The Genetic Architecture of Climatic Adaptation of Tropical Cattle

Adaptation of global food systems to climate change is essential to feed the world. Tropical cattle production, a mainstay of profitability for farmers in the developing world, is dominated by heat, lack of water, poor quality feedstuffs, parasites, and tropical diseases. In these systems European cattle suffer significant stock loss, and the cross breeding of taurine x indicine cattle is unpredictable due to the dilution of adaptation to heat and tropical diseases. We explored the genetic architecture of ten traits of tropical cattle production using genome wide association studies of 4,662 animals varying from 0% to 100% indicine. We show that nine of the ten have genetic architectures that include genes of major effect, and in one case, a single location that accounted for more than 71% of the genetic variation. One genetic region in particular had effects on parasite resistance, yearling weight, body condition score, coat colour and penile sheath score. This region, extending 20 Mb on BTA5, appeared to be under genetic selection possibly through maintenance of haplotypes by breeders. We found that the amount of genetic variation and the genetic correlations between traits did not depend upon the degree of indicine content in the animals. Climate change is expected to expand some conditions of the tropics to more temperate environments, which may impact negatively on global livestock health and production. Our results point to several important genes that have large effects on adaptation that could be introduced into more temperate cattle without detrimental effects on productivity.

Reconfiguring agriculture through the relocation of production systems for water, environment and food security under climate change

The prospect of climate change has revived both fears of food insecurity and its corollary, market opportunities for agricultural production. In Australia, with its long history of state-sponsored agricultural development, there is renewed interest in the agricultural development of tropical and sub-tropical northern regions. Climate projections suggest that there will be less water available to the main irrigation systems of the eastern central and southern regions of Australia, while net rainfall could be sustained or even increase in the northern areas. Hence, there could be more intensive use of northern agricultural areas, with the relocation of some production of economically important commodities such as vegetables, rice and cotton. The problem is that the expansion of cropping in northern Australia has been constrained by agronomic and economic considerations. The present paper examines the economics, at both farm and regional level, of relocating some cotton production from the east-central irrigation areas to the north where there is an existing irrigation scheme together with some industry and individual interest in such relocation. Integrated modelling and expert knowledge are used to examine this example of prospective climate change adaptation. Farm-level simulations show that without adaptation, overall gross margins will decrease under a combination of climate change and reduction in water availability. A dynamic regional Computable General Equilibrium model is used to explore two scenarios of relocating cotton production from south east Queensland, to sugar-dominated areas in northern Queensland. Overall, an increase in real economic output and real income was realized when some cotton production was relocated to sugar cane fallow land/new land. There were, however, large negative effects on regional economies where cotton production displaced sugar cane. It is concluded that even excluding the agronomic uncertainties, which are not examined here, there is unlikely to be significant market-driven relocation of cotton production.

On Systems Thinking, Systems Biology, and the in Silico Plant

The recent summary report of a Department of Energy Workshop on Plant Systems Biology (P.V. Minorsky [2003] Plant Physiol 132: 404-409) offered a welcomed advocacy for systems analysis as essential in understanding plant development, growth, and production. The goal of the Workshop was to consider methods for relating the results of molecular research to real-world challenges in plant production for increased food supplies, alternative energy sources, and environmental improvement. The rather surprising feature of this report, however, was that the Workshop largely overlooked the rich history of plant systems analysis extending over nearly 40 years (Sinclair and Seligman, 1996) that has considered exactly those challenges targeted by the Workshop. Past systems research has explored and incorporated biochemical and physiological knowledge into plant simulation models from a number of perspectives. The research has resulted in considerable understanding and insight about how to simulate plant systems and the relative contribution of various factors in influencing plant production. These past activities have contributed directly to research focused on solving the problems of increasing biomass production and crop yields. These modeling approaches are also now providing an avenue to enhance integration of molecular genetic technologies in plant improvement (Hammer et al., 2002).

Evaluation of three storage systems used for chilling and holding swordfish

Swordfish are kept chilled, not frozen, for up to 15 days before being unloaded at Australian ports. Swordfish landed alive, and to a lesser extent prerigor, have better quality when unloaded. Warmer fishing waters did not lead to poorer quality at unloading. There was a serious loss of quality during long fishing trips. Sex had no influence on swordfish quality. Three methods of chilling were evaluated: refrigerated seawater (RSW) chilling for up to 2 days followed by storage under ice, refrigerated brine (seawater with extra salt added) for up to 2 days followed by storage in a freshwater ice slurry, and ice slurry (freshwater ice mixed with seawater) for up to 2 days followed by storage under ice only. Two fishing trips were monitored for each method. The freshness indicator K value was used to determine which method produced the best quality swordfish when unloaded at the factory. Storage method played a larger role in quality loss than capture conditions. Refrigerated brine produced the best quality swordfish when the machinery functioned properly closely followed by RSW. Ice slurry chilling of large fish such as swordfish exhibited initial delays in the reduction of core temperature which led to lower quality. This method could be improved with the addition of mechanical circulation. Mechanical problems, which resulted in minor increases of temperature during brine storage, led to a much larger loss of quality than would be expected.

Influence of food supplementation on the fitness of two biological control agents: a predatory nabid bug and a bollworm pupal parasitoid

Many arthropod predators and parasitoids exhibit either stage-specific or lifetime omnivory, in that they include extra-floral nectar, floral nectar, honeydew or pollen in their immature and/or adult diet. Access to these plant-derived foods can enhance pest suppression by increasing both the individual fitness and local density of natural enemies. Commercial products such as Amino-Feed®, Envirofeast®, and Pred-Feed® can be applied to crops to act as artificial-plant-derived foods. In laboratory and glasshouse experiments we examined the influence of carbohydrate and protein rich Amino-Feed UV® or Amino-Feed, respectively, on the fitness of a predatory nabid bug Nabis kinbergii Reuter (Hemiptera: Nabidae) and bollworm pupal parasitoid Ichneumon promissorius (Erichson) (Hymenoptera: Ichneumonidae). Under the chosen conditions, the provision of either wet or dry residues of Amino-Feed UV had no discernable effect on immediate or longer-term survival and immature development times of N. kinbergii. In contrast, the provision of honey, Amino-Feed plus extrafloral nectar, and extrafloral nectar alone had a marked effect on the longevity of I. promissorius, indicating that they were limited by at least carbohydrates as an energy source, but probably not protein. Compared with a water only diet, the provision of Amino-Feed plus extrafloral nectar increased the longevity of males and females of I. promissorius by 3.0- and 2.4-fold, respectively. Not only did female parasitoids live longer when provided food, but the total number of eggs laid and timing of deposition was affected by diet under the chosen conditions. Notably, females in the water and honey treatments deposited greater numbers of eggs earlier in the trial, but this trend was unable to be sustained over their lifetime. Egg numbers in these treatments subsequently fell below the levels achieved by females in the Amino-Feed plus extrafloral nectar and cotton extrafloral nectar only treatments. Furthermore, there were times when the inclusion of the Amino-Feed was beneficial compared with cotton extrafloral nectar only. Artificial food supplements and plant-derived foods are worthy of further investigation because they have potential to improve the ecosystem service of biological pest control in targeted agroecosystems by providing natural enemies with an alternative source of nutrition, particularly during periods of prey/host scarcity.

Simulating pasture growth rates in Australian and New Zealand grazing systems

DairyMod, EcoMod, and the SGS Pasture Model are mechanistic biophysical models developed to explore scenarios in grazing systems. The aim of this manuscript was to test the ability of the models to simulate net herbage accumulation rates of ryegrass-based pastures across a range of environments and pasture management systems in Australia and New Zealand. Measured monthly net herbage accumulation rate and accumulated yield data were collated from ten grazing system experiments at eight sites ranging from cool temperate to subtropical environments. The local climate, soil, pasture species, and management (N fertiliser, irrigation, and grazing or cutting pattern) were described in the model for each site, and net herbage accumulation rates modelled. The model adequately simulated the monthly net herbage accumulation rates across the range of environments, based on the summary statistics and observed patterns of seasonal growth, particularly when the variability in measured herbage accumulation rates was taken into account. Agreement between modelled and observed growth rates was more accurate and precise in temperate than in subtropical environments, and in winter and summer than in autumn and spring. Similarly, agreement between predicted and observed accumulated yields was more accurate than monthly net herbage accumulation. Different temperature parameters were used to describe the growth of perennial ryegrass cultivars and annual ryegrass; these differences were in line with observed growth patterns and breeding objectives. Results are discussed in the context of the difficulties in measuring pasture growth rates and model limitations.

Global banana disease management - getting serious with sustainability and food security

Much research in understanding plant diseases has been undertaken, but there has been insufficient attention given to dealing with coordinated approaches to preventing and managing diseases. A global management approach is essential to the long-term sustainability of banana production. This approach would involve coordinated surveys, capacity building in developing countries, development of disease outbreak contingency plans and coordinated quarantine awareness, including on-line training in impact risk assessment and web-based diagnostic software. Free movement of banana plants and products between some banana-producing countries is causing significant pressure on the ability to manage diseases in banana. The rapid spread of Fusarium oxysporum f. sp. cubense 'tropical race 4' in Asia, bacterial wilts in Africa and Asia and black leaf streak [Mycosphaerella fijiensis] in Brazil and elsewhere are cases in point. The impact of these diseases is devastating, severely cutting family incomes and jeopardising food security around the globe. Agreements urgently need to be reached between governments to halt the movement of banana plants and products between banana-producing countries before it is too late and global food security is irreparably harmed. Black leaf streak, arguably the most serious banana disease, has become extremely difficult to control in commercial plantations in various parts of the world. Sometimes in excess of 50 fungicide sprays have to be applied each year. Disease eradication and effective disease control is not possible because there is no control of disease inoculum in non-commercial plantings in these locations. Additionally, there have been enormous sums of money invested in international banana breeding programmes over many years only to see the value of hybrid products lost too soon. 'Goldfinger' (AAAB, syn. 'FHIA-01'), for example, has recently been observed severely affected by black leaf streak in Samoa. Resistant cultivars alone cannot be relied upon in the fight against this disease. Real progress in control may only come when the local communities are engaged and become actively involved in regional programmes. Global recommendations are long overdue and urgently needed to help ensure the long-term sustainable utilisation of the products of the breeding programmes.

Duckweed-based Wastewater Treatment Systems: Design Aspects and Integrated Reuse Options for Queensland Conditions

Point sources of wastewater pollution, including effluent from municipal sewage treatment plants and intensive livestock and processing industries, can contribute significantly to the degradation of receiving waters (Chambers et al. 1997; Productivity Commission 2004). This has led to increasingly stringent local wastewater discharge quotas (particularly regarding Nitrogen, Phosphorous and suspended solids), and many municipal authorities and industry managers are now faced with upgrading their existing treatment facilities in order to comply. However, with high construction, energy and maintenance expenses and increasing labour costs, traditional wastewater treatment systems are becoming an escalating financial burden for the communities and industries that operate them. This report was generated, in the first instance, for the Burdekin Shire Council to provide information on design aspects and parameters critical for developing duckweed-based wastewater treatment (DWT) in the Burdekin region. However, the information will be relevant to a range of wastewater sources throughout Queensland. This information has been collated from published literature and both overseas and local studies of pilot and full-scale DWT systems. This report also considers options to generate revenue from duckweed production (a significant feature of DWT), and provides specifications and component cost information (current at the time of publication) for a large-scale demonstration of an integrated DWT and fish production system.

Integrated Cotton Farming Systems for Central Queensland

This project has delivered outcomes that address major agronomic and crop protection issues closely linked to the profitability and sustainability of cotton production enterprises in CQ. From an agronomic perspective, the CQ environment was always though to support economically viable cotton production in a wide sowing window from the middle of September to early January prior to this research. The ideal positioning of Bollgard II varieties in the CQ planting window was, therefore, critical to the future of the local cotton industry because growers needed baseline information to determine how best to take advantage of the higher yield potential offered by the Bt cotton technology, optimise irrigation water use and fibre characteristics. The project’s outputs include a number of key agronomic findings. Over three growing seasons, Bollgard II crop planted in the traditional sowing window from the middle of September to the end of October consistently produced the highest yields. The project delivers a clear and quantitative assessment of the impacts of planting outside the traditional cropping window - a yield penalty of between 1-4 bales/ha for November and December planted cotton. Whilst yield penalties associated with December-planted crops are clearly linked to declining heat units in the second half of the crop and a cool finish, those associated with November-planted cotton are not consistent with the theoretical yield potential for this sowing date. Further research to understand and minimize the physiological constraints on November-planted cotton would give CQ cotton growers far greater flexibility to develop mixed/double/rotation cropping farming systems that are relevant to the rapidly evolving nature of Agricultural production in Australia. The equivalence of cultivar types with clearly distinguishable, genetically based growth habits, demonstrated in this project, gives growers important information for making varietal choices. The entomological outcomes of this project represent strategic and tactical tools that are highly relevant to the viability and profitability of the cotton industry in Australia. The future of the cotton industry is inextricably linked to the survival and efficacy of GM cotton. Research done in the Callide irrigation area demonstrates the unquestionable potential for development of alternative and highly effective resistance management strategies for Bollgard II using novel technologies and strategies based on products such as Magnet®. Magnet® and similar technologies will be increasingly important in strategies to preserve the shelf life and efficacy of current and future generations of GM technology. However, more research will be required to address logistical and operational issues related to these new technologies before they can be fully exploited in commercial production systems. From an economic perspective, SLW is the sleeping giant in terms of insect nemeses of cotton, particularly from the standpoint of climate change and an increasingly warmer production environment. An effective sampling and management strategy for SLW which has been delivered by this project will go a long way towards minimising production costs in an environment characterised by rapidly rising input costs. SLW has the potential to permanently debilitate the national cotton industry by influencing market sentiment and quality perceptions. Field validation of the SLW population sampling models and management options in the Dawson irrigation area cotton and southern Queensland during 2006-07 documents the robustness of the entomological research outcomes achieved through this project.

Maximising profitability with limited water in cotton farming systems

Diminishing water supply, changing weather patterns and pressure to enhance environmental flows are making it imperative to optimise water use efficiency (WUE) on cotton/grain farming systems. Growers are looking for better strategies to make the best use of limited water, but it is still not clear how to best use the available water at farm and field scale. This research project investigated the impact of management strategies to deal with limited water supplies on the yield and quality of irrigated cotton and wheat. The objectives were: (1) to develop irrigation management guidelines for the main irrigated crops on the Darling Downs for full- and deficitirrigation scenarios, taking into account the critical factors that affect irrigation decisions at the local level, (2) to quantify the evapotranspiration (ET) of Bollgard II cotton and wheat and its relationship to yield and quality under full- and deficit-irrigation scenarios, and (3) to increase industry awareness and education of farming systems practises for optimised economic water use efficiency.Objective (1) was addressed by (A) collaborating with ASPRU to develop the APSFarm model within APSIM to be able to perform multi-paddock simulations. APSFarm was then tested by conducting a case study at a farm near Dalby, and (B) conducting semi-structured interviews with individual farmers and crop consultants on the Darling Downs to document the strategies they are using to deal with limited water. Objective (2) was addressed by (A) building and installing 12 large (1 m x 1m x 1.5 m) weighing lysimeters to measure crop evapotranspiration. The lysimeters were installed at the Agri-Science Queensland research station at Kingsthorpe in November 2008, (B) conducting field experiments to measure crop evapotranspiration and crop development under four irrigation treatments, including dryland, deficit-irrigation, and full irrigation. Field experiments were conducted with cotton in 2007-08 and 2008-09, and with wheat in 2008 and 2009, and (C) collaborating with USQ on a PhD thesis to quantify the impact of crop stress on crop evapotranspiration and canopy temperature. Glasshouse experiments were conducted with wheat in 2008 and with cotton in 2008-09. Objective (3) was addressed by (A) conducting a field day at Kingsthorpe in 2009, which was attended by 80 participants, (B) presenting information in conferences in Australia and overseas, (D) presenting information at farmers meeting, (E) making presentations to crop consultants, and (F) preparing extension publications.As part of this project we contributed to the development of APSfarm, which has been successfully applied to evaluate the feasibility of practices at the whole-farm scale. From growers and crop consultants interviews we learned that there is a great variety of strategies, at different scales, that they are using to deal with limited water situation. These strategies will be summarised in the "e;Limited Water Guidelines for the Darling Downs"e; that we are currently preparing. As a result of this project, we now have a state-of-the-art lysimeter research facility (23 large weighing lysimeters) to be able to conduct replicated experiments to investigate daily water use of a variety of crops under different irrigation regimes and under different environments. Under this project, a series of field and glasshouse experiments were conducted with cotton and wheat, investigating aspects like: (A) quantification of daily and seasonal crop water use under nonstressed and stressed conditions, (B) impact of row configuration on crop water use, (C) impact of water stress on yield, evapotranspiration, crop vegetative and reproductive development, soil water extraction pattern, yield and yield quality. The information obtained from this project is now being used to develop web-based tools to help growers make planning and day-to-day irrigation decisions.

Grazing for Healthy Coastal Wetlands: Guidelines for managing coastal wetlands in grazing systems.

Grazing for Healthy Coastal Wetlands has been developed to provide graziers, landowners and extension officers with information on managing grazing in and around Queensland’s coastal wetlands to maintain healthy coastal wetlands and productive grazing enterprises. It provides practical advice on how grazing and associated land management practices can be implemented to support the long-term health of coastal wetlands whilst maintaining production. The guidelines have been compiled from published literature, grazier knowledge, wetlands managers and the experience of extension and natural resource management professionals. They reflect the current knowledge of suitable management practices for coastal wetlands. They are designed to complement and be considered in conjunction with existing information resources including the EDGEnetwork Grazing Land Management series and best management practice guidelines from regional Natural Resource Management (NRM) groups. While the recommendations apply broadly to Queensland’s coastal wetlands, regional, catchment and landscape-scale variations in wetland characteristics and the objectives of the individual grazing enterprise should be taken into account in planning and deciding management actions for wetlands. An individual grazing property may even have a range of wetland types with different management needs and objectives which should be identified during whole of property planning. Specific land and wetland management advice should also be sought from local grazing extension officers and NRM professionals.

AQUAMAN: a web-based decision support system for irrigation scheduling in peanuts

Peanut (Arachis hypogaea L.) is an economically important legume crop in irrigated production areas of northern Australia. Although the potential pod yield of the crop in these areas is about 8 t ha(-1), most growers generally obtain around 5 t ha(-1), partly due to poor irrigation management. Better information and tools that are easy to use, accurate, and cost-effective are therefore needed to help local peanut growers improve irrigation management. This paper introduces a new web-based decision support system called AQUAMAN that was developed to assist Australian peanut growers schedule irrigations. It simulates the timing and depth of future irrigations by combining procedures from the food and agriculture organization (FAO) guidelines for irrigation scheduling (FAO-56) with those of the agricultural production systems simulator (APSIM) modeling framework. Here, we present a description of AQUAMAN and results of a series of activities (i.e., extension activities, case studies, and a survey) that were conducted to assess its level of acceptance among Australian peanut growers, obtain feedback for future improvements, and evaluate its performance. Application of the tool for scheduling irrigations of commercial peanut farms since its release in 2004-2005 has shown good acceptance by local peanuts growers and potential for significantly improving yield. Limited comparison with the farmer practice of matching the pan evaporation demand during rain-free periods in 2006-2007 and 2008-2009 suggested that AQUAMAN enabled irrigation water savings of up to 50% and the realization of enhanced water and irrigation use efficiencies.

APSIM – Evolution towards a new generation of agricultural systems simulation

Agricultural systems models worldwide are increasingly being used to explore options and solutions for the food security, climate change adaptation and mitigation and carbon trading problem domains. APSIM (Agricultural Production Systems sIMulator) is one such model that continues to be applied and adapted to this challenging research agenda. From its inception twenty years ago, APSIM has evolved into a framework containing many of the key models required to explore changes in agricultural landscapes with capability ranging from simulation of gene expression through to multi-field farms and beyond. Keating et al. (2003) described many of the fundamental attributes of APSIM in detail. Much has changed in the last decade, and the APSIM community has been exploring novel scientific domains and utilising software developments in social media, web and mobile applications to provide simulation tools adapted to new demands. This paper updates the earlier work by Keating et al. (2003) and chronicles the changing external challenges and opportunities being placed on APSIM during the last decade. It also explores and discusses how APSIM has been evolving to a “next generation” framework with improved features and capabilities that allow its use in many diverse topics.

Can sustainable cotton production systems be developed for tropical northern Australia?

This article reviews research coordinated by the Australian Cotton Cooperative Research Centre (CRC) that investigated production issues for irrigated cotton at five targeted sites in tropical northern Australia, north of 21°S from Broome in Western Australia to the Burdekin in Queensland. The biotic and abiotic issues for cotton production were investigated with the aim of defining the potential limitations and, where appropriate, building a sustainable technical foundation for a future industry if it were to follow. Key lessons from the Cotton CRC research effort were: (1) limitations thought to be associated with cotton production in northern Australia can be overcome by developing a deep understanding of biotic and environmental constraints, then tailoring and validating production practices; and (2) transplanting of southern farming practices without consideration of local pest, soil and climatic factors is unlikely to succeed. Two grower guides were published which synthesised the research for new growers into a rational blueprint for sustainable cotton production in each region. In addition to crop production and environmental impact issues, the project identified the following as key elements needed to establish new cropping regions in tropical Australia: rigorous quantification of suitable land and sustainable water yields; support from governments; a long-term funding model for locally based research; the inclusion of traditional owners; and development of human capacity.

Legume pastures can reduce N2O emissions intensity in subtropical cereal cropping systems

Alternative sources of N are required to bolster subtropical cereal production without increasing N2O emissions from these agro-ecosystems. The reintroduction of legumes in cereal cropping systems is a possible strategy to reduce synthetic N inputs but elevated N2O losses have sometimes been observed after the incorporation of legume residues. However, the magnitude of these losses is highly dependent on local conditions and very little data are available for subtropical regions. The aim of this study was to assess whether, under subtropical conditions, the N mineralised from legume residues can substantially decrease the synthetic N input required by the subsequent cereal crop and reduce overall N2O emissions during the cereal cropping phase. Using a fully automated measuring system, N2O emissions were monitored in a cereal crop (sorghum) following a legume pasture and compared to the same crop in rotation with a grass pasture. Each crop rotation included a nil and a fertilised treatment to assess the N availability of the residues. The incorporation of legumes provided enough readily available N to effectively support crop development but the low labile C left by these residues is likely to have limited denitrification and therefore N2O emissions. As a result, N2O emissions intensities (kgN2O-N yield-1ha-1) were considerably lower in the legume histories than in the grass. Overall, these findings indicate that the C supplied by the crop residue can be more important than the soil NO3 - content in stimulating denitrification and that introducing a legume pasture in a subtropical cereal cropping system is a sustainable practice from both environmental and agronomic perspectives.