the application of this knowledge to commercial-scale breeding programs has been limited. Detached leaf assays were first demonstrated more than 40 years ago and reliable data suggesting a single gene determining susceptibility has been emerging for at least 20 years. However it is only recently that the requirement for genetic resistance in new hybrids has become a priority, following increased disease prevalence in Australian mandarin production areas previously considered too dry for the pathogen. Almost all of the high-fruit-quality parents developed so far by the Queensland-based breeding program are susceptible to ABS necessitating the screening of their progeny to avoid commercialisation of susceptible hybrids. This is done effectively and efficiently by spraying 3-6 month old hybrid seedlings with a spore suspension derived from a toxin-producing field isolate of Alternaria alternate, then incubating these seedlings in a cool room at 25°C and high humidity for 5 days. Susceptible seedlings show clear disease symptoms and are discarded. Analysis of observed and expected segregation ratios loosely support the hypothesis for a single dominant gene for susceptibility, but do not rule out the possibility of alternative genetic models. After implementing the routine screening for ABS resistance for three seasons we now have more than 20,000 hybrids growing in field progeny blocks that have been screened for resistance to the ABS disease.

Inheritance and Characterization of Strong Resistance to Phosphine in Sitophilus oryzae(L.)

Sitophilus oryzae (Linnaeus) is a major pest of stored grain across Southeast Asia and is of increasing concern in other regions due to the advent of strong resistance to phosphine, the fumigant used to protect stored grain from pest insects. We investigated the inheritance of genes controlling resistance to phosphine in a strongly resistant S. oryzae strain (NNSO7525) collected in Australia and find that the trait is autosomally inherited and incompletely recessive with a degree of dominance of -0.66. The strongly resistant strain has an LC50 52 times greater than a susceptible reference strain (LS2) and 9 times greater than a weakly resistant strain (QSO335). Analysis of F2 and backcross progeny indicates that two or more genes are responsible for strong resistance, and that one of these genes, designated Sorph1, not only contributes to strong resistance, but is also responsible for the weak resistance phenotype of strain QSO335. These results demonstrate that the genetic mechanism of phosphine resistance in Soryzae is similar to that of other stored product insect pests. A unique observation is that a subset of the progeny of an F1 backcross generation are more strongly resistant to phosphine than the parental strongly resistant strain, which may be caused by multiple alleles of one of the resistance genes.

Novel species of Cercospora and Pseudocercospora (Capnodiales, Mycosphaerellaceae) from Australia

Novel species of Cercospora and Pseudocercospora are described from Australian native plant species. These taxa are Cercospora ischaemi sp. nov. on Ischaemum australe (Poaceae); Pseudocercospora airliensis sp. nov. on Polyalthia nitidissima (Annonaceae); Pseudocercospora proiphydis sp. nov. on Proiphys amboinensis (Amaryllidaceae); and Pseudocercospora jagerae sp. nov. on Jagera pseudorhus var. pseudorhus (Sapindaceae). These species were characterised by morphology and an analysis of partial nucleotide sequence data for the three gene loci, ITS, LSU and EF-1α. Recent divergence of closely related Australian species of Pseudocercospora on native plants is proposed.

Complete genome sequence and intracellular protein localization of Datura yellow vein nucleorhabdovirus

A limited number of plant rhabdovirus genomes have been fully sequenced, making taxonomic classification, evolutionary analysis and molecular characterization of this virus group difficult. We have for the first time determined the complete genome sequence of 13,188 nucleotides of Datura yellow vein nucleorhabdovirus (DYVV). DYVV genome organization resembles that of its closest relative, Sonchus yellow net virus (SYNV), with six ORFs in antigenomic orientation, separated by highly conserved intergenic regions and flanked by complementary 3′ leader and 5′ trailer sequences. As is typical for nucleorhabdoviruses, all viral proteins, except the glycoprotein, which is targeted to the endoplasmic reticulum, are localized to the nucleus. Nucleocapsid (N) protein, matrix (M) protein and polymerase, as components of nuclear viroplasms during replication, have predicted strong canonical nuclear localization signals, and N and M proteins exclusively localize to the nucleus when transiently expressed as GFP fusions. As in all nucleorhabdoviruses studied so far, N and phosphoprotein P interact when co-expressed, significantly increasing P nuclear localization in the presence of N protein. This research adds to the list of complete genomes of plant-infecting rhabdoviruses, provides molecular tools for further characterization and supports classification of DYVV as a nucleorhabdovirus closely related to but with some distinct differences from SYNV.

Bactrocera frauenfeldi (Diptera: Tephritidae), an invasive fruit fly in Australia that may have reached the extent of its spread due to environmental variables

Bactrocera frauenfeldi (Schiner), the ‘mango fruit fly’, is a horticultural pest originating from the Papua New Guinea region. It was first detected in Australia on Cape York Peninsula in north Queensland in 1974 and had spread to Cairns by 1994 and Townsville by 1997. Bactrocera frauenfeldi has not been recorded further south since then despite its invasive potential, an absence of any controls and an abundance of hosts in southern areas. Analysis of cue-lure trapping data from 1997 to 2012 in relation to environmental variables shows that the distribution of B. frauenfeldi in Queensland correlates to locations with a minimum temperature for the coldest month >13.2°C, annual temperature range <19.3°C, mean temperature of the driest quarter >20.2°C, precipitation of the wettest month >268 mm, precipitation of the wettest quarter >697 mm, temperature seasonality <30.9°C (i.e. lower temperature variability) and areas with higher human population per square kilometre. Annual temperature range was the most important variable in predicting this species' distribution. Predictive distribution maps based on an uncorrelated subset of these variables reasonably reflected the current distribution of this species in northern Australia and predicted other areas in the world potentially at risk from invasion by this species. This analysis shows that the distribution of B. frauenfeldi in Australia is correlated to certain environmental variables that have most likely limited this species' spread southward in Queensland. This is of importance to Australian horticulture in demonstrating that B. frauenfeldi is unlikely to establish in horticultural production areas further south than Townsville.

First report of Cotton leafroll dwarf virus in Thailand using a species-specific PCR validated with isolates from Brazil

Partial virus genome sequence with high nucleotide identity to Cotton leafroll dwarf virus (CLRDV) was identified from two cotton (Gossypium hirsutum) samples from Thailand displaying typical cotton leaf roll disease symptoms. We developed and validated a PCR assay for the detection of CLRDV isolates from Thailand and Brazil.

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.

Distribution and characterization of Poleroviruses affecting food legumes in Central/West Asia and North Africa (CWANA) region and Australia

During the past 15 years, surveys to identify virus diseases affecting cool-season food legume crops in Australia and 11 CWANA countries (Algeria, China, Egypt, Ethiopia, Lebanon, Morocco, Sudan, Syria, Tunisia, Uzbekistan and Yemen) were conducted. More than 20,000 samples were collected and tested for the presence of 14 legume viruses by the tissue-blot immunoassay (TBIA) using a battery of antibodies, including the following Luteovirus monoclonal antibodies (McAbs): a broad-spectrum legume Luteovirus (5G4), BLRV, BWYV, SbDV and CpCSV. A total of 195 Luteovirus samples were selected for further testing by RT-PCR using 7 primers (one is degenerate, and can detect a wide range of Luteoviridae virus species and the other six are species-specific primers) at the Virology Laboratory, QDAF, Australia, during 2014. A total of 145 DNA fragments (represented 105 isolates) were sequenced. The following viruses were characterized based on molecular analysis: BLRV from Lebanon, Morocco, Tunisia and Uzbekistan; SbDV from Australia, Syria and Uzbekistan; BWYV from Algeria, China, Ethiopia, Lebanon, Morocco, Sudan, Tunisia and Uzbekistan; CABYV from Algeria, Lebanon, Syria, Sudan and Uzbekistan; CpCSV from Algeria, Ethiopia, Lebanon, Morocco, Syria and Tunisia, and unknown Luteoviridae species from Algeria, Ethiopia, Morocco, Sudan, Uzbekistan and Yemen. This study has clearly shown that there are a number of Polerovirus species, in addition to BWYV, all can produce yellowing/stunting symptoms in pulses (e.g. CABYV, CpCSV, and other unknown Polerovirus species). Based on our knowledge this is the first report of CABYV affecting food legumes. Moreover, there was about 95% agreement between results obtained from serological analysis (TBIA) and molecular analysis for the detection of BLRV and SbDV. Whereas, TBIA results were not accurate when using CpCSV and BWYV McAbs . It seems that the McAbs for CpCSV and BWYV used in this study and those available worldwide, are not virus species specific. Both antibodies, reacted with other Polerovirus species (e.g. CABYV, and unknown Polerovirus). This highlights the need for more accurate characterization of existing antibodies and where necessary the development of better, virus-specific antibodies to enable their use for accurate diagnosis of Poleroviruses.

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.

Exotic plant pests–a threat to the sustainability of Australia’s grains industry

Exotic plant pests (EPPs) threaten production, market access and sustainability of Australian plant production systems. For the grains industry there are over 600 identified EPPs of which 54 are considered high priority, posing a significant threat. Despite Australia’s geographical isolation and strong quarantine systems, the threat from EPPs has never been higher with the increasing levels of travel and trade, emphasising the need for improving our efforts in prevention, preparedness and surveillance for EPPs.

Field evaluation of tolerance to Tobacco streak virus in sunflower germplasm, and observations of seasonal disease spread

Strong statistical evidence was found for differences in tolerance to natural infections of Tobacco streak virus (TSV) in sunflower hybrids. Data from 470 plots involving 23 different sunflower hybrids tested in multiple trials over 5 years in Australia were analysed. Using a Bayesian Hierarchical Logistic Regression model for analysis provided: (i) a rigorous method for investigating the relative effects of hybrid, seasonal rainfall and proximity to inoculum source on the incidence of severe TSV disease; (ii) a natural method for estimating the probability distributions of disease incidence in different hybrids under historical rainfall conditions; and (iii) a method for undertaking all pairwise comparisons of disease incidence between hybrids whilst controlling the familywise error rate without any drastic reduction in statistical power. The tolerance identified in field trials was effective against the main TSV strain associated with disease outbreaks, TSV-parthenium. Glasshouse tests indicate this tolerance to also be effective against the other TSV strain found in central Queensland, TSV-crownbeard. The use of tolerant germplasm is critical to minimise the risk of TSV epidemics in sunflower in this region. We found strong statistical evidence that rainfall during the early growing months of March and April had a negative effect on the incidence of severe infection with greatly reduced disease incidence in years that had high rainfall during this period.