Australian Department of Primary Industries and Fisheries

Melbourne, Australia

Australian Department of Primary Industries and Fisheries

Melbourne, Australia
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Grant
Agency: European Commission | Branch: FP7 | Program: CSA-CA | Phase: KBBE-2008-1-2-02 | Award Amount: 1.15M | Year: 2009

BrightAnimal will contribute to economically, socially and environmentally sustainable development by outlining a practical and acceptable methodology for precision livestock farming. To achieve this goal, BrightAnimal has the following mission: To produce a framework for European and non-European small and medium enterprises on effective and acceptable precision livestock farming and to create an international, interdisciplinary network for further development and dissemination. The main activity and achievement of BrightAnimal will be the elaboration of a book on effective Precision Livestock Farming in Europe and world-wide with special consideration of small and medium enterprises. The book aims at describing current and near-future techniques in PLF, especially taking into account both the practicality for SMEs as well as their acceptability (in the broader sense). The book will also try to set the scene for future developments. As the second component of the framework, BrightAnimal will produce best precision livestock farming practices (BPLFP) in a series of problematic areas such as aquaculture, beef, sheep and chicken. These best practice guides will be released to the public domain in the form of booklets. A third deliverable of the project will be a practical showcase activity showing the Good Practices in action in the European Centre of Excellence of Automatic Identification and Data Capture in the UK. BrightAnimal will organise interdisciplinary conferences for opinion exchange and cross-disciplinary discussions. It is of great importance to include opinions from outside Europe. We have been pleased to accept partners from the following ICPC countries: Thailand, Malaysia, South Africa, Brazil and China and from Australia as a third country. Other non-funded partners from third countries will also join the project.


Powell J.E.,Queensland Institute of Medical Research | Visscher P.M.,Queensland Institute of Medical Research | Goddard M.E.,University of Melbourne | Goddard M.E.,Australian Department of Primary Industries and Fisheries
Nature Reviews Genetics | Year: 2010

Identity by descent (IBD) is a fundamental concept in genetics and refers to alleles that are descended from a common ancestor in a base population. Identity by state (IBS) simply refers to alleles that are the same, irrespective of whether they are inherited from a recent ancestor. In modern applications, IBD relationships are estimated from genetic markers in individuals without any known relationship. This can lead to erroneous inference because a consistent base population is not used. We argue that the purpose of most IBD calculations is to predict IBS at unobserved loci. Recognizing this aim leads to better methods to estimating IBD with benefits in mapping genes, estimating genetic variance and predicting inbreeding depression. © 2010 Macmillan Publishers Limited. All rights reserved.


Wilkinson K.G.,Australian Department of Primary Industries and Fisheries
Biomass and Bioenergy | Year: 2011

This review examines the drivers behind the adoption of on-farm anaerobic digestion in Germany where there were more than 4000 plants operating in 2009. In Australia, only one plant is operating, at a piggery in the State of Victoria. Germany's generous feed-in-tariffs for renewable energy are typically given the credit for promoting investment in on-farm anaerobic digestion. But the particular biophysical and socio-economic character of farming in the country provided the fertile ground for these financial incentives to take root. Energy security has also been a major driver for the promotion of renewable energy in Germany since it imports over 60% of its energy needs. In contrast, Australia is a net energy exporter, exporting about two-thirds of its domestic energy. Although it has considerable potential for application in Australia, anaerobic digestion is unlikely to be widely adopted unless new incentives emerge to strongly encourage investment. Stronger Australian regulation of manures and effluent may serve as an incentive to a limited extent in the future. Yet the experience in Germany suggests that regulation on its own was not sufficient to encourage large numbers of farmers to invest in anaerobic digestion. Even with generous incentives from the German government, increasing construction costs and the rising cost of energy crops can put the financial viability of anaerobic digestion plants at risk. Unless improvements in efficiency are found and implemented, these pressures could lead to unsustainable rises in the cost of the incentive schemes that underpin the development of renewable energy technologies. © 2011.


Lee S.H.,Queensland Institute of Medical Research | Wray N.R.,Queensland Institute of Medical Research | Goddard M.E.,Australian Department of Primary Industries and Fisheries | Goddard M.E.,University of Melbourne | Visscher P.M.,Queensland Institute of Medical Research
American Journal of Human Genetics | Year: 2011

Genome-wide association studies are designed to discover SNPs that are associated with a complex trait. Employing strict significance thresholds when testing individual SNPs avoids false positives at the expense of increasing false negatives. Recently, we developed a method for quantitative traits that estimates the variation accounted for when fitting all SNPs simultaneously. Here we develop this method further for case-control studies. We use a linear mixed model for analysis of binary traits and transform the estimates to a liability scale by adjusting both for scale and for ascertainment of the case samples. We show by theory and simulation that the method is unbiased. We apply the method to data from the Wellcome Trust Case Control Consortium and show that a substantial proportion of variation in liability for Crohn disease, bipolar disorder, and type I diabetes is tagged by common SNPs. © 2011 The American Society of Human Genetics.


Stewart J.,Australian Department of Primary Industries and Fisheries
Fisheries Research | Year: 2011

Exploited reef-associated species in south-eastern Australia have evolved life-history strategies to ensure population persistence through periods that are unsuitable for recruitment. They are characterized by considerable potential longevity (20-50 years), sexual maturation at relatively young ages (2-4 years old) and variable recruitment patterns. The age compositions in landings of the major reef-associated species in this region were used to demonstrate that some species have been subjected to significant age-class truncation. Species with long histories of exploitation had age compositions with relatively few fish greater than 5 years old. It is suggested that the removal of older age classes from the most heavily exploited populations has lowered their resilience to environmental change and that remedial management action may be required to rebuild reserves of older individuals. It is argued that the management options that are most likely to succeed in achieving this objective for populations of offshore reef-associated species include reducing rates of exploitation to very low levels, protecting larger/older fish through regulated maximum length limits and/or changes to gear selectivity and no take marine protected areas. The most appropriate management options will depend on the life-history of the species being considered. © 2010 Elsevier B.V.


Yang J.,Queensland Institute of Medical Research | Lee S.H.,Queensland Institute of Medical Research | Goddard M.E.,University of Melbourne | Goddard M.E.,Australian Department of Primary Industries and Fisheries | Visscher P.M.,Queensland Institute of Medical Research
American Journal of Human Genetics | Year: 2011

For most human complex diseases and traits, SNPs identified by genome-wide association studies (GWAS) explain only a small fraction of the heritability. Here we report a user-friendly software tool called genome-wide complex trait analysis (GCTA), which was developed based on a method we recently developed to address the "missing heritability" problem. GCTA estimates the variance explained by all the SNPs on a chromosome or on the whole genome for a complex trait rather than testing the association of any particular SNP to the trait. We introduce GCTA's five main functions: data management, estimation of the genetic relationships from SNPs, mixed linear model analysis of variance explained by the SNPs, estimation of the linkage disequilibrium structure, and GWAS simulation. We focus on the function of estimating the variance explained by all the SNPs on the X chromosome and testing the hypotheses of dosage compensation. The GCTA software is a versatile tool to estimate and partition complex trait variation with large GWAS data sets. © 2011 The American Society of Human Genetics.


Daniells I.G.,Australian Department of Primary Industries and Fisheries
Soil Research | Year: 2012

Hardsetting soils have been defined as soils that set to a hard, structureless mass during drying and are thereafter difficult or impossible to cultivate until the profile is rewetted. Soil strength increases rapidly as the soil dries, and so seedlings must grow quickly before soil strength becomes too high for root growth or shoot emergence. Recent work on the mechanisms of hardsetting confirms that aggregate disruption through slaking and dispersion on wetting leads to coalescence. Bridging by dispersed particles under matric potential makes a soil hardset. Failure to recover from a coalesced state as the soil dries leaves it with a massive structure. This paper reviews the worldwide occurrence of hardsetting soils, the evolution of definitions of hardsetting, and the use of those definitions in soil classification with particular emphasis on Australia. Measurement of hardsetting includes methods such as visual score of slaking and dispersion, penetration resistance, fall-cone penetration, dispersion, fractions of soil organic matter, friability index, modulus of rupture, and a particular use of the soil water retention curve. Overcoming problems associated with hardsetting soils and their ongoing management is difficult. Further work is needed on the reasons for variable responses to tillage, no tillage, and pasture. Modifying soil texture has limited application, and increasing soil organic matter under cropping is difficult in low-rainfall areas. Polymers have been shown to be beneficial. Mulching maintains higher soil moisture and therefore a softer surface, while biochar shows inconsistent effects. Controlled traffic is a key to reducing recompaction. Management of a hardsetting soil must include the whole rotation, including when to till, when to crop, and when to graze or not. © CSIRO 2012.


Levot G.W.,Australian Department of Primary Industries and Fisheries
Australian Veterinary Journal | Year: 2012

Objective: To investigate the cause of cyromazine failure to protect lambs from flystrike. Methods: Lucilia cuprina larvae from a Nimmitabel (New South Wales) population associated with failure of a cyromazine spray-on to protect lambs from flystrike were compared with larvae from a susceptible field strain and a reference susceptible laboratory strain in laboratory bioassays. Batches of neonate blowfly larvae were transferred onto homogenised bovine liver containing varying concentrations of cyromazine or dicyclanil and the numbers of larvae pupating and completing development were recorded. Results: Based on the ability of larvae to complete development on liver homogenate containing 1mg/kg cyromazine, the phenotypic frequency of resistance in the Nimmitabel population was estimated to be approximately 4%. Compared with a susceptible field strain, the Nimmitabel population was 3-fold more resistant to cyromazine and twice as resistant to dicyclanil at the LC95 level (lethal concentration killing 95% of larvae). In the laboratory, the Nimmitabel strain responded to sequential exposure of larvae to food containing cyromazine by becoming more resistant. Resistance to cyromazine was incompletely dominant, giving resistant larvae a survival advantage over susceptible types over a relatively narrow range of cyromazine concentrations. Conclusion: Cyromazine resistance was detected in a field population of L. cuprina. Low-level cross-resistance to dicyclanil was also confirmed. Until more is known about the resistance, the prudent recommendation to control flystrike by this blowfly population is topical treatment with ivermectin. © 2012 The Authors. Australian Veterinary Journal © 2012 Australian Veterinary Association.


Ross E.M.,Australian Department of Primary Industries and Fisheries
BMC microbiology | Year: 2013

The bovine rumen hosts a diverse and complex community of Eukarya, Bacteria, Archea and viruses (including bacteriophage). The rumen viral population (the rumen virome) has received little attention compared to the rumen microbial population (the rumen microbiome). We used massively parallel sequencing of virus like particles to investigate the diversity of the rumen virome in thirteen lactating Australian Holstein dairy cattle all housed in the same location, 12 of which were sampled on the same day. Fourteen putative viral sequence fragments over 30 Kbp in length were assembled and annotated. Many of the putative genes in the assembled contigs showed no homology to previously annotated genes, highlighting the large amount of work still required to fully annotate the functions encoded in viral genomes. The abundance of the contig sequences varied widely between animals, even though the cattle were of the same age, stage of lactation and fed the same diets. Additionally the twelve animals which were co-habited shared a number of their dominant viral contigs. We compared the functional characteristics of our bovine viromes with that of other viromes, as well as rumen microbiomes. At the functional level, we found strong similarities between all of the viral samples, which were highly distinct from the rumen microbiome samples. Our findings suggest a large amount of between animal variation in the bovine rumen virome and that co-habiting animals may have more similar viromes than non co-habited animals. We report the deepest sequencing to date of the rumen virome. This work highlights the enormous amount of novelty and variation present in the rumen virome.


Reconstructions of the Cambrian-Silurian tectonic evolution of eastern Gondwanaland, when the Australian Tasmanides and Antarctic Ross Orogen developed, rely on correlation between structural elements in SE Australia and Northern Victoria Land (NVL), Antarctica. A variety of published models exist but none completely solve the tectonic puzzle that is the Delamerian-Lachlan transition in the Tasmanides. This paper summarizes the understanding of Cambrian (Delamerian) to Silurian (Lachlan) geological evolution of the eastern Tasmanides, taking into account new deep seismic data that clarifies the geological connection between Victoria and Tasmania - the 'Selwyn Block' model. It evaluates previous attempts at correlation between NVL, Tasmania and Victoria, and presents a new scenario that encompasses the most robust correlations. Tasmania together with the Selwyn Block is reinterpreted as an exotic Proterozoic microcontinental block - 'VanDieland' - that collided into the east Gondwanaland margin south of western Victoria, and north of NVL in the Late Cambrian, perhaps terminating the Delamerian Orogeny in SE Australia. Subsequent north-east 'tectonic escape' of VanDieland in the Early Ordovician explains the present-day outboard position of Tasmania with respect to the rest of the Delamerian orogen, the origin of the hiatus that separates the Delamerian and Lachlan orogenic cycles in Australia, and how western Lachlan oceanic crust developed as a 'trapped plate-segment'. The model establishes a new structural template for subsequent Lachlan Orogen development and Mesozoic Australia-Antarctica separation. © 2010.

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