Agriculture and Food Systems - Theses

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    New Technologies and Yam Production Efficiency in Nigeria: Potential for Improved Farm Household Wellbeing
    Amaefula, Adanma ( 2018)
    Nigeria is an agrarian economy with over seventy percent of the population engaged in agriculture. However, the nation depends heavily on food imports. Nigerian food producers are predominantly resource-constrained poor farmers, who are the most food insecure. Nigerian agriculture is chiefly conducted to meet household food requirement but is gradually transitioning to semi-subsistence agriculture. Agriculture was once the mainstay of Nigeria. The Nigerian agricultural sector was abandoned for the oil sector in the early 1970s. This neglect has negative consequences on the country’s agriculture. Presently, Nigerian agriculture is characterized by low performance. Nigeria, once a net food exporter has become a net food importer. With a view to enhancing the performance of Nigeria farmers, improved technologies have been developed and disseminated to farmers. In spite of this, there is food insecurity and poverty intensification in the country. This raises the questions whether or not farmers are adopting these technologies and the efficacy of these technologies in enhancing farmer performance and alleviating poverty in the country. Yam is a significant crop in Nigeria. It is a highly prized crop in the country. It has sociocultural, medicinal, nutritional and economic value. It is nutritionally superior to comparable crops including sweet potato and taro. Notwithstanding, yam farmers in Nigeria are performing poorly. Yam production in Nigeria is mainly impeded by high cost, unavailability of planting material, and over reliance on labour-intensive traditional yam production methods which are expensive, encourage the use of low quality planting materials, and inhibit mechanization of yam production. Yam Minisett Technology (YMT) is an on-farm yam multiplication technique which enables development of high quality planting materials for yam production. The aim of this project is to ascertain the potential of new technology and increased farmers efficiency for wellbeing improvement with reference to yam production and YMT in Nigeria. The specific objectives of this project are to: (i) describe yam production in Nigeria; (ii) compare farm activities and yam production systems in Nigeria; (iii) examine indicators and determinants of performance of yam producers (performance indicators being technical and economic); (iv) examine the role of technology adoption on farmer performance and wellbeing; (v) assess the superiority of seed yam from YMT over other planting materials; and (vi) ascertain determinants of adoption of improved technology. A multi-stage sampling technique was adopted to elicit cross-sectional data from three hundred and sixty yam farmers (120 respondents per State) in three yam-producing States of Nigeria. The States were Benue, Enugu and Ondo. The States are located in different agro-ecological zones of Nigeria and use different methods for yam production. Data were drawn from two Local Government Areas (LGAs) in each State. The LGAs were Katsina-Ala and Buruku in Benue State, Nkanu-east and Uzo-Uwani in Enugu State, and Ose and Owo in Ondo State. Primary and secondary data were used in this investigation. Primary data were collected from the respondents by using a well-structured questionnaire, direct observation and by interviewing farmers. Secondary data were obtained from databases, websites and literature. Data collected include socioeconomic data, resource endowment and utilization data, input and output data, data on farming systems and techniques, attitudinal data, environmental data and health data. Data were analyzed with descriptive statistics, econometrics and economic models. Descriptive statistics were used to describe yam production. An econometric model (stochastic frontier analysis) was used to evaluate the indicators of performance of yam farmers. Two functional forms, the Cobb-Douglas and the Translog production and cost functions, were used to investigate the production and cost of yam. The models were compared for goodness-of-fit. The best functional form was used to determine the technical and economic efficiency and factors influencing efficiency. Metafrontier analysis was used to test the presence of environment/technology gaps between States. The impact of YMT adoption on yam farmer performance was investigated using Propensity Score Matching. Factors influencing adoption were determined with Probit model. Gross Margin (GM) analysis was used to determine the profitability of yam with and without YMT. Partial budgeting was also performed to confirm the profitability of YMT. Net return was used to compare the yam cropping systems. The stochastic frontier analysis showed that, on average, Nigerian yam farmers in those States were not fully efficient in yam production. Benue State was technically efficient in yam production. Both Benue and Enugu yam farmers were relatively economically efficient. The performance (technical and economic efficiency) of Nigerian yam farmers is influenced by farmer’s socioeconomic profile, decisions, and access to inputs and facilities. Yam production is affected by farm size, quantity of planting material, labour and capital input. Cost of yam is determined by output, capital input, rent on land, planting material, wage rate and price of fertilizer. The result of the metafrontier analysis revealed that the production environment and technology for yam differ between States in Nigeria. Benue and Ondo States have more favourable environments for yam production. Enugu yam farmers are operating in a more restrictive environment. GM analysis established that yam production is relatively profitable. Yam had a higher GM than other root and tuber crops. Yam/Maize is the most profitable cropping system in Nigeria. Embracing Yam/Maize intercrop and increased investment in yam production can contribute to improving the poverty status in Nigeria. The adoption of YMT has the potential to improve farmer performance and wellbeing in Nigeria. YMT is a viable seed yam production technique. Yam production using YMT is more profitable than the traditional yam production techniques. Adopters of YMT in Nigeria outperformed non-adopters.
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    Molecular and functional genomic analysis of Phytochrome Interacting Factor 4 during the floral transition of soybean
    Arya, Hina ( 2019)
    Climate change is adversely affecting global food production. Reduced crop yields and increasing food demands are presenting new challenges for developing resilient crop varieties. Legume plant soybean is an important food crop next to cereals. Soybean is a rich source of high-quality vegetable oils, protein, nutraceuticals, and it is widely cultivated across the globe for both human and animal consumption. According to the Australian oilseed federation, soybean cultivation strengthens regional economies and contributes to 2.5 billion dollars of the Australian oilseed industry. To breed better soybean crops, a study of light and temperature perception is important, as these events control the process of flowering which is the first step towards total seed production. On the molecular level, light and temperature signal control is a complex process mediated by a network of photoreceptors and transducers. One such transducer is Phytochrome Interacting Factor 4 (PIF4). It is involved in the perception of external environmental stimuli to integrate the information of daily light and temperature fluctuations with the internal physiology of plants. PIF4 has been studied in the model plant Arabidopsis thaliana, but knowledge about its counterparts in soybean is limited. To understand the function of PIF4 in soybean, an integrated genomics, molecular, and functional characterization approach was employed. The genomic analysis show that there are seven active copies of PIF4 gene in the genome of the cultivated soybean (Glycine max). The seven soybean PIF4 genes have evolved at different time points during the soybean genome duplication events, and phylogeny is suggestive of the existence of a conserved PIF4 clade (PIF4 I), which includes Arabidopsis PIF4 and a clade that groups only the PIF4s of legumes (PIF4II). To assess the gene expression patterns of soybean PIF4s during variable photoperiods and temperature conditions, quantitative RT-PCR was performed. Quantitative RT-PCR results showed that three PIF4s belonging to the PIF4I clade (i.e. GmPIF4a, GmPIF4b, and GmPIF4c) had conserved PIF4 like expression (consistent with Arabidopsis pif4) in inductive photoperiod (short day; SD), whereas two soybean PIF4s belonging to the PIF4II clade (i.e. GmPIF4f and GmPIF4g) exhibited reduced to nil sensitivity to short-days. The mRNA transcript levels of three PIF4s were elevated at 35-degree centigrade as compared to 25-degrees centigrade in short days. In non-inductive photoperiod (long day; LD), all soybean PIF4s were responsive to extended light phase suggesting their functional role in long photoperiods. Further, no significant transcript variation was observed at elevated temperatures in long days, except one PIF4, which expressed at higher levels at 30-degrees centigrade as compared to 25-degrees centigrade. Mining of previously published RNA sequencing data obtained from leaf samples of a short-day soybean cultivar (Bragg) undergoing floral transition showed that one of the PIF4s was differentially regulated with high differences in transcript read values on consecutive short days. This soybean PIF4 was designated as GmPIF4b. GmPIF4b was functionally characterized using ectopic expression in Arabidopsis, mutant complementation in Arabidopsis pif4-101 mutants and gene over-expression in the soybean cultivar, Bragg. Ectopic expression of GmPIF4b in Arabidopsis resulted in elongated hypocotyls and early flowering responses suggesting the function of GmPIF4b in hypocotyl elongation and flowering responses. Arabidopsis pif4-101 mutant contains a mutation in the exon-5 of pif4 gene. This mutant is characterized by shorter hypocotyls and a compact rosette size. Complementation of GmPIF4b in Arabidopsis pif4-101 mutant partially rescued the short hypocotyl and compact rosette phenotypes of pif4-101 mutant. The results were suggestive of both conservation and divergence of GmPIF4b. To gain insights into the function of GmPIF4b in soybean, constitutive overexpression of GmPIF4b in soybean (Bragg) was undertaken. Constitutive overexpression resulted in decreased plant height, reduced leaf surface area, decline in total number of branches per plant, and early flowering in transgenic soybean plants as compared to the wild type. Quantitative RT-PCR was performed to study the transcript levels of soybean florigens; GmFT2a and GmFT5a in the transgenic plants (over expressing GmPIF4b). The transcript levels of GmFT2a and GmFT5a were significantly elevated in transgenic lines compared to the wild type. Late maturing soybean varieties, such as Bragg, can terminate flowering in sub-optimal photoperiods. To study the effect of GmPIF4b over-expression on termination of flowering, transgenic soybean plants (over expressing GmPIF4b) grown in short days were transitioned to non-inductive photoperiod (for 10 long days) at full bloom stage. Interestingly, wild type Bragg plants terminated flowers and produced less pods. Transgenic plants did not terminate their reproductive activity and gave rise to a higher number of pods per plant. To study the dynamics of GmPIF4b protein, immunoblot analysis was undertaken. The results showed that on protein level, GmPIF4b follows a strict diurnal expression pattern under both long and short days, suggesting the involvement of biological clock in regulating GmPIF4b protein expression. Chromatin immunoprecipitation was performed to study the protein-DNA interaction of GmPIF4b protein with the promoters of soybean florigens GmFT2a and GmFT5a. The results suggested that GmPIF4b interacts with the promoters of GmFT2a in short-day treated plants, whereas it interacts with the promoter of GmFT5a in a photoperiod insensitive manner. PIF4 is shown to be involved in nitrate assimilation and phosphate acquisition pathways. Soybeans plants were treated with nitrates or orthophosphates under inductive short days to analyse the GmPIF4b gene expression by RT-PCR. The results showed that the application of nitrates and orthophosphates can affect the levels of GmPIF4b transcript and can modulate the expression pattern of soybean floral identity marker gene, GmAP1. Hence, the outcome of this study can contribute towards developing climate-resilient varieties for the future.
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    The functional analysis of soybean (Glycine max L.) flowering genes
    Lee, Sangil ( 2019)
    Soybean (Glycine max L.) is one of the major crop plants since its seeds contain high levels of oil and protein. In addition, soybean’s unique ability in fixing nitrogen makes it a key plant for sustainable agriculture due to the increasing cost of nitrogen fertilizers caused by continuing depletion of petroleum. The demand for improvement of soybean yield has been rapidly growing due to the plant’s high nutritional values and its significance in sustainable agriculture. Flowering is a major step in plant life cycles as it plays crucial roles in reproductive success. Late flowering under favourable conditions allow plants to maximize their vegetative growth, which ultimately leads to improved seed production, whilst early flowering allows plants to secure their progenies under adverse growth environments. Comparative analysis of flowering genes between Arabidopsis and soybean has revealed conservation of most flowering genes. However, functions of most flowering genes in soybean are still unknown. Therefore, investigation of soybean flowering genes is expected to provide insight into flowering mechanisms of soybean. Plant genetic transformation is an important tool to improve agricultural traits and investigate functions of genes. Since reported success in soybean genetic transformation has been limited to inferior-breeding cultivars, development of stable transformation systems for commercial soybean cultivars will provide a new solution to meet the ever-increasing demand for soybean. In the present study, transformation systems for commercial cultivars of soybean were developed using the Agrobacterium-mediated transformation method. Transgenic soybean plants (cv. Bragg) containing yellow fluorescence protein (YFP) and herbicide resistant gene (bar) were produced using half-seed transformation method. Shoot elongation efficiency was increased (6 fold) by addition of phenolic compound inhibitors [adenine hemisulfate (40mg/L) and PVP 40,000 (500 mg/L)] during shoot elongation, resulting in improvements in the growth of transgenic shoots. Total 23 independent T0 putative transgenic lines were produced and herbicide resistance was confirmed via basta brush test (100mg/L glufosinate). Total two basta resistance lines exhibited YFP expression in leaves. Stable expressions of transgenes were observed in T1 and T2 generations. The roles of soybean LFY homolog (Glyma.06G163600.1) in flowering initiation was confirmed in this study. LEAFY gene (LFY) is one of floral meristem identity genes and plays essential roles in flowering. In soybean, two LFY homologs (Glyma.04G202000.1 and Glyma.06G163600.1) are annotated and they show high sequence similarity (Glyma.04G202000.1: 73.4% and Glyma.06G163600.1: 69.5%) with Arabidopsis LFY (AtLFY). Furthermore, soybean LFY homologs have two conserved DNA-binding domains (N- and C-domains). The expression levels of both soybean LFY homologs gradually increased in flowering inductive conditions and Glyma.06G163600.1(GmLFY1) showed a higher expression than Glyma.04G202000.1 (GmLFY2). These high sequence conservation and expression patterns of soybean LFY homologs suggested GmLFY genes may have roles in flowering initiation. Ectopic expression of GmLFY1 in transgenic Arabidopsis and tobacco plants induced early flowering phenotypes. Moreover, up-regulations of genes (AP1, SOC1 and LFY) involved in flowering were also detected in transgenic plants. These results suggest that GmLFY1 may regulate flowering time via the conserved process as in Arabidopsis. Besides, tissue-specific GUS expressions on sepals were detected in flowers of transgenic tobacco plants (GmLFY1::GUS), indicating that GmLFY1 is also involved in flower development. The ageing pathway is one of the identified flowering genetic pathways and the miR156-miR172 module plays major roles in this process via repression of their target genes. In this study, expression patterns of soybean miR156 and miR172 (gma-miR156a, gma-miR172a) in vegetative and reproductive developments were confirmed. Expression of gma-miR156a was higher than that of gma-miR172a in the vegetative developmental stage and it decreased with ageing. On the other hand, expression of gma-miR172a was elevated under flowering inductive conditions. These expression patterns of soybean miR156a and miR172a genes suggest that they may be involved in the developmental process. Ectopic expression of gma-miR156a in transgenic tobacco plants caused significant delays in flowering initiation with extended juvenile developmental traits (round shape of leaves). In contrast, transgenic tobacco plants overexpressing gma-miR172a exhibited early flowering phenotypes with adult traits on leaves (narrow shape). Significant down-regulations of miR156 target genes (SPL transcription factor family) and miR172 target genes (AP2-like genes) were detected in transgenic tobacco plants. These results showed that gma-miR156a and gma-miR172a may regulate ageing process via repressions of their target genes. In the present study, transgenic commercial soybean cultivar (cv. Bragg) was produced using the Agrobacterium-mediated method. In addition, this study provided evidence of conserved roles of GmLFY1, gma-miR156a and gma-miR172a in flowering and plant developments via heterologous expressions in transgenic Arabidopsis and tobacco plants. GmLFY1 is involved in floral meristem development and initiation of flowering. gma-miR156a is responsible for juvenile developments via repression of SPL transcription factor family. In contrast, gma-miR172a plays major roles in adult developmental phase by down-regulations of its target genes. These results will provide new insights on the genetic improvement of soybean.
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    Economic analysis of ameliorating subsoil constraints using subsoil manure in a cropping system
    Henty, Sam James ( 2019)
    To date, no studies have accounted for the effects of the yield and/or price risks that will occur over a run of years on the profitability of investing in ameliorating subsoil constraints within a cropping system. While addressing subsoil constraints is likely to increase grain yield, the key economic question for a grower is whether the income from extra grain produced covers the extra costs of ameliorating the subsoil. The focus of this thesis was the likely profit and risk of investing in ameliorating subsoil constraints. Investment costs and annual activity gross margins for a set rotation were used to estimate the economic performance of subsoil amelioration. The marginal change to the gross margin as a result of subsoil amelioration was assessed using partial discounted cashflow budgets. Risk analysis was used to assess the effect of price and yield variability on the mean and variance of outcomes from an investment in ameliorating subsoil constraints in cropping. This study shows an investment in subsoil amelioration was more profitable on average than an alternative investment earning 6% (real). The size of the expected extra yield benefits and longevity of these benefits are the most important factors for a grower to consider when assessing the likely merit (return and risk) of investing in subsoil amelioration in their own situations.
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    Understanding small and large milk fat globule phenotype variation in dairy cows through milk lipidomic characterisation
    Walter, Leonie ( 2019)
    Milk fat globules (MFGs) are spherical structures comprising a neutral lipid core that is surrounded by a three-layer membrane. This MFG membrane is of nutritional benefit for infants and adult consumers. Individual variation in the size of MFGs is observed within a herd of the same breed, and this milk production trait, if selected for through breeding programs, could be exploited for a more targeted milk production for specific technological streams. For example, large MFGs are desirable for butter making, whereas small MFGs are preferred for cheese making and direct consumption due to improved sensory properties and increased relative abundance of the beneficial membrane material. The initial experiment of this work aimed to determine how much the average MFG size is affected by on-farm and animal related factors within a herd subjected to the same diet and environmental conditions. Milk fat globule size of the whole herd was repeatedly measured over a one-year period and the effects of these parameters were estimated using a linear mixed effect model. This analysis showed that stage of lactation, parity and milk yield can affect MFG size, while the impact of fat yield, concentrate intake and number of milkings per day was limited. However, the individual variation within the herd outweighed the effect of individual factors, supporting the possibility of a genetically determined regulation of MFG size. Based on the data collected for the first experimental chapter, cows were selected for the second and third experiment, which aimed to characterise the small and large MFG phenotypes through an in-depth lipidomics analysis. This analysis included the characterisation of the fatty acid (FA) profile of the MFG core by gas chromatography and the identification of the whole milk lipidome through targeted liquid chromatography tandem mass spectrometry. The analysis of the MFG core FA profile revealed that the cows with the small MFG (SMFG) phenotype produced milk with higher proportions of unsaturated FAs compared to large MFG (LMFG) cows. This was related to an increased uptake of preformed FAs with a chain length of 18 or more carbons, which are sourced directly from the diet or from lipid mobilisation. This characteristic of the SMFG group could potentially lead to the production of milk with an improved nutritional profile. The results of the third experiment present the most extensive milk lipidomic analysis in the literature to date, with 301 detected lipid species. The results also revealed, for the first time, a potential role for ether phosphatidylethanolamine (ePE) in the regulation of MFG size, showing a higher relative abundance of ePE in the milk from LMFG cows. Ether PEs can reduce the fluidity of biological membranes and are predicted to promote lipid droplet fusion. The milk from SMFG cows, on the other hand, contained higher total phosphatidylcholine (PC) to PE ratios and a higher relative abundance of unsaturated PC species, both attributes that are predicted to prevent lipid droplet fusion. In the final experiment of this thesis an in vitro model using cells purified from raw milk and grown on permeable membrane supports was established, which offers the potential to test some of the novel findings of this thesis in future experiments.
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    Amelioration of the effects of cyclic heat stress in broiler chickens with dietary betaine and antioxidants
    Shakeri, Majid ( 2019)
    Controlling and managing environmental conditions is crucial to avoid hyperthermia and heat stress, and hence to successful poultry production and welfare. Heat stress (HS) is one of the most important environmental factors challenging poultry production globally. The detrimental effects of HS on broilers range from reduced growth rate to decreased poultry meat quality. Increasingly, there has been a focus on the use of nutritional supplements as a cost effective HS amelioration strategy. The use of antioxidants such as selenium, vitamin E and polyphenols to improve productivity via reduced levels of oxidative stress in tissues when broiler chickens were exposed to cyclic HS. Another molecule of interest is the osmolyte betaine, which is accumulated in cells under osmotic stress, but also has properties as a methyl donor and antioxidant. The principal findings were that cyclic HS impaired growth performance and physiological responses as increased respiratory rate and rectal temperature caused alteration in blood haematology as pCO2 reduced and blood pH increased which could lead to impaired product quality. While supplementation of betaine improved growth performance, including improved final body weight and this effect was observed irrespective of HS or additional antioxidants supplementation where it had no impact on blood haematology. The effects of HS and betaine were investigated on meat quality and it was found that HS reduced moisture content, increased lipid oxidation and reduced myofibril degradation, indicating reduced post-mortem proteolysis. This indicates worsening of meat quality as increased lipid oxidation reduces shelf life and myofibrillar degradation is important for the meat tenderisation process. When supplemented betaine was distributed to the breast muscle, and corresponded to improvements in meat quality. This was evidenced by reduced drip loss, lipid oxidation and reduction of Evans Blue dye (EBD) concentration in the breast muscle. Most importantly, supplementation of betaine reduced EBD concentration in vital organs such as kidney and ileum, indicating that betaine could have protective effects under HS. Furthermore, supplementation of betaine improved intestinal and breast muscle structure, including improved villous length and increased muscle fibre diameters which contribute to better growth performance and meat quality. Betaine supplementation was also performed against or with selenium, vitamin E or polyphenols. In general, selenium and vitamin E did not have additive effects on growth, whereas some benefits were iv observed for preventing lipid oxidation. The use of polyphenols improved growth rates to levels seen with betaine, indicating that they may also be useful nutritional agents for the amelioration of HS. Many studies have investigated the effects of the mentioned additives individually, but limited studies are available that whether the combination of them at different ages could ameliorate the negative effects of HS. This thesis aimed to investigate the effects of betaine alone or in combination with antioxidants on growth performance, meat quality and involved mechanisms to provide a better understanding on HS and betaine effects. In conclusion, betaine is a promising additive that can partially ameliorate HS effects. Despite of positive effects of antioxidants on meat quality, the additional effects of antioxidants warrant further investigation, particularly with respect to shelf life and oxidation.
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    Counterfeiting and Design-Driven Deterrents: Trust perceptions of anti-counterfeiting strategies for food and product packaging
    Francis, Caroline Maree ( 2019)
    Premium international goods are sought after by quality-concerned Chinese consumers who are increasingly turning towards cross-border e-Commerce and social media platforms with the expectation to avoid local food safety scares. Online retail of foreign brands however, does not guarantee protection against fraud. Counterfeit products are now commonly placed and are marketed equally besides the genuine items exposing consumers to vulnerabilities and heightening their perceived risk prior to purchase. Products are forensically scrutinised on multiple levels of security and further judged on authenticity. Australian Small-to-Medium Enterprises (SMEs), which make up 97% of all Australia’s workforce, are not well represented in the encouraged export trade opportunities as they fear export pathways that are increasingly complicated and changing. Compounding the problem is SMEs limited investment funds to upscale with expensive anti-counterfeiting solutions that may not clearly deliver on counterfeiting deterrent effectiveness and appropriateness to build consumer’s ‘initial trust’. This paper seeks to shed light on three key principles of the food counterfeiting phenomenon. Firstly, to map literature on food fraud, packaging counterfeiting with a focus on deceptive counterfeiting operations and tactics. Secondly, to investigate the unique trust relationship formation between risk adverse consumers and emerging, unfamiliar SME brands. Finally, the research will appraise anti-counterfeiting responses, from two perspectives: technological and design-driven, with a primary focus on cost-effective deterrent strategies catering to SMEs. Design/methodology/approach – A Mixed Methods approach was adopted to integrate the Participatory Action Research (PAR) methodology and co-creation strategies to later inform the larger online survey, triangulating the overall findings through qualitative and quantitative studies. Comparisons were made between Consumer and Industry insights as well as a cross-cultural study between Australia (low risk) and China (high risk) representing diverse levels of Risk Societies. The three studies investigated trust influences and drivers of Security Elements applied to food packaging founded on Technology and/or Design applications. The studies consisted of: (1) a Qualitative Multivariate Analysis, identifying the 5 Design-Driven Influencing Factors (DDIFs), (2) an Anti-Counterfeiting Workshop Model testing 30 security elements through the Case Study methodology, and finally (3) a Quantitative Online Study comparing two populations trust propensities and expectations of security elements on food packaging. Overall, the research identified that consumers acceptance of anti-counterfeiting elements can be strongly influenced by DDIFs that are appropriate for the food category (Fitted), multiple authenticity checks (Layered), connected to the country of origin (Identity Links), presents a reward attraction (User-Purposed), and technologies use a holistic design (Embedded). Design-Driven elements were identified as strong applicable to SME needs and were perceived as strong deterrent hurdles against counterfeiting threats. Future research is needed in developing education for designers to become the trust design guardians for the expansion and protection of the Australian food exporting industry.
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    Prevalence and Transmission of Antibiotic Resistance Genes in the Soil Environment
    Zhang, Yu Jing ( 2019)
    The increasing prevalence of antibiotic resistance genes (ARGs) in environmental settings and their potential acquisition by human and animal pathogens have become a global public health concern in the 21st century. The use of antibiotics in livestock industry and the enrichment of ARGs in animal manure and arable soils have engendered the concern that recycling of manure onto agricultural land could disseminate antimicrobial resistance to crops/vegetables, which might represent a potential route for migration of environmental ARGs from farm to fork. However, the pathways for transmission of ARGs from soil to plant remain unclear. Growing evidence points to the pivotal role of the environmental factors in influencing the prevalence of ARGs in the natural environment, while our understanding of the ecological and evolutionary environmental factors that contribute to the development and dissemination of antibiotic resistance in natural environment is lacking. It is imperative to decipher the diversity, prevalence, and environmental determinants of antibiotic resistance before we could design management approaches to control the transmission of environmental resistomes. A soil microcosm incubation experiment was conducted to compare the effects of poultry, cattle and swine manures spiked with or without the antibiotic tylosin on the temporal changes of soil ARGs. The high-throughput quantitative PCR detected a total of 185 unique ARGs (out of 295 targeted genes) among all the soil samples. The diversity and abundance of ARGs significantly increased following manure application. The level of antibiotic resistance gradually decreased over time in all the manured soils but was still significantly higher in the soils treated with swine and poultry manures than in the untreated soils after 130 days’ incubation. Tylosin-amended soils consistently showed higher abundances of ARGs than soils treated with manure only, suggesting a strong selection pressure of antibiotic-spiked manure on soil ARGs. The relative abundance of ARGs had significantly positive correlations with integrase and transposase genes, indicative of horizontal transfer potential of ARGs in the manure and tylosin treated soils. A glasshouse pot experiment explored the impacts of manure fertilization on the incidence of ARGs in the plant-associated microbiomes. Rhizosphere and phyllosphere microbiomes of cherry radish harbored significantly higher diversity and abundance of ARGs than root endophytic microbiomes. Manure application significantly increased the abundance of ARGs in the rhizosphere and phyllosphere, but not in the root endosphere, which is the edible part of cherry radish. Soil and plant microbiomes changed dramatically after manure applications. The bacterial abundance was the most important factor modulating the distribution patterns of soil and plant resistomes after accounting for multiple drivers. For the pot experiment of lettuce, rhizosphere soil samples harbored the most diverse ARGs compared with other components of lettuce. Comparing with cattle manure, poultry manure had a stronger impact on lettuce resistomes, reflecting by the significant increase of ARGs in rhizosphere, root endophyte and phyllosphere in the poultry manure treatment. Moreover, the overlaps of ARGs between lettuce tissues and soil were identified to propose two potential transmission routes (internal and external pathway) of ARGs from manured soils to different compartments of lettuce. A field survey experiment investigated the abundance, diversity and environmental determinants of ARGs in ocean and river beach soils. A total of 61 soil samples were collected from ocean and river beaches, which are hotspots for human activities and platforms for potential transmission of environmental ARGs to human pathogens. A total of 110 ARGs conferring resistance to eight major categories of antibiotics were detected. The core resistome including all the abundant and prevalent ARG subtypes was identified, which accounted for 66.9% of the total abundance of ARGs. The relative abundances of ARGs were significantly correlated with salinity-related properties including electrical conductivity and concentrations of sodium and chloride. Random forest analysis and structural equation modeling revealed that salinity was the most important factor modulating the distribution patterns of beach soil ARGs after accounting for multiple drivers. These findings suggest that beach soil is a rich reservoir of ARGs, and that salinity is a predominant factor shaping the distribution patterns of soil resistome. Overall, this research provided solid evidence that manure application may result in a significant increase of ARGs in agricultural soil and different parts of vegetables. The shared ARGs in the soil-plant system suggested a potential route of ARGs transfer from manure/soil to vegetables and highlighted the potential threats to human health by consuming raw vegetables grown in manure-amended soils. Soil salinity has been identified as the most important environmental factor in shaping the ARGs in beach soil environments, highlighting the importance of understanding the environmental stresses that maintain the environmental ARGs and developing effective strategies to minimize the dissemination of ARGs.
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    Regulation of Leaf Vein Density in C3 Rice
    Nawarathna, Ruwanthi Nayananjalee ( 2019)
    Stagnation of rice yield over last few decades is a major concern for food security, especially in Asia. A large part of the yield increase in food crops has come from breeding for abiotic and biotic stresses and responsiveness to nutrients. However, next step of change in rice yield should target improving photosynthetic capacity, better utilising the major inputs of sunlight and/or carbon dioxide. C4 species are efficient in utilising both sunlight and carbon dioxide and therefore, engineering or breeding of C4 like traits into C3 crop plants are major pathways to increase the yield potential. Reduced interveinal spacing or enhanced leaf vein density is known to be a primary prerequisite for C4 evolution. This study is carried out to identify the potential high vein density candidates in Sri Lankan traditional rice germplasm and rice from different regions of origin and further screened for variation in their other anatomical and physiological mechanisms that are associated with enhanced photosynthesis and crop production. We have successfully identified high vein density candidates in this study and investigated their changes of leaf vein density for exogenous application of Phytohormone, Brassinosteroid (Brassinolide), a Brassinosteroid inhibitor (Brassinazole) and Auxin (Indole-3-butyric acid), and for abiotic stress; elevated carbon dioxide levels, elevated temperature and water limited conditions to identify regulatory mechanism of leaf vein density. This study is providing insight to underpin regulatory mechanism of rice leaf vein density and further, pave a foundation to develop C4 like rice to meet future food demand while mitigating the impact of climate change.
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    Objective measures of sparkling wine quality
    Conde Lima, Bruna Cristina ( 2019)
    Sparkling wines are economically significant for the Australian wine economy. It is the only sector in the Australian wine industry that has been increasing in volume and value when compared to a decreasing fortified wine sector and the still wine sector. In Australia, sparkling wines are distinguished from other wine categories by the presence of carbonation, which is introduced naturally or artificially to still wines. And so, the appearance of a sparkling wine is of great importance as the presence of bubbles and foam changes the sensory experience of the wine consumer. The scientific community and industry have a great interest in uncovering the process and compounds which results in foam and bubble formation. Furthermore, although proteins are an excellent candidate to stabilize bubbles and foam, an official methodology for quantification of soluble protein content in sparkling wines has not been implemented. This thesis aims to uncover objective measures for quality assessment of sparkling wines by developing a robust, fast, accurate, and repeatable method to assess foam quality. Additionally, the specific objectives were i) to develop a robotic pourer to uniform and standardize the pouring process; ii) to develop a non-sparging automated methodology to quantify/assess foam characteristics of sparkling wines, using computer vision algorithms; iii) to quantify total soluble proteins in sparkling wines; iv) to uncover compounds other than proteins related to foam characteristics. Therefore, a novel methodology to characterize foam and bubbles in sparkling white wines was developed. The research presents a non-sparging technique to minimize product losses, that uses a robotic pourer to standardize the volume of wine poured with an automated arm, coupled with computer vision and image analysis to quantify and characterize foam in sparkling white wines. The method was successfully applied to find compounds influencing bubbles and sparkling wine foam. The compounds uncovered included proteins, amino acids, and polyphenols, which was validated by the addition of target compounds to sparkling wines. Modifications for the bicinchoninic protein assay was presented to application in wine, and the soluble protein content was correlated to foam parameters obtained by the robotic pourer and computer vision algorithms. Finally, preliminary results on the effects of wine ageing was presented. In summary, this research has uncovered objective measures of sparkling wine quality, providing practical information for industry and research centres, to allow monitoring and control of wine quality and uncovering compounds influencing foam and bubble characteristics.