Genomic regions influencing seminal root traits in barley

Water availability is a major limiting factor for crop production, making drought adaptation and its many component traits a desirable attribute of plant cultivars. Previous studies in cereal crops indicate that root traits expressed at early plant developmental stages, such as seminal root angle and root number, are associated with water extraction at different depths. Here, we conducted the first study to map seminal root traits in barley (Hordeum vulgare L.). Using a recently developed high-throughput phenotyping method, a panel of 30 barley genotypes and a doubled-haploid (DH) population (ND24260 × 'Flagship') comprising 330 lines genotyped with diversity array technology (DArT) markers were evaluated for seminal root angle (deviation from vertical) and root number under controlled environmental conditions. A high degree of phenotypic variation was observed in the panel of 30 genotypes: 13.5 to 82.2 and 3.6 to 6.9° for root angle and root number, respectively. A similar range was observed in the DH population: 16.4 to 70.5 and 3.6 to 6.5° for root angle and number, respectively. Seven quantitative trait loci (QTL) for seminal root traits (root angle, two QTL; root number, five QTL) were detected in the DH population. A major QTL influencing both root angle and root number (RAQ2/RNQ4) was positioned on chromosome 5HL. Across-species analysis identified 10 common genes underlying root trait QTL in barley, wheat (Triticum aestivum L.), and sorghum [Sorghum bicolor (L.) Moench]. Here, we provide insight into seminal root phenotypes and provide a first look at the genetics controlling these traits in barley.

Physical Oceanographic Influences on Queensland Reef Fish and Scallops : Final Report FRDC 2013/020

The project examined coastal and physical oceanographic influences on the catch rates of coral trout (Plectropomus leopardus) and saucer scallops (Amusium balloti) in Queensland. The research was undertaken to explain variation observed in the catches, and to improve quantitative assessment of the stocks and management advice. 3.1 OBJECTIVES 1. Review recent advances in the study of physical oceanographic influences on fisheries catch data, and describe the major physical oceanographic features that are likely to influence Queensland reef fish and saucer scallops. 2. Collate Queensland’s physical oceanographic data and fisheries (i.e. reef fish and saucer scallops) data. 3. Develop stochastic population models for reef fish and saucer scallops, which can link physical oceanographic features (e.g. sea surface temperature anomalies) to catch rates, biological parameters (e.g. growth, reproduction, natural mortality) and ecological aspects (e.g. spatial distribution).

Molecular Breeding for Complex Adaptive Traits: How Integrating Crop Ecophysiology and Modelling Can Enhance Efficiency

Progress in crop improvement is limited by the ability to identify favourable combinations of genotypes (G) and management practices (M) in relevant target environments (E) given the resources available to search among the myriad of possible combinations. To underpin yield advance we require prediction of phenotype based on genotype. In plant breeding, traditional phenotypic selection methods have involved measuring phenotypic performance of large segregating populations in multi-environment trials and applying rigorous statistical procedures based on quantitative genetic theory to identify superior individuals. Recent developments in the ability to inexpensively and densely map/sequence genomes have facilitated a shift from the level of the individual (genotype) to the level of the genomic region. Molecular breeding strategies using genome wide prediction and genomic selection approaches have developed rapidly. However, their applicability to complex traits remains constrained by gene-gene and gene-environment interactions, which restrict the predictive power of associations of genomic regions with phenotypic responses. Here it is argued that crop ecophysiology and functional whole plant modelling can provide an effective link between molecular and organism scales and enhance molecular breeding by adding value to genetic prediction approaches. A physiological framework that facilitates dissection and modelling of complex traits can inform phenotyping methods for marker/gene detection and underpin prediction of likely phenotypic consequences of trait and genetic variation in target environments. This approach holds considerable promise for more effectively linking genotype to phenotype for complex adaptive traits. Specific examples focused on drought adaptation are presented to highlight the concepts.

Seed bank persistence and germination of chinee apple (Ziziphus mauritiana Lam.)

Chinee apple (Ziziphus mauritiana Lam.) is a thorny tree that is invading tropical woodlands of northern Australia. The present study reports three experiments related to the seed dynamics of chinee apple. Experiment 1 and 2 investigated persistence of seed lots under different soil types (clay and river loam), levels of pasture cover (present or absent) and burial depths (0, 2.5, 10 and 20 cm). Experiment 3 determined the germination response of chinee apple seeds to a range of alternating day/night temperatures (11/6°C up to 52/40°C). In the longevity experiments (Expts 1 and 2), burial depth, soil type and burial duration significantly affected viability. Burial depth had the greatest influence, with surface located seeds generally persisting for longer than those buried below ground. Even so, no viable seeds remained after 18 and 24 months in the first and second experiment, respectively. In Expt 3 seeds of chinee apple germinated under a wide range of alternating day/night temperatures ranging from 16/12°C to 47 /36°C. Optimal germination (77%) occurred at 33/27°C and no seeds germinated at either of the lowest (11/6°C) or highest (52/40°C) temperature regimes tested. These findings indicated that chinee apple has the potential to expand its current distribution to cooler areas of Australia. Control practices need to be undertaken for at least two years to exhaust the seed bank.

Germination Biology and Occurrence of Polyembryony in Two Forms of Cats Claw Creeper Vine, Dolichandra unguis-cati (Bignoniaceae): Implications for Its Invasiveness and Management

Cat’s claw creeper vine, Dolichandra unguis-cati (L.) Lohmann (syn. Macfadyena unguis-cati (L.) Gentry), is a major environmental weed in Australia. Two forms of the weed with distinctive leaf morphology and reproductive traits, including varying fruit size, occur in Queensland, Australia. The long pod form occurs in a few localities in Queensland, while the short pod form is widely distributed in Queensland and northern part of New South Wales. This investigation aimed to evaluate germination behavior and occurrence of polyembryony (production of multiple seedlings from a single seed) in the two forms of the weed. Seeds were germinated in growth chambers set to 10/20°C, 15/25°C, 20/30°C, 30/45°C and 25°C, representing ambient temperature conditions of the region. Germination and polyembryony were monitored over a period of 12 weeks. For all the treatments in this study, seeds from short pod plants exhibited significantly higher germination rates and higher occurrence of polyembryony than those from long pod plants. Seeds from long pod plants did not germinate at the lowest temperature of 10/20°C; in contrast, those of the short pod form germinated under this condition, albeit at a lower rate (reaching a maximum 45% germination at week 12). Results from this study could explain why the short pod form of D. unguis-cati is the more widely distributed plants in Australia, while the long pod is confined to a few localities. The results have implication in predicting future range of both forms of the invasive D. unguis-cati, as well as inform management decisions for control of the weed.

A network forensics tool for precise data packet capture and replay in cyber-physical systems

Network data packet capture and replay capabilities are basic requirements for forensic analysis of faults and security-related anomalies, as well as for testing and development. Cyber-physical networks, in which data packets are used to monitor and control physical devices, must operate within strict timing constraints, in order to match the hardware devices' characteristics. Standard network monitoring tools are unsuitable for such systems because they cannot guarantee to capture all data packets, may introduce their own traffic into the network, and cannot reliably reproduce the original timing of data packets. Here we present a high-speed network forensics tool specifically designed for capturing and replaying data traffic in Supervisory Control and Data Acquisition systems. Unlike general-purpose "packet capture" tools it does not affect the observed network's data traffic and guarantees that the original packet ordering is preserved. Most importantly, it allows replay of network traffic precisely matching its original timing. The tool was implemented by developing novel user interface and back-end software for a special-purpose network interface card. Experimental results show a clear improvement in data capture and replay capabilities over standard network monitoring methods and general-purpose forensics solutions.

Thermal stabilization of glucose oxidase and glucoamylase by physical entrapment

Physical entrapment was used as an approach to achieve thermal stabilization of enzymes. The ti values for the thermoinactivation of glucose oxidase and glucoamylase were increased several-fold by their entrapment in polyacrylamide gels. In polyacrylate gels the individual enzymes behaved differently, probably owing to microenvironmental effects arising by the polyelectrolyte nature of the carrier.

Fine Mapping of qDor7, a Major QTL Affecting Seed Dormancy in Sorghum (Sorghum bicolor (L.) Moench)

Seed dormancy is a key domestication trait for major crops, which is acquired in long-term systems development processes and enables the survival of plants in adverse natural conditions. It is a complex trait under polygenic control and is affected by endogenous and environmental factors. In the present study, a major seed dormancy QTL in sorghum (Sorghum bicolor (L.) Moench), qDor7, detected previously, was fine mapped using a large, multi-generational population. The qDor7 locus was delimited to a 96-kb region which contains 16 predicted gene models. These results lay a solid foundation for cloning qDor7. In addition, the functional markers tightly linked to the seed dormancy QTL may be used in marker-assisted selection for seed dormancy in sorghum.

Bringing nature to schools to promote children’s physical activity

Physical activity (PA) is essential for human health and wellbeing across all age, socioeconomic and ethnic groups. Engagement with the natural world is a new defining criterion for enhancing the benefits of PA particularly for children and young people. Interacting with nature benefits children’s social and emotional wellbeing, develops resilience and reduces the risk of obesity and type 2 diabetes across all population groups. Governments around the world are now recognising the importance of children spending more active time outdoors. However, children’s outdoor activities, free play and nature-related exploration are often structured and supervised by adults due to safety concerns and risks. In this context schools become more accessible and safe options for children to engage in PA outdoors with the presence of nature features. Research on school designs involving young children has revealed that children prefer nature-related features in school environments. Affordances in nature may increase children’s interest in physically active behaviours. Given that present school campuses are designed for operational efficiency and economic reasons there is a need to re-design schools responding to the positive role of nature on human health. If schools were re-designed to incorporate diverse natural features children’s PA and consequent health and wellbeing would likely improve markedly.

Mixed reality stories: How creative writers integrate virtual and physical realities

Mixed reality stories (MRS) unfold simultaneously in the physical and the virtual world. Advancements in digital technologies, which are now able to capture more contextual information about our physical environments, are enabling novel ways of blending the two worlds. To explore the process of creating stories from this perspective, we conducted a study with creative writers, in which we asked them to write a MRS script for outdoor running. While we saw instances of intentional connections between physical and virtual worlds in their work, we also observed the use of ambiguity or even deliberate contradiction with available contextual information. In this paper we discuss how these approaches can be beneficial for MRS and propose directions for future work.

Dispersal and related life history traits in the Glanville fritillary butterfly

Most studies of life history evolution are based on the assumption that species exist at equilibrium and spatially distinct separated populations. In reality, this is rarely the case, as populations are often spatially structured with ephemeral local populations. Therefore, the characteristics of metapopulations should be considered while studying factors affecting life history evolution. Theoretical studies have examined spatial processes shaping the evolution of life history traits to some extent, but there is little empirical data and evidence to investigate model predictions. In my thesis I have tried to bridge the gap between theoretical and empirical studies by using the well-known Glanville fritillary (Melitaea cinxia) metapopulation as a model system. The long-term persistence of classic metapopulations requires sufficient dispersal to establish new local populations to compensate for local extinctions. Previous studies on the Glanville fritillary have shown that females establishing new populations are not a random sample from the metapopulation, but they are in fact more dispersive than females in old populations. Many other life-history traits, such as body size, fecundity and lifespan, may be related to dispersal rate. Therefore, I examined a range of correlated traits for their evolutionary and ecological consequences. I was particularly interested in how the traits vary under natural environmental conditions, hence all studies were conducted in a large (32 x 26 m) outdoor population cage built upon a natural habitat patch. Individuals for the experiments were sampled from newly-established and old populations within a large metapopulation. Results show that females originating from newly-established populations had higher within-habitat patch mobility than females from old populations. I showed that dispersal rate is heritable and that flight activity is related to variation in a gene encoding the glycolytic enzyme phosphoglucose isomerase. Both among-individual and among-population variation in dispersal are correlated with the reproductive performance of females, though I found no evidence for a trade-off between dispersal and fecundity in terms of lifetime egg production or clutch size. Instead, the results suggest that highly dispersive females from newly-established populations have a shorter lifespan than females from old populations, and that dispersive females may pay a cost in terms of reduced lifetime reproductive success due to increased time spent outside habitat patches. In summary, the results of this thesis show that genotype-dependent dispersal rate correlates with other life history traits in the Glanville fritillary, and that the rapid turnover of local populations (extinctions and re-colonisations) is likely to be the mechanism that maintains phenotypic variation in many life history traits at the metapopulation level.