Quantitative trait loci and epistatic interactions in barley conferring resistance to net type net blotch (Pyrenophora teres f. teres) isolates.

Net type net blotch (NTNB) is an important barley disease in Australia and elsewhere, with significant yield reduction. This trait is important in selection along with other traits of quality and agronomic value. Two-hundred doubled-haploid lines were generated through anther culture from a cross between 'Pompadour' and 'Stirling'. Quantitative trait loci (QTL) were identified against five isolates of Pyrenophora teres f. teres, which represent virulences across Australia. QTL were mapped on chromosomes 3H and 6H using simple sequence repeat (SSR) markers. The resistance locus on 6H was detected with all isolates while the 3H locus was detected with two isolates. The 6H QTL from 'Pompadour' contributed resistance to isolates 97NB1, 95NB100 and NB81, whereas 6H QTL from 'Stirling' contributed resistance to isolates NB50 and NB52B. The 3H QTL from 'Pompadour' contributed resistance to NB50 and NB52B. Significant epistatic interactions were detected between QTL on 3H and 6H. These resistance QTL are a useful resource and identifying closely linked SSR markers with allelic combinations will facilitate in marker-assisted selection to develop NTNB resistant breeding lines.

Environment characterization as an aid to wheat improvement: interpreting genotype-environment interactions by modelling water-deficit patterns in North-Eastern Australia.

Genotype-environment interactions (GEI) limit genetic gain for complex traits such as tolerance to drought. Characterization of the crop environment is an important step in understanding GEI. A modelling approach is proposed here to characterize broadly (large geographic area, long-term period) and locally (field experiment) drought-related environmental stresses, which enables breeders to analyse their experimental trials with regard to the broad population of environments that they target. Water-deficit patterns experienced by wheat crops were determined for drought-prone north-eastern Australia, using the APSIM crop model to account for the interactions of crops with their environment (e.g. feedback of plant growth on water depletion). Simulations based on more than 100 years of historical climate data were conducted for representative locations, soils, and management systems, for a check cultivar, Hartog. The three main environment types identified differed in their patterns of simulated water stress around flowering and during grain-filling. Over the entire region, the terminal drought-stress pattern was most common (50% of production environments) followed by a flowering stress (24%), although the frequencies of occurrence of the three types varied greatly across regions, years, and management. This environment classification was applied to 16 trials relevant to late stages testing of a breeding programme. The incorporation of the independently-determined environment types in a statistical analysis assisted interpretation of the GEI for yield among the 18 representative genotypes by reducing the relative effect of GEI compared with genotypic variance, and helped to identify opportunities to improve breeding and germplasm-testing strategies for this region.

Utilisation of local ingredients in commercial pig feeds

The long-term competitiveness of the both the Vietnamese feed and pig production industries are constrained and under pressure whilst the industry is dependent on the use of imported feed ingredients in diets for animal production. These cost pressures are a result of import taxes, transport costs, currency fluctuations and feed supply limitations. By undertaking studies on available resources which are currently under-utilised and with potential as local feeds, we can prove their suitability for use as feedstuffs in pig diets and as replacements for imported feed ingredients. In undertaking this process we can lower feeding costs for pig production in Vietnam by the use of local feeds which are cheaper, generate new industries in Vietnam harvesting or processing these feeds and increase the incomes of Vietnamese workers who are involved in producing these by-products. Our project has shown that rubber seed, when processed correctly to lower the hydrogen cyanide content, is a safe and suitable protein meal feedstuff for use in pig diets with the potential to replace significant quantities of imported soybean and fishmeal in Vietnamese pig diets as long as diets are balanced for any amino acid shortfalls. Our peanut studies have shown that use of binders can help alleviate pig production problems with aflatoxin content in peanut meals. Further work is needed to characterise the fate of the bound aflatoxin to see if there is any meat residue risk. Cassava residue is a resultant by-product from starch extraction in both large and small cassava processing factories. Sub-samples from these two mill types were collected and evaluated for residue HCN. Analyses has shown that the processing and sun drying results in a product with relatively consistent low HCN content. Chemical analyses also reveal that significant residual starch also remains in this by-product. Digestibility studies and pig performance feeding studies have shown that cassava residue can be included in diets at 30% with no adverse effect, although the higher fibre content of this product means that strategically, cassava residue is more suitably used in finisher and sow diets. Research has examined the digestible energy content of a number of sunflower meal types available in Australia and identified major differences in their energy value based on processing, additionally, amino acid analysis has shown a significantly lower lysine content than previous reported. We also examined the digestible energy content of a number of Australian stylo forage legume harvest batches and identified the differences in their energy value based on age/harvest time of the forage legume. Analysis results of various stylo cuts showed that the early cut stylo has a higher starch content and lower fibre fraction content than observed in late and recut stylo which were allowed to grow longer. As a result the faecal digestible energy content was higher for the early cut stylo than for the subsequent cut stylo material which had been allowed to become woody. The results have shown that feeding of stylo meal does provide some nutritive value to the pig with increased energy and nitrogen supply, with a portion of the nitrogen presented which the pig is able to retain. Based on nutrient and fibre content stylo could have a useful role in sow feeding and satiety under non-stall housing situations. With increasing Vietnamese investment in rubber production seen with larger areas under plantations the amounts of rubber seed available for animal feeding will grow significantly over the next 15 years and the importance of the by-product ie rubber seed meal as a protein source in diets for Vietnamese pigs.

Assessment of novel gear designs to reduce interactions between species

This project tested modified gillnets designed by commercial net fishers in the Queensland East Coast Inshore Finfish Fishery (ECIFF) to try and identify gears that would mitigate and/or improve interactions between fishing nets and Species of Conservation Interest (SOCI). The study also documents previously unrecognised initiatives by pro-active commercial net fishers that reflect a conservation-minded approach to their fishing practices, which is the opposite of what is perceived publicly. Between 2011 and 2014, scientists from James Cook University and the Queensland Department of Agriculture and Fisheries teamed with commercial fishers representing the Queensland Seafood Industry Association and the Moreton Bay Seafood Industry Association to conduct field trials of various modified net designs under normal fishery conditions. Trials were conducted in Moreton Bay (southern part of the fishery) and Bowling Green Bay (northern) and tested different net designs developed by fishers to improve the nature of interactions between net fishing gear and SOCI.

Hardwoods Nutrient/Disease Interactions

Interactions of nutrients and disease expression in hardwood plantations.

Cellular and molecular interactions of rhabdoviruses

Cellular and molecular interactions of rhabdoviruses with their plant hosts and insect vectors.

Interactions between a Trawl fishery and spatial closures for biodiversity conservation in the Great Barrier Reef World Heritage Area, Australia.

Background: The Queensland East Coast Otter Trawl Fishery (ECOTF) for penaeid shrimp fishes within Australia's Great Barrier Reef World Heritage Area (GBRWHA). The past decade has seen the implementation of conservation and fisheries management strategies to reduce the impact of the ECOTF on the seabed and improve biodiversity conservation. New information from electronic vessel location monitoring systems (VMS) provides an opportunity to review the interactions between the ECOTF and spatial closures for biodiversity conservation. Methodology and Results: We used fishing metrics and spatial information on the distribution of closures and modelled VMS data in a geographical information system (GIS) to assess change in effort of the trawl fishery from 2001-2009 and to quantify the exposure of 70 reef, non-reef and deep water bioregions to trawl fishing. The number of trawlers and the number of days fished almost halved between 2001 and 2009 and new spatial closures introduced in 2004 reduced the area zoned available for trawl fishing by 33%. However, we found that there was only a relatively minor change in the spatial footprint of the fishery as a result of new spatial closures. Non-reef bioregions benefited the most from new spatial closures followed by deep and reef bioregions. Conclusions/Significance: Although the catch of non target species remains an issue of concern for fisheries management, the small spatial footprint of the ECOTF relative to the size of the GBRWHA means that the impact on benthic habitats is likely to be negligible. The decline in effort as a result of fishing industry structural adjustment, increasing variable costs and business decisions of fishers is likely to continue a trend to fish only in the most productive areas. This will provide protection for most benthic habitats without any further legislative or management intervention.

In planta localization and interactions of impatiens necrotic spot tospovirus proteins

Impatiens necrotic spot tospovirus (INSV) is a significant pathogen of ornamentals. The tripartite negative- and ambi-sense RNA genome encodes six proteins that are involved in cytoplasmic replication, movement, assembly, insect transmission and defence. To gain insight into the associations of these viral proteins, we determined their intracellular localization and interactions in living plant cells. Nucleotide sequences encoding the nucleoprotein N, non-structural proteins NSs and NSm, and glycoproteins Gn and Gc of a Kentucky isolate of INSV were amplified by RTPCR, cloned, sequenced and transiently expressed as fusions with autofluorescent proteins in leaf epidermal cells of Nicotiana benthamiana. All proteins accumulated at the cell periphery and co-localized with an endoplasmic reticulum marker. The Gc protein fusion also localized to the nucleus. N and NSm protein self-interactions and an NSm-N interaction were observed by using bimolecular fluorescence complementation. A tospovirus NSm homotypic interaction had not been reported previously.

Classifying genotype by environment interactions for targeted germplasm deployment with a focus on Eucalyptus

A novel methodology for describing genotype by environment interactions estimated from multi-environment field trials is described and an empirical example using an extensive trial network of eucalypts is presented. The network of experiments containing 65 eucalypts was established in 38 replicated field trials across the tropics and subtropics of eastern Australia, with a selection of well-tested species used to provide a more detailed examination of productivity differentials across environmental gradients. By focusing on changes in species’ productivity across environmental gradients, the results are applicable for all species established across the range of environments evaluated in the trial network and simultaneously classify species and environments so that results may be applied across the landscape. The methodology developed was able to explain most (93 %) of the variation in the selected species relative changes in productivity across the various environmental variables examined. Responses were primarily regulated by changes in variables related to water availability and secondarily by temperature related variables. Clustering and ordination can identify groups of species with similar physiological responses to environment and may also guide the parameterisation and calibration of process based models of plant growth. Ordination was particularly useful in the identification of species with distinct environmental response patterns that would be useful as probes for extracting more information from future trials.

Phosphine Resistance in the Rust Red Flour Beetle, Tribolium castaneum (Coleoptera: Tenebrionidae): Inheritance, Gene Interactions and Fitness Costs

The recent emergence of heritable high level resistance to phosphine in stored grain pests is a serious concern among major grain growing countries around the world. Here we describe the genetics of phosphine resistance in the rust red flour beetle Tribolium castaneum (Herbst), a pest of stored grain as well as a genetic model organism. We investigated three field collected strains of T. castaneum viz., susceptible (QTC4), weakly resistant (QTC1012) and strongly resistant (QTC931) to phosphine. The dose-mortality responses of their test- and inter-cross progeny revealed that most resistance was conferred by a single major resistance gene in the weakly (3.2x) resistant strain. This gene was also found in the strongly resistant (431x) strain, together with a second major resistance gene and additional minor factors. The second major gene by itself confers only 12-206x resistance, suggesting that a strong synergistic epistatic interaction between the genes is responsible for the high level of resistance (431x) observed in the strongly resistant strain. Phosphine resistance is not sex linked and is inherited as an incompletely recessive, autosomal trait. The analysis of the phenotypic fitness response of a population derived from a single pair inter-strain cross between the susceptible and strongly resistant strains indicated the changes in the level of response in the strong resistance phenotype; however this effect was not consistent and apparently masked by the genetic background of the weakly resistant strain. The results from this work will inform phosphine resistance management strategies and provide a basis for the identification of the resistance genes.

Corymbia phloem phenolics, tannins and terpenoids: interactions with a cerambycid borer

Plant secondary chemistry mediates the ability of herbivores to locate, accept and survive on potential host plants. We examined the relationship between attack by the cerambycid beetle Phoracantha solida and the chemistry of the secondary phloem (inner bark) of two differentially attacked plantation forestry taxa, Corymbia variegata and its hybrid with C. torelliana. We hypothesised that this differential rate of attack may have to do with differences in secondary chemistry between the taxa. We found differences in the bark chemistry of the taxa, both with respect to phenolic compounds and terpenoids. We could detect no difference between bored and non-bored C. variegata trees (the less preferred, but co-evolved host). Hybrid trees were not different in levels of total polyphenols, flavanols or terpenes according to attack status, but acetone extracts were significantly different between bored and non-bored trees. We propose that variations in the bark chemistry explain the differential attack rate between C. variegata and the hybrid hosts.

Modelling interactions between farm-level structural adjustment and a regional economy: A case of the Australian rice industry

Climate change and on-going water policy reforms will likely contribute to on-farm and regional structural adjustment in Australia. This paper gathers empirical evidence of farm-level structural adjustments and integrates these with a regional equilibrium model to investigate sectoral and regional impacts of climate change and recent water use policy on rice industry. We find strong evidence of adjustments to the farming system, enabled by existing diversity in on-farm production. A further loss of water with additional pressures to adopt less intensive and larger-scale farming, will however reduce the net number of farm businesses, which may affect regional rice production. The results from a regional CGE model show impacts on the regional economy over and above the direct cost of the environmental water, although a net reduction in real economic output and real income is partially offset by gains in rest of the Australia through the reallocation or resources. There is some interest within the industry and from potential new corporate entrants in the relocation of some rice production to the north. However, strong government support would be crucial to implement such relocation.

Weed–pathogen interactions and elevated CO2: growth changes in favour of the biological control agent

In this study, we used Parthenium hysterophorus and one of its biological control agents, the winter rust (Puccinia abrupta var. partheniicola) as a model system to investigate how the weed may respond to infection under a climate change scenario involving an elevated atmospheric CO2 (550 μmol mol−1) concentration. Under such a scenario, P. hysterophorus plants grew significantly taller (52%) and produced more biomass (55%) than under the ambient atmospheric CO2 concentration (380 μmol mol−1). Following winter rust infection, biomass production was reduced by 17% under the ambient and by 30% under the elevated atmospheric CO2 concentration. The production of branches and leaf area was significantly increased by 62% and 120%, under the elevated as compared with ambient CO2 concentration, but unaffected by rust infection under either condition. The photosynthesis and water use efficiency (WUE) of P. hysterophorus plants were increased by 94% and 400%, under the elevated as compared with the ambient atmospheric CO2 concentration. However, in the rust-infected plants, the photosynthesis and WUE decreased by 18% and 28%, respectively, under the elevated CO2 and were unaffected by the ambient atmospheric CO2 concentration. The results suggest that although P. hysterophorus will benefit from a future climate involving an elevation of the atmospheric CO2 concentration, it is also likely that the winter rust will perform more effectively as a biological control agent under these same conditions.

Effect of Broadcast Baiting on Abundance Patterns of Red Imported Fire Ants (Hymenoptera: Formicidae) and Key Local Ant Genera at Long-Term Monitoring Sites in Brisbane, Australia

In 2001, the red imported fire ant (Solenopsis invicta Buren) was identified in Brisbane, Australia. An eradication program involving broadcast bait treatment with two insect growth regulators and a metabolic inhibitor began in September of that year and is currently ongoing. To gauge the impacts of these treatments on local ant populations, we examined long-term monitoring data and quantified abundance patterns of S. invicta and common local ant genera using a linear mixed-effects model. For S. invicta, presence in pitfalls reduced over time to zero on every site. Significantly higher numbers of S. invicta workers were collected on high-density polygyne sites, which took longer to disinfest compared with monogyne and low-density polygyne sites. For local ants, nine genus groups of the 10 most common genera analyzed either increased in abundance or showed no significant trend. Five of these genus groups were significantly less abundant at the start of monitoring on high-density polygyne sites compared with monogyne and low-density polygyne sites. The genus Pheidole significantly reduced in abundance over time, suggesting that it was affected by treatment efforts. These results demonstrate that the treatment regime used at the time successfully removed S. invicta from these sites in Brisbane, and that most local ant genera were not seriously impacted by the treatment. These results have important implications for current and future prophylactic treatment efforts, and suggest that native ants remain in treated areas to provide some biological resistance to S. invicta.

Interactions between two naturalised invasive predators in Australia: are feral cats suppressed by dingoes?

Top-predators can play important roles in terrestrial food webs, fuelling speculation that top-predators might be used as biocontrol tools against invasive mesopredators. Feral cats are believed to be largely responsible for the current declines of native fauna across tropical northern Australia, where substantial beef cattle production occurs. Dingoes are known to impact cattle production there and are predicted to impact native fauna also. However, dingoes are forecasted to curtail the impacts of cats and reverse native fauna declines. We review (1) empirical studies investigating the relationships between dingoes and cats, and dingo control and cats, (2) records of cat remains in dingo diets, and (3) historical records of lethal dingo control using 1080-poisoned baits across Australia between 1999 and 2008 to show how two naturalised invasive species can interact in dynamic agro-ecological landscapes. From the 35 studies assessed, most reported no detectable relationship between dingoes and cats; negative or positive relationships were seldom detected. Dingoes do not appear to exclude cats beyond fine scales, but may alter cat activity periods under certain conditions. Cat remains were found in only 0.63 % of over 31,000 dingo diet records. Lethal dingo control occurs (in varying degrees) across about two-thirds of Australia and does not appear to substantially influence dingo-cat relationships. We conclude that the presently available data provides little evidence that bolstering dingo populations will reduce the impacts of cats. Much more work is needed to identify situations where top-predators might be used as effective biocontrol tools against invasive mesopredators in agro-ecological systems.