Water and thermal regimes for field pea in Australia and their implications for breeding.

There is a large gap between the refined approaches to characterise genotypes and the common use of location and season as a coarse surrogate for environmental characterisation of breeding trials. As a framework for breeding, the aim of this paper is quantifying the spatial and temporal patterns of thermal and water stress for field pea in Australia. We compiled a dataset for yield of the cv. Kaspa measured in 185 environments, and investigated the associations between yield and seasonal patterns of actual temperature and modelled water stress. Correlations between yield and temperature indicated two distinct stages. In the first stage, during crop establishment and canopy expansion before flowering, yield was positively associated with minimum temperature. Mean minimum temperature below similar to 7 degrees C suggests that crops were under suboptimal temperature for both canopy expansion and radiation-use efficiency during a significant part of this early growth period. In the second stage, during critical reproductive phases, grain yield was negatively associated with maximum temperature over 25 degrees C. Correlations between yield and modelled water supply/demand ratio showed a consistent pattern with three phases: no correlation at early stages of the growth cycle, a progressive increase in the association that peaked as the crop approached the flowering window, and a progressive decline at later reproductive stages. Using long-term weather records (1957-2010) and modelled water stress for 104 locations, we identified three major patterns of water deficit nation wide. Environment type 1 (ET1) represents the most favourable condition, with no stress during most of the pre-flowering phase and gradual development of mild stress after flowering. Type 2 is characterised by increasing water deficit between 400 degree-days before flowering and 200 degree-days after flowering and rainfall that relieves stress late in the season. Type 3 represents the more stressful condition with increasing water deficit between 400 degree-days before flowering and maturity. Across Australia, the frequency of occurrence was 24% for ET1, 32% for ET2 and 43% for ET3, highlighting the dominance of the most stressful condition. Actual yield averaged 2.2 t/ha for ET1, 1.9 t/ha for ET2 and 1.4 t/ha for ET3, and the frequency of each pattern varied substantially among locations. Shifting from a nominal (i.e. location and season) to a quantitative (i.e. stress type) characterisation of environments could help improving breeding efficiency of field pea in Australia.

Harvest strategy evaluations and co-management for the Moreton Bay Trawl Fishery

Non-Technical Summary Seafood CRC Project 2009/774. Harvest strategy evaluations and co-management for the Moreton Bay Trawl Fishery Principal Investigator: Dr Tony Courtney, Principal Fisheries Biologist Fisheries and Aquaculture, Agri-Science Queensland Department of Agriculture, Fisheries and Forestry Level B1, Ecosciences Precinct, Joe Baker St, Dutton Park, Queensland 4102 Email: tony.courtney@daff.qld.gov.au Project objectives: 1. Review the literature and data (i.e., economic, biological and logbook) relevant to the Moreton Bay trawl fishery. 2. Identify and prioritise management objectives for the Moreton Bay trawl fishery, as identified by the trawl fishers. 3. Undertake an economic analysis of Moreton Bay trawl fishery. 4. Quantify long-term changes to fishing power for the Moreton Bay trawl fishery. 5. Assess priority harvest strategies identified in 2 (above). Present results to, and discuss results with, Moreton Bay Seafood Industry Association (MBSIA), fishers and Fisheries Queensland. Note: Additional, specific objectives for 2 (above) were developed by fishers and the MBSIA after commencement of the project. These are presented in detail in section 5 (below). The project was an initiative of the MBSIA, primarily in response to falling profitability in the Moreton Bay prawn trawl fishery. The analyses were undertaken by a consortium of DAFF, CSIRO and University of Queensland researchers. This report adopted the Australian Standard Fish Names (http://www.fishnames.com.au/). Trends in catch and effort The Moreton Bay otter trawl fishery is a multispecies fishery, with the majority of the catch composed of Greasyback Prawns (Metapenaeus bennettae), Brown Tiger Prawns (Penaeus esculentus), Eastern King Prawns (Melicertus plebejus), squid (Uroteuthis spp., Sepioteuthis spp.), Banana Prawns (Fenneropenaeus merguiensis), Endeavour Prawns (Metapenaeus ensis, Metapenaeus endeavouri) and Moreton Bay bugs (Thenus parindicus). Other commercially important byproduct includes blue swimmer crabs (Portunus armatus), three-spot crabs (Portunus sanguinolentus), cuttlefish (Sepia spp.) and mantis shrimp (Oratosquilla spp.). Logbook catch and effort data show that total annual reported catch of prawns from the Moreton Bay otter trawl fishery has declined to 315 t in 2008 from a maximum of 901 t in 1990. The number of active licensed vessels participating in the fishery has also declined from 207 in 1991 to 57 in 2010. Similarly, fishing effort has fallen from a peak of 13,312 boat-days in 1999 to 3817 boat-days in 2008 – a 71% reduction. The declines in catch and effort are largely attributed to reduced profitability in the fishery due to increased operational costs and depressed prawn prices. The low prawn prices appear to be attributed to Australian aquacultured prawns and imported aquacultured vannamei prawns, displacing the markets for trawl-caught prawns, especially small species such as Greasyback Prawns which traditionally dominated landings in Moreton Bay. In recent years, the relatively high Australian dollar has resulted in reduced exports of Australian wild-caught prawns. This has increased supply on the domestic market which has also suppressed price increases. Since 2002, Brown Tiger Prawns have dominated annual reported landings in the Moreton Bay fishery. While total catch and effort in the bay have declined to historically low levels, the annual catch and catch rates of Brown Tiger Prawns have been at record highs in recent years. This appears to be at least partially attributed to the tiger prawn stock having recovered from excessive effort in previous decades. The total annual value of the Moreton Bay trawl fishery catch, including byproduct, is about $5 million, of which Brown Tiger Prawns account for about $2 million. Eastern King Prawns make up about 10% of the catch and are mainly caught in the bay from October to December as they migrate to offshore waters outside the bay where they contribute to a large mono-specific trawl fishery. Some of the Eastern King Prawns harvested in Moreton Bay may be growth overfished (i.e., caught below the size required to maximise yield or value), although the optimum size-at-capture was not determined in this study. Banana Prawns typically make up about 5% of the catch, but can exceed 20%, particularly following heavy rainfall. Economic analysis of the fishery From the economic survey, cash profits were, on average, positive for both fleet segments in both years of the survey. However, after the opportunity cost of capital and depreciation were taken into account, the residual owner-operator income was relatively low, and substantially lower than the average share of revenue paid to employed skippers. Consequently, owner-operators were earning less than their opportunity cost of their labour, suggesting that the fleets were economically unviable in the longer term. The M2 licensed fleet were, on average, earning similar boat cash profits as the T1/M1 fleet, although after the higher capital costs were accounted for the T1/M1 boats were earning substantially lower returns to owner-operator labour. The mean technical efficiency for the fleet as a whole was estimated to be 0.67. That is, on average, the boats were only catching 67 per cent of what was possible given their level of inputs (hours fished and hull units). Almost one-quarter of observations had efficiency scores above 0.8, suggesting a substantial proportion of the fleet are relatively efficient, but some are also relatively inefficient. Both fleets had similar efficiency distributions, with median technical efficiency score of 0.71 and 0.67 for the M2 and T1/M1 boats respectively. These scores are reasonably consistent with other studies of prawn trawl fleets in Australia, although higher average efficiency scores were found in the NSW prawn trawl fleet. From the inefficiency model, several factors were found to significantly influence vessel efficiency. These included the number of years of experience as skipper, the number of generations that the skipper’s family had been fishing and the number of years schooling. Skippers with more schooling were significantly more efficient than skippers with lower levels of schooling, consistent with other studies. Skippers who had been fishing longer were, in fact, less efficient than newer skippers. However, this was mitigated in the case of skippers whose family had been involved in fishing for several generations, consistent with other studies and suggesting that skill was passed through by families over successive generations. Both the linear and log-linear regression models of total fishing effort against the marginal profit per hour performed reasonably well, explaining between 70 and 84 per cent of the variation in fishing effort. As the models had different dependent variables (one logged and the other not logged) this is not a good basis for model choice. A better comparator is the square root of the mean square error (SMSE) expressed as a percentage of the mean total effort. On this criterion, both models performed very similarly. The linear model suggests that each additional dollar of average profits per hour in the fishery increases total effort by around 26 hours each month. From the log linear model, each percentage increase in profits per hour increases total fishing effort by 0.13 per cent. Both models indicate that economic performance is a key driver of fishing effort in the fishery. The effect of removing the boat-replacement policy is to increase individual vessel profitability, catch and effort, but the overall increase in catch is less than that removed by the boats that must exit the fishery. That is, the smaller fleet (in terms of boat numbers) is more profitable but the overall catch is not expected to be greater than before. This assumes, however, that active boats are removed, and that these were also taking an average level of catch. If inactive boats are removed, then catch of the remaining group as a whole could increase by between 14 and 17 per cent depending on the degree to which costs are reduced with the new boats. This is still substantially lower than historical levels of catch by the fleet. Fishing power analyses An analysis of logbook data from 1988 to 2010, and survey information on fishing gear, was performed to estimate the long-term variation in the fleet’s ability to catch prawns (known as fishing power) and to derive abundance estimates of the three most commercially important prawn species (i.e., Brown Tiger, Eastern King and Greasyback Prawns). Generalised linear models were used to explain the variation in catch as a function of effort (i.e., hours fished per day), vessel and gear characteristics, onboard technologies, population abundance and environmental factors. This analysis estimated that fishing power associated with Brown Tiger and Eastern King Prawns increased over the past 20 years by 10–30% and declined by approximately 10% for greasybacks. The density of tiger prawns was estimated to have almost tripled from around 0.5 kg per hectare in 1988 to 1.5 kg/ha in 2010. The density of Eastern King Prawns was estimated to have fluctuated between 1 and 2 kg per hectare over this time period, without any noticeable overall trend, while Greasyback Prawn densities were estimated to have fluctuated between 2 and 6 kg per hectare, also without any distinctive trend. A model of tiger prawn catches was developed to evaluate the impact of fishing on prawn survival rates in Moreton Bay. The model was fitted to logbook data using the maximum-likelihood method to provide estimates of the natural mortality rate (0.038 and 0.062 per week) and catchability (which can be defined as the proportion of the fished population that is removed by one unit of effort, in this case, estimated to be 2.5 ± 0.4 E-04 per boat-day). This approach provided a method for industry and scientists to develop together a realistic model of the dynamics of the fishery. Several aspects need to be developed further to make this model acceptable to industry. Firstly, there is considerable evidence to suggest that temperature influences prawn catchability. This ecological effect should be incorporated before developing meaningful harvest strategies. Secondly, total effort has to be allocated between each species. Such allocation of effort could be included in the model by estimating several catchability coefficients. Nevertheless, the work presented in this report is a stepping stone towards estimating essential fishery parameters and developing representative mathematical models required to evaluate harvest strategies. Developing a method that allowed an effective discussion between industry, management and scientists took longer than anticipated. As a result, harvest strategy evaluations were preliminary and only included the most valuable species in the fishery, Brown Tiger Prawns. Additional analyses and data collection, including information on catch composition from field sampling, migration rates and recruitment, would improve the modelling. Harvest strategy evaluations As the harvest strategy evaluations are preliminary, the following results should not be adopted for management purposes until more thorough evaluations are performed. The effects, of closing the fishery for one calendar month, on the annual catch and value of Brown Tiger Prawns were investigated. Each of the 12 months (i.e., January to December) was evaluated. The results were compared against historical records to determine the magnitude of gain or loss associated with the closure. Uncertainty regarding the trawl selectivity was addressed using two selectivity curves, one with a weight at 50% selection (S50%) of 7 g, based on research data, and a second with S50% of 14 g, put forward by industry. In both cases, it was concluded that any monthly closure after February would not be beneficial to the industry. The magnitude of the benefit of closing the fishery in either January or February was sensitive to which mesh selectivity curve that was assumed, with greater benefit achieved when the smaller selectivity curve (i.e., S50% = 7 g) was assumed. Using the smaller selectivity (S50% = 7 g), the expected increase in catch value was 10–20% which equates to $200,000 to $400,000 annually, while the larger selectivity curve (S50% = 14 g) suggested catch value would be improved by 5–10%, or $100,000 to $200,000. The harvest strategy evaluations showed that greater benefits, in the order of 30–60% increases in the tiger annual catch value, could have been obtained by closing the fishery early in the year when annual effort levels were high (i.e., > 10,000 boat-days). In recent years, as effort levels have declined (i.e., ~4000 boat-days annually), expected benefits from such closures are more modest. In essence, temporal closures offer greater benefit when fishing mortality rates are high. A spatial analysis of Brown Tiger Prawn catch and effort was also undertaken to obtain a better understanding of the prawn population dynamics. This indicated that, to improve profitability of the fishery, fishers could consider closing the fishery in the period from June to October, which is already a period of low profitability. This would protect the Brown Tiger Prawn spawning stock, increase catch rates of all species in the lucrative pre-Christmas period (November–December), and provide fishers with time to do vessel maintenance, arrange markets for the next season’s harvest, and, if they wish, work at other jobs. The analysis found that the instantaneous rate of total mortality (Z) for the March–June period did not vary significantly over the last two decades. As the Brown Tiger Prawn population in Moreton Bay has clearly increased over this time period, an interesting conclusion is that the instantaneous rate of natural mortality (M) must have increased, suggesting that tiger prawn natural mortality may be density-dependent at this time of year. Mortality rates of tiger prawns for June–October were found to have decreased over the last two decades, which has probably had a positive effect on spawning stocks in the October–November spawning period. Abiotic effects on the prawns The influence of air temperature, rainfall, freshwater flow, the southern oscillation index (SOI) and lunar phase on the catch rates of the four main prawn species were investigated. The analyses were based on over 200,000 daily logbook catch records over 23 years (i.e., 1988–2010). Freshwater flow was more influential than rainfall and SOI, and of the various sources of flow, the Brisbane River has the greatest volume and influence on Moreton Bay prawn catches. A number of time-lags were also considered. Flow in the preceding month prior to catch (i.e., 30 days prior, Logflow1_30) and two months prior (31–60 days prior, Logflow31_60) had strong positive effects on Banana Prawn catch rates. Average air temperature in the preceding 4-6 months (Temp121_180) also had a large positive effect on Banana Prawn catch rates. Flow in the month immediately preceding catch (Logflow1_30) had a strong positive influence on Greasyback Prawn catch rates. Air temperature in the preceding two months prior to catch (Temp1_60) had a large positive effect on Brown Tiger Prawn catch rates. No obvious or marked effects were detected for Eastern King Prawns, although interestingly, catch rates declined with increasing air temperature 4–6 months prior to catch. As most Eastern King Prawn catches in Moreton Bay occur in October to December, the results suggest catch rates decline with increasing winter temperatures. In most cases, the prawn catch rates declined with the waxing lunar phase (high luminance/full moon), and increased with the waning moon (low luminance/new moon). The SOI explains little additional variation in prawn catch rates (~ <2%), although its influence was higher for Banana Prawns. Extrapolating findings of the analyses to long-term climate change effects should be interpreted with caution. That said, the results are consistent with likely increases in abundance in the region for the two tropical species, Banana Prawns and Brown Tiger Prawns, as coastal temperatures rise. Conversely, declines in abundance could be expected for the two temperate species, Greasyback and Eastern King Prawns. Corporate management structures An examination of alternative governance systems was requested by the industry at one of the early meetings, particularly systems that may give them greater autonomy in decision making as well as help improve the marketing of their product. Consequently, a review of alternative management systems was undertaken, with a particular focus on the potential for self-management of small fisheries (small in terms of number of participants) and corporate management. The review looks at systems that have been implemented or proposed for other small fisheries internationally, with a particular focus on self-management as well as the potential benefits and challenges for corporate management. This review also highlighted particular opportunities for the Moreton Bay prawn fishery. Corporate management differs from other co-management and even self-management arrangements in that ‘ownership’ of the fishery is devolved to a company in which fishers and government are shareholders. The company manages the fishery as well as coordinates marketing to ensure that the best prices are received and that the catch taken meets the demands of the market. Coordinated harvesting will also result in increased profits, which are returned to fishers in the form of dividends. Corporate management offers many of the potential benefits of an individual quota system without formally implementing such a system. A corporate management model offers an advantage over a self-management model in that it can coordinate both marketing and management to take advantage of this unique geographical advantage. For such a system to be successful, the fishery needs to be relatively small and self- contained. Small in this sense is in terms of number of operators. The Moreton Bay prawn fishery satisfies these key conditions for a successful self-management and potentially corporate management system. The fishery is small both in terms of number of participants and geography. Unlike other fisheries that have progressed down the self-management route, the key market for the product from the Moreton Bay fishery is right at its doorstep. Corporate management also presents a number of challenges. First, it will require changes in the way fishers operate. In particular, the decision on when to fish and what to catch will be taken away from the individual and decided by the collective. Problems will develop if individuals do not join the corporation but continue to fish and market their own product separately. While this may seem an attractive option to fishers who believe they can do better independently, this is likely to be just a short- term advantage with an overall long-run cost to themselves as well as the rest of the industry. There are also a number of other areas that need further consideration, particularly in relation to the allocation of shares, including who should be allocated shares (e.g. just boat owners or also some employed skippers). Similarly, how harvesting activity is to be allocated by the corporation to the fishers. These are largely issues that cannot be answered without substantial consultation with those likely to be affected, and these groups cannot give these issues serious consideration until the point at which they are likely to become a reality. Given the current structure and complexity of the fishery, it is unlikely that such a management structure will be feasible in the short term. However, the fishery is a prime candidate for such a model, and development of such a management structure in the future should be considered as an option for the longer term.

Effect of physiological and experiential state of Bactrocera tryoni flies on intra-tree foraging behavior for food (bacteria) and host fruit

Using caged guava trees in Queensland, Australia, provided with food and oviposition sites, the foraging behaviour of females of the tephritid Bactrocera tryoni was investigated in relation to hunger for protein, the presence or absence of bacteria as a source of protein, the degree of prior experience with host fruit and quality of host fruit for oviposition. One aim was to evaluate whether it is immature or mature B. tryoni females that are responsible for initially inoculating host fruit surfaces with "fruit-fly-type" bacteria, the odour of which is known to attract B. tryoni females. Three-week-old immature females provided with sucrose but deprived of protein from eclosion had a much greater propensity than 3-week-old protein-fed mature females to visit vials containing fruit-fly-type bacteria, irrespective of whether vials were associated with adjacent host fruit or not. In the absence of associated bacteria in vials, immature females had a much lower propensity than mature females to visit host fruit. In the presence of bacteria in vials, however, propensity of immature and mature females to visit fruit was about equal. Mature (but not immature) females were more inclined to visit fruit that ranked higher for oviposition (nectarines) than fruit that ranked lower (sweet oranges). Mature females that attempted oviposition during a single 3-min exposure period to a nectarine prior to release were much more likely to find a nectarine than were mature females naive to fruit or immature females with or without prior contact with fruit. Exposure to a nectarine before release did not affect the propensity of either mature or immature females to alight on an odourless visual model of a nectarine, however. As judged by numbers of leaves visited, protein-deprived immature females were more active than protein-fed mature females, irrespective of the sorts of resources on a tree. It was concluded that: the 1st B. tryoni females to arrive on the fruit of a host tree and therefore inoculate the fruit with fruit-fly-type bacteria were unlikely to be sexually immature, but to be mature as a result of having earlier acquired protein elsewhere; the odour of colonies of fruit-fly-type bacteria when associated with host fruit attracted protein-hungry but not protein-fed females; and the odour of the fruit itself attracted mature females (especially experienced ones) but not immature females.

Inheritance and relative dominance, expressed as toxicity response and delayed development, of phosphine resistance in immature stages of Rhyzopertha dominica (F.) (Coleoptera: Bostrichidae)

Fumigation of stored grain with phosphine (PH 3) is used widely to control the lesser grain borer Rhyzopertha dominica. However, development of high level resistance to phosphine in this species threatens control. Effective resistance management relies on knowledge of the expression of resistance in relation to dosage at all life stages. Therefore, we determined the mode of inheritance of phosphine resistance and strength of the resistance phenotype at each developmental stage. We achieved this by comparing mortality and developmental delay between a strongly resistant strain (R-strain), a susceptible strain (S-strain) and their F 1 progenies. Resistance was a maternally inherited, semi-dominant trait in the egg stage but was inherited as an autosomal, incompletely recessive trait in larvae and pupae. The rank order of developmental tolerance in both the sensitive and resistant strains was eggs > pupae > larvae. Comparison of published values for the response of adult R. dominica relative to our results from immature stages reveals that the adult stage of the S-strain is more sensitive to phosphine than are larvae. This situation is reversed in the R-strain as the adult stage is much more resistant to phosphine than even the most tolerant immature stage. Phosphine resistance factors at LC 50 were eggs 400×, larvae 87× and pupae 181× with respect to reference susceptible strain (S-strain) adults indicating that tolerance conferred by a particular immature stage neither strongly nor reliably interacts with the genetic resistance element. Developmental delay relative to unfumigated control insects was observed in 93% of resistant pupae, 86% of resistant larvae and 41% of resistant eggs. Increased delay in development and the toxicity response to phosphine exposure were both incompletely recessive. We show that resistance to phosphine has pleiotropic effects and that the expression of these effects varies with genotype and throughout the life history of the insect. © 2012.

Biology, ecology and conservation of the Mobulidae

The Mobulidae are zooplanktivorous elasmobranchs comprising two recognized species of manta rays (Manta spp.) and nine recognized species of devil rays (Mobula spp.). They are found circumglobally in tropical, subtropical and temperate coastal waters. Although mobulids have been recorded for over 400 years, critical knowledge gaps still compromise the ability to assess the status of these species. On the basis of a review of 263 publications, a comparative synthesis of the biology and ecology of mobulids was conducted to examine their evolution, taxonomy, distribution, population trends, movements and aggregation, reproduction, growth and longevity, feeding, natural mortality and direct and indirect anthropogenic threats. There has been a marked increase in the number of published studies on mobulids since c. 1990, particularly for the genus Manta, although the genus Mobula remains poorly understood. Mobulid species have many common biological characteristics although their ecologies appear to be species-specific, and sometimes region-specific. Movement studies suggest that mobulids are highly mobile and have the potential to rapidly travel large distances. Fishing pressure is the major threat to many mobulid populations, with current levels of exploitation in target fisheries unlikely to be sustainable. Advances in the fields of population genetics, acoustic and satellite tracking, and stable-isotope and fatty-acid analyses will provide new insights into the biology and ecology of these species. Future research should focus on the uncertain taxonomy of mobulid species, the degree of overlap between their large-scale movement and human activities such as fisheries and pollution, and the need for management of inter-jurisdictional fisheries in developing nations to ensure their long-term sustainability. Closer collaboration among researchers worldwide is necessary to ensure standardized sampling and modelling methodologies to underpin global population estimates and status.

Estimating Hydrogen Cyanide in Forage Sorghum (Sorghum bicolor) by Near-Infrared Spectroscopy

Hydrogen cyanide (HCN) is a toxic chemical that can potentially cause mild to severe reactions in animals when grazing forage sorghum. Developing technologies to monitor the level of HCN in the growing crop would benefit graziers, so that they can move cattle into paddocks with acceptable levels of HCN. In this study, we developed near-infrared spectroscopy (MRS) calibrations to estimate HCN in forage sorghum and hay. The full spectral NIRS range (400-2498 nm) was used as well as specific spectral ranges within the full spectral range, i.e., visible (400-750 nm), shortwave (800-1100 nm) and near-infrared (NIR) (1100-2498 nm). Using the full spectrum approach and partial least-squares (PLS), the calibration produced a coefficient of determination (R-2) = 0.838 and standard error of cross-validation (SECV) = 0.040%, while the validation set had a R-2 = 0.824 with a low standard error of prediction (SEP = 0.047%). When using a multiple linear regression (MLR) approach, the best model (NIR spectra) produced a R-2 = 0.847 and standard error of calibration (SEC) = 0.050% and a R-2 = 0.829 and SEP = 0.057% for the validation set. The MLR models built from these spectral regions all used nine wavelengths. Two specific wavelengths 2034 and 2458 nm were of interest, with the former associated with C=O carbonyl stretch and the latter associated with C-N-C stretching. The most accurate PLS and MLR models produced a ratio of standard error of prediction to standard deviation of 3.4 and 3.0, respectively, suggesting that the calibrations could be used for screening breeding material. The results indicated that it should be feasible to develop calibrations using PLS or MLR models for a number of users, including breeding programs to screen for genotypes with low HCN, as well as graziers to monitor crop status to help with grazing efficiency.

Urinary excretion of antioxidants in healthy humans following queen garnet plum juice ingestion: a new plum variety rich in antioxidant compounds

In recent years, there has been intense interest in the potential health benefits of dietary derived plant polyphenols and antioxidants. A new variety of Prunus salicina, Queen Garnet plum (QGP), was developed as a high anthocyanin, high antioxidant plum, in a Queensland Government breeding program. Following consumption of 400 mL QGP juice (QGPJ; 1,117 mg anthocyanins) by two healthy male subjects, QGP anthocyanins (cyanidin-3-glucoside and cyanidin-3-rutinoside) were excreted mainly as methylated and glucuronidated metabolites in urine (0.5% of the ingested dose within 24 h). Furthermore, QGPJ intake resulted in a threefold increase in hippuric acid excretion (potential biomarker for total polyphenols intake and metabolite), an increased urinary antioxidant capacity and a decreased malondialdehyde excretion (biomarker for oxidative stress) within 24 h as compared with the polyphenol-/antioxidant-free control. Results from this pilot study suggest that metabolites, and not the native QGP anthocyanins/polyphenols, are most likely the bioactive compounds in vivo.

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.

Resistance gene analogues in sugarcane and sorghum and their association with quantitative trait loci for rust resistance

Fifty-four different sugarcane resistance gene analogue (RGA) sequences were isolated, characterized, and used to identify molecular markers linked to major disease-resistance loci in sugarcane. Ten RGAs were identified from a sugarcane stem expressed sequence tag (EST) library; the remaining 44 were isolated from sugarcane stem, leaf, and root tissue using primers designed to conserved RGA motifs. The map location of 31 of the RGAs was determined in sugarcane and compared with the location of quantitative trait loci (QTL) for brown rust resistance. After 2 years of phenotyping, 3 RGAs were shown to generate markers that were significantly associated with resistance to this disease. To assist in the understanding of the complex genetic structure of sugarcane, 17 of the 31 RGAs were also mapped in sorghum. Comparative mapping between sugarcane and sorghum revealed syntenic localization of several RGA clusters. The 3 brown rust associated RGAs were shown to map to the same linkage group (LG) in sorghum with 2 mapping to one region and the third to a region previously shown to contain a major rust-resistance QTL in sorghum. These results illustrate the value of using RGAs for the identification of markers linked to disease resistance loci and the value of simultaneous mapping in sugarcane and sorghum.

Ecological significance of rice (Oryza sativa) planting density and nitrogen rates in managing the growth and competitive ability of itchgrass (Rottboellia cochinchinensis) in direct-seeded rice systems

Current understanding is that high planting density has the potential to suppress weeds and crop-weed interactions can be exploited by adjusting fertilizer rates. We hypothesized that (a) high planting density can be used to suppress Rottboellia cochinchinensis growth and (b) rice competitiveness against this weed can be enhanced by increasing nitrogen (N) rates. We tested these hypotheses by growing R. cochinchinensis alone and in competition with four rice planting densities (0, 100, 200, and 400 plants m-2) at four N rates (0, 50, 100, and 150 kg ha-1). At 56 days after sowing (DAS), R. cochinchinensis plant height decreased by 27-50 %, tiller number by 55-76 %, leaf number by 68-84 %, leaf area by 70-83 %, leaf biomass by 26-90 %, and inflorescence biomass by 60-84 %, with rice densities ranging from 100 to 400 plants m-2. All these parameters increased with an increase in N rate. Without the addition of N, R. cochinchinensis plants were 174 % taller than rice; whereas, with added N, they were 233 % taller. Added N favored more weed biomass production relative to rice. R. cochinchinensis grew taller than rice (at all N rates) to avoid shade, which suggests that it is a "shade-avoiding" plant. R. cochinchinensis showed this ability to reduce the effect of rice interference through increased leaf weight ratio, specific stem length, and decreased root-shoot weight ratio. This weed is more responsive to N fertilizer than rice. Therefore, farmers should give special consideration to the application timing of N fertilizer when more N-responsive weeds are present in their field. Results suggest that the growth and seed production of R. cochinchinensis can be decreased considerably by increasing rice density to 400 plants m-2. There is a need to integrate different weed control measures to achieve complete control of this noxious weed.

Fate of key food-borne pathogens associated with intensive pig and poultry farming environments

Intensive pig and poultry farming in Australia can be a source of pathogens with implications for food-safety and/or human illness. Seven studies were undertaken with the following objectives: · Assess the types of zoonotic pathogens in waste · Assess the transfer of pathogens during re-use both within the shed and externally in the environment · The potential for movement of pathogens via aerosols In the first and second studies the extent of zoonotic pathogens was evaluated in both piggery effluent and chicken litter and Salmonella and Campylobacter were detected in both wastes. In the third study the dynamics of Salmonella during litter re-use was examined and results showed a trend for lower Salmonella levels and serovar diversity in re-used litter compared to new litter. Thus, re-use within the poultry farming system posed no increased risk. The fourth study addressed the direct risks of pathogens to farm workers due to reuse of piggery effluent within the pig shed. Based on air-borne Escherichia coli (E. coli) levels, re-using effluent did not pose a risk. In the fifth study high levels of Arcobacter spp. were detected in effluent ponds and freshly irrigated soils with potential food-safety risks during the irrigation of food-crops and pasture. The sixth and seventh studies addressed the risks from aerosols from mechanically ventilated sheds. Staphylococci were shown to have potential as markers, with airborne levels gradually dropping and reaching background levels at 400 m distance. Salmonella was detected (at low levels) both inside and outside the shed (at 10 m). Campylobacter was detected only once inside the shed during the 3-year period (at low levels). Results showed there was minimal risk to humans living adjacent to poultry farms This is the first comprehensive analysis studying key food-safety pathogens and potential public health risks associated with intensively farmed pigs and poultry in Australia.

Drafting the Kensington Pride Mango Genome

The mango industry in Australia is worth in excess of $150 million annually with the Kensington Pride (KP) cultivar capturing 60% of the domestic market. Valued by consumers for desirable taste and colour characteristics, KP has been used extensively as a parent in the Department of Agriculture and Fisheries’ (Queensland, Australia) mango breeding program with over 400 hybrid trees sharing KP as the male parent. In order to gain a better understanding of Australia’s most significant mango variety, Horticulture Innovation Australia had led an international collaboration between the Queensland Department of Agriculture and Fisheries (Australia), the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT, India) and the Beijing Genomics Institute (China) to sequence the KP genome. Preliminary de novo assembly of illumina short read sequence data suggests that the KP genome is highly heterozygous and has an estimated genome size of 407 Mb. As refinements and additional sequence data are added to the assembly, a more complete picture of the mango genome will be elucidated.

Inventories and significance of the genetic resources of an African mahogany species (Khaya senegalensis (Desr.) A. Juss.) assembled and further developed in Australia.

The forest tree species Khaya senegalensis (Desr.) A. Juss. occurs in a belt across 20 African countries from Senegal-Guinea to Sudan-Uganda where it is a highly important resource. However, it is listed as Vulnerable (IUCN 2015-3). Since introduction in northern Australia around 1959, the species has been planted widely, yielding high-value products. The total area of plantations of the species in Australia exceeds 15,000 ha, mostly planted in the Northern Territory since 2006, and includes substantial areas across 60-70 woodlots and industrial plantations established in north-eastern Queensland since the early-1990s and during 2005-2007 respectively. Collaborative conservation and tree improvement by governments began in the Northern Territory and Queensland in 2001 based on provenance and other trials of the 1960s-1970s. This work has developed a broad base of germplasm in clonal seed orchards, hedge gardens and trials (clone and progeny). Several of the trials were established collaboratively on private land. Since the mid-2000s, commercial growers have introduced large numbers of provenance-bulk and individual-tree seedlots to establish industrial plantations and trials, several of the latter in collaboration with the Queensland Government. Provenance bulks (>140) and families (>400) from 17 African countries are established in Australia, considered the largest genetic base of the species in a single country outside Africa. Recently the annual rate of industrial planting of the species in Australia has declined, and R&D has been suspended by governments and reduced by the private sector. However, new commercial plantings in the Northern Territory and Queensland are proposed. In domesticating a species, the strategic importance of a broad genetic base is well known. The wide range of first- and advanced-generation germplasm of the species established in northern Australia and documented in this paper provides a sound basis for further domestication and industrial plantation and woodlot expansion, when investment conditions are favourable