Agriculture and Food Systems - Theses
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ItemSurface Modification of Coal and its Application to Mitigate Ammonia Loss from Livestock Manure( 2022)Nearly all global ammonia (NH3) emissions are emitted from agricultural sources, including ammonia-based fertilizers and livestock manure, which can have significant negative impacts on both human health and the natural environment. Ammonia emissions from livestock manure represent a large loss of nitrogen (N) nutrients that would otherwise be available for plant growth. Application of lignite has been demonstrated to be a practical and cost-effective method to reduce NH3 emissions from cattle feedlots. However, widescale implementation of such technology is limited because lignite mines and intensive livestock production systems are not always located near each other and the high water content of lignite makes the long distance transport uneconomical. Therefore, this thesis investigates the feasibility of using a thermal air oxidation method to dewater lignite and to surface modify the more commonly occurring and geologically abundant black coal (BC) and coal tailings (CTs) from coal washing process as alternative materials to lignite to reduce NH3 loss from livestock manure. The first phase of the research determined the optimum oxidation temperature for lignite dewatering and BC surface modification and evaluated the gaseous NH3 and aqueous ammonium (NH4+) adsorption before and after treatment. Lignite treated at 200 degrees Celsius exhibited the highest adsorption capacities of 76.4 and 3.7 mg g-1 for NH3 and NH4+, respectively. The water content of lignite was decreased from 61.6 to 4.2% with an enhanced apparent activation energy of combustion, suggesting that the thermal oxidation process would not increase the spontaneous combustion risk of lignite. Characterization of the surface chemistry indicated that these enhancements originated from the partial oxidation of lignite surfaces. The acidic surface functional groups on lignite played an important role in NH4+ adsorption. Similarly, the thermal air oxidation method used in lignite dewatering was then employed for the surface modification of a BC. The NH3 adsorption capacity of BC treated at 300 degrees Celsius achieved an 11-fold increase (49.7 mg g-1) compared with the untreated BC. The concentration of acidic surface functional groups on BC was significantly increased after treatment. Moreover, NH3 adsorption capacity showed a linear relationship with the concentration of acidic surface functional groups, indicating NH3 adsorption of BC was enhanced due to interactions between NH3 and acidic functional groups from thermal air oxidation. In the second phase, the dewatered lignite and surface-modified BC (treated at 200 and 300 degrees Celsius, respectively) displayed the greatest NH3 adsorption capacity were chosen to investigate the capacity of these materials (applied at 30%) to reduce NH3 loss from livestock manure through a laboratory incubation experiment. Results showed that dewatered lignite and surface-modified BC reduced NH3 volatilization from cattle manure to a similar extent as the raw lignite. Moreover, the adsorption and immobilization of manure ammoniacal N induced by coal materials were identified as key drivers in reducing NH3 loss from manure, outweighing the pH effect. In the phase three, CTs were treated at different temperatures and varying duration to investigate the reaction kinetics of formation of acidic surface functional groups on coal surfaces and elucidate the NH3 adsorption mechanisms. The CT treated at 300 degrees Celsius for 5 hours showed an NH3 uptake of up to 52.5 mg g-1, which was a 25-fold increase in comparison to the untreated CT. Spectroscopic analysis showed that the acidic surface functional groups such as carboxylic groups present on treated CT surfaces could react with NH3 via an acid-base reaction leading to the formation of NH4+ but they were also involved in the formation of amides. A relatively low activation energy of 50.2 kJ mol-1 for the formation of acidic surface functional groups on CTs was obtained using an Arrhenius analysis in the temperature range of 200 – 300 degrees Celsius of oxidation, indicating that thermal air oxidation is a simple, rapid, and effective surface modification method to generate acidic surface functional groups on coal surfaces to capture NH3. Overall, the findings of this study provide a fundamental insight into the effectively design and development of coal-derived adsorbent materials to capture NH3 and show promise for future utilization of modified coal materials for mitigation of manure NH3 emissions in livestock farms.
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ItemPositive Human-Animal Interactions, Early Life Experiences and Stress Resilience in Pigs( 2022)Pigs in intensive production systems routinely encounter several challenging situations including abrupt weaning, painful husbandry procedures, intense contact with stockpeople, and exposure to novel social and physical environments. The ability of pigs to cope with these routine stressors has implications for their welfare and productivity and may be affected by their previous experiences with humans. Furthermore, experiences that occur early in life, including interactions with the dam, the physical environment as well as early experiences with humans, may have a profound effect on the development of stress coping mechanisms that impacts how pigs cope with stress throughout their lives. The aim of this thesis was to examine the effects of positive interactions with humans and early life human and housing experiences on stress resilience in pigs. Stress resilience was measured based on: 1. behavioural and physiological responses to stressors such as routine husbandry and management practices, isolation, novelty, and humans; 2. basal behavioural and physiological measurements that reflect how pigs cope with their general environment; and 3. measurements of biological fitness. Overall, positive interactions with humans, including patting, stroking and scratching pigs, reduced pigs’ fear of humans and their stress responses to routine husbandry and management practices imposed by stockpeople. Sows that received 2 min of daily positive human contact during gestation showed less avoidance of and more interaction with stockpeople imposing pregnancy testing and vaccination in the home pens, and piglets that received 3 or 5 minutes of regular positive human contact showed less escape behaviour and vocalisations during husbandry procedures in the lactation period. Providing opportunities for positive human interaction from 0-4 wk of age was extremely effective in reducing fear of humans, based on positively handled piglets showing increased approach and interaction with an unfamiliar human at 2 and 3 wk of age. Although the effects of handling on fear of humans appeared to weaken over time, there was evidence of early positive human contact resulting in pigs showing less fearful responses to a human at 6, 9 and 14 wk of age, indicating that some reduction in fear of humans lasted well beyond the period when the handling treatment was imposed. In addition to reducing fear of humans, there was evidence that early positive human contact conferred broader effects on stress resilience. Early positive handling reduced pigs’ fear of a novel object at 3 wk of age, escape behaviour after weaning, and cortisol concentrations after weaning and after isolation at 7 wk of age. Furthermore, early positive handling reduced pigs’ injuries and increased serum concentrations of brain-derived neurotrophic factor (BDNF) at 4 wk of age, with limited evidence indicating similar effects on these measurements much later in life at 17 wk of age. The early housing environment had a considerable effect on the human-animal relationship, with pigs reared in farrowing crates showing less fear of humans at 2, 3, 4 and 6 wk of age compared to pigs reared in loose farrowing and lactation pens with more space, physical complexity, and opportunity for interaction with the sow. During the lactation period, piglets in loose pens showed more play behaviour and less repetitive nosing of pen mates and had higher concentrations of serum BDNF compared to piglets in farrowing crates, but surprisingly, they were less able to cope with several stressors before and after weaning. During the lactation period, loose pen piglets showed more avoidance of a novel object, a greater intensity of escape behaviour during capture by a stockperson, and more injuries at 2 wk of age. After weaning, loose pen pigs showed more escape behaviour, less inactivity and had higher cortisol concentrations. At 7 wk of age, loose pen pigs showed more vocalising in a novel area and had higher cortisol concentrations after isolation, and at 21 wk of age, they showed more baulking when being moved out of the home pen by a stockperson. This research showed that positive interactions with humans can ameliorate the stress associated with routine husbandry practices involving stockpeople. When imposed early in life, positive handling had an extended effect on reducing pigs’ fear of humans and appeared to foster stress resilience in a general capacity, based on fewer injuries, higher BDNF concentrations and reduced responses to challenges such as novelty, weaning and isolation in positively handled pigs. In addition to reducing fear of humans through habituation and conditioning, brief and regular close human contact early in life may provide a minor challenge to overcome, that improves the competence of pigs to cope with other types of challenges faced in the future. This research also demonstrated considerable differences in the stress resilience of pigs reared in the two housing treatments studied. While piglets in the loose system showed more play behaviour and had higher BDNF concentrations during the lactation period (both of which are linked to stress resilience) they showed far less flexibility in response to stressors such as routine husbandry practices, weaning, isolation, and exposure to novelty and humans. Piglets in the loose system were reared in a more isolated environment with less contact with people and other pigs and less visual stimulation in general. This may have resulted in loose pen piglets having fewer opportunities to learn to cope with small challenges such as frequent and/or close exposure to stockpeople and other pigs, thus increasing their vulnerability to stress. In addition, heightened maternal responses of loose pen sows towards stockpeople may have increased loose pen piglets’ fear of humans. More research is needed to determine the specific features of the early housing environment that affect both immediate and long-term fear and stress responses of pigs. Overall, this research: 1. showed that the early human and housing environment for pigs can have both immediate and longer-term consequences on stress resilience; and 2. contributed to a growing body of work showing that humans are a key determining factor in the welfare of pigs.
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ItemEffect of Heat Stress on Sheep Meat Quality( 2022)Heat stress (HS) is one of the greatest challenges facing the global livestock industry. An increase in global temperature and relative humidity (RH) is likely to compromise animal welfare, production, and meat quality during hot summer months. While the negative effects of chronic HS on sheep are well established, the influence of short-term HS are comparatively less known and especially, there are few studies reporting impact of HS on sheep meat quality which is still not clear. Therefore, this PhD project was designed to demonstrate the effect of various heat exposure durations on meat quality of sheep and identify the differences, if any, among different sheep breeds. This PhD thesis consists of three animal experiments designed to investigate the effect of short-term HS on physiology and meat quality of different sheep breeds. Because the duration of heat exposure which could lead to negative impact of HS on meat quality of different sheep breeds was not clear, the first animal study was a preliminary experiment to confirm the negative effects of HS period on different sheep breeds meat quality. In this experiment, two wool type (Merino, Southdown) and two hair type (Dorper and Wiltshire) breeds of sheep (n=5 of each breed) were allocated to either thermoneutral [TN; 18-21 C, 45-55% relative humidity (RH)], or heat stress (HS; 28 C-38 C, 40-60% RH) conditions (n=10 of each group) for two weeks to assess the effect of two weeks HS on physiological, blood, and meat quality parameters. Compared with TN, two weeks HS significantly increased the respiration rate (RR) and rectal temperature (RT) of sheep but had no impact on retail meat colour, water holding capacity (WHC) and Warner-bratzler shear force (WBSF) for five days high oxygen map packaging display. Among four breeds, Merino showed higher L*, b* and purge loss than other breeds, Merino and Dorper had higher cooking loss than Southdown and Wiltshire. This study provided some preliminary evidence that HS can cause negative effects on meat quality of sheep and needs to be investigated further to select an adaptive and productive sheep breed for changing climate. The second animal experiment compared the heat tolerance capacity of 2nd cross and Dorper lambs after two weeks HS treatment based on growth, physiological and retail meat quality parameters. Forty-eight Dorper and 2nd cross [Poll Dorset x (Border Leicester x Merino)] lambs (38-42 kg; 4-5 months old) were allocated to either TN (18-21 C, 45-55% RH), or HS (28 C–38 C, 40-60% RH) conditions in a 2 x 2 factorial design for two weeks. Compared with 2nd cross, Dorper lambs had a lower (RR) and rectal temperature (RT) and exhibited less decline in body weight under HS. 2nd cross lambs showed a higher body weight gain than Dorper under TN conditions. HS increased a* and chroma of the Longissimus thoracis et lumborum (LTL) of second cross lambs over 10 days retail display but had no impact on Dorper lambs. In conclusion, Dorpers showed higher heat tolerance compared with second cross lambs during the two weeks HS exposure condition. The third animal experiment assessed the influence of short duration heatwaves (HW) on sheep physiological, blood biochemical profile and retail meat quality parameters. Seventy-two second-cross lambs (Poll Dorset x (Border Leicester x Merino)) were selected and exposed to either one, three or five days of stimulation heatwaves (HW) or TN (28-38 C and 40-60% RH; 18-21 C, 40-55% RH) conditions in climate-controlled chambers. Lambs exposed to one to five days of HW exhibited higher RR, RT, skin temperatures (ST) and heart rates (HR) compared to lambs exposed to an equal duration of TN conditions. HW also had significant impact on blood gas parameters which included higher blood pH, and lower CO2, Ca2+, Na+, HCO3- and Cl-. However, lambs’ ileal histology and GSSG:GSH of intestine and muscle was not influenced by HW. Longissimus thoracis (LT) muscle showed higher total antioxidant capacity (TAC) in HW condition, but the TAC of intestine and blood had no difference between HW and TN groups. In terms of determinants of meat quality, HWs had no significant effects on muscle metabolism (rate and extent of pH decline, muscle glycogen and lactate content) and meat quality (cooking loss and shear force). Similarly, there were limited impacts of one to five days of HW on the colour (L*, a*, b* and R630/580) and drip loss of the LTL and semimembranosus (SM) muscles during four days’ overwrap retail display. These results suggest that short-duration HWs (one to five days) lead to significant negative effects on sheep physiology but may not effect postmortem muscle metabolism and meat quality. In conclusion, this thesis demonstrated that short-term HS (less than two weeks) are a significant challenge for sheep physiology and welfare but have limited impact on some of the meat quality attributes while have no impact on other meat quality parameters (water holding capacity, shear force etc). These results are explained by the fact that sheep can cope with short duration by recruiting some physiological and behavioral responses which are not severe enough to cause oxidative damage to muscle or intestinal tissues which are seen under chronic heat stress. Compared with wool type breeds, hair type breeds have better heat tolerance and are less affected by short-term heat stress.
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ItemEvaluation of nitrogen fertiliser decisions by rice farmers: accounting for the effects of nitrate on water quality for communities in cascaded village tank systems in Sri Lanka( 2022)Nitrogen fertiliser is an essential input to agriculture and contributes to enhancing the productivity of cereal production around the world. The use of Nitrogen fertilisers has caused environmental pollution, especially water pollution, which has impacted the ecology of waterways and human health. Rice is a staple food in Sri Lanka and fertiliser application to rice has been supported by fertiliser subsidy policies since the 1960s. Nitrogen fertiliser management in rice fields is one of the causes that can contribute to elevating the Nitrate in water bodies in Sri Lanka, especially in Dry Zone areas. Hence evaluations of fertiliser applications to rice are important for sustaining rice production while reaching environmental standards. A literature review suggested that the link between source and sink is important in managing water pollution by Nitrogen fertiliser. Nitrate is highly soluble and mobile, hence easily lost from the agricultural soil. Leaching, runoff, and lateral flows of Nitrate are the most common pathways for Nitrate discharge and transport from source to sink. Fertiliser management has been identified as the most common, feasible and viable solution for addressing agricultural Nitrate water pollution. Experimental evidence has confirmed that reduction of Nitrogen fertiliser on agricultural lands can reduce Nitrate discharge and yield losses from such fertiliser reductions are small. Experimental evidence from field studies shows that the biophysical trade-off between reduction of discharge and rice yield is low. However, those studies have lacked proper quantification of stochastic variability, economic evaluation and link between source and sink. Most have not considered the Nitrate load at the source and transport to the sink. Therefore, this study aimed to quantify the implications for stochastic crop profit when improving water quality through crop fertiliser management practices and policies. The study analysed key underlying bio-physical processes linked to the dynamics of Nitrogen in the soil and water and the rice yield responses to Nitrogen fertiliser applications in Thirappane Tank Cascade in the Dry Zone of Sri Lanka. Soil-plant agronomic and Nitrate transport models were coupled to obtain response functions which were integrated into the economic model with the objective of profit maximization. Farm household level data were obtained from a survey of around 50% of farmers in the Cascade. The rice yield and Nitrate discharge responses to applied Nitrogen fertiliser were identified across the different seasons and soil types using the Agricultural Production Systems sIMulator (APSIM)- Oryza model for the main season of rice cultivation, Maha or wet season and Yala or dry season. The simulated yields were validated with the temporal district average rice yields and rice yields at farmer’s field in 2018 for three soil types. The validation confirmed that the simulated yields are representative of the study area. Further, simulated rice yields increased at a decreasing rate for increased Nitrogen applications. In contrast, simulated Nitrate leaching and runoff increased at an increasing rate for increased Nitrogen applications. Rice yield and Nitrogen discharge varied across the soil types and seasons over time. Potential rice yields were higher in Low Humic Gley (LHG) poorly drained soil compared to Reddish Brown Earth (RBE) imperfectly drained soil. RBE well-drained soil had the lowest yield potential. Higher Nitrate leaching was observed in RBE soils compared to LHG soil in both seasons. In comparison to leaching, the runoff was small and occurred only in the Maha season. Nitrate transport within the Cascade was predicted using coupled water balance and Nitrate transport models for varied Nitrogen rates. The results showed that Nitrate transported into sink tanks from the rice cultivation areas in the source tank varied with the rate of Nitrogen fertiliser application and the area of rice cultivation at the source tank. Nitrate discharge at the source did not vary much between tanks. However, seasonal Nitrate transport was substantially different among tanks in the Cascade Simulations of Nitrate-N revealed that the Nitrate-Nitrogen concentrations exceeded the minimum limit for eutrophication but did not exceed the drinking water quality level (10 mg of Nitrate-N/l). The economic evaluation used the production function approach with the profit maximization objective. When considering spatial and climatic variability, uniform Nitrogen management can be economically and environmentally inefficient. Low, medium, and high yield outcomes were defined based on climatic variability over the years using the 10th, 50th and 90th yield percentiles of yield responses to Nitrogen fertiliser. Further, optimal rates of Nitrogen were identified for the specific soil types and seasons. The rice yield responses to Nitrogen were statistically significant except for the lowest yield percentile in the RBE well-drained soil in the Maha season. The fertiliser price plays a vital role in deciding optimal Nitrogen rates. Fertiliser prices were varied in the analysis considering policy regulations and market prices. The estimated Economic Optimum Rate of Nitrogen (EORN) and Social Optimum Rate of Nitrogen (SORN) confirmed that the optimal rates varied with season, soil type, yield outcome and Nitrogen price. Higher levels of Nitrogen fertiliser were needed to achieve maximum profit in LHG soil than in RBE soil. But comparably higher profits can be generated in LHG soil compared to RBE soil. Further, the optimal rate of Nitrogen declined with improving seasonal climatic conditions. The respective rice yields were increased. When seasonal climatic conditions are more favourable, higher rice yields can be achieved with a lower Nitrogen rate and vice-versa. The Nitrogen fertiliser price is vital for fertiliser decisions and profitability in rice cultivation. When the price of Nitrogen is subsidized, the optimal rate of Nitrogen is higher than under the market price. Most farmers in the Cascade applied Nitrogen fertiliser at rates below both the EORN and SORN. These decisions could be due to farmers' risk aversion and the affordability of fertiliser by farmers. However, a small fraction of farmers applied Nitrogen above the EORN and SORN. Operating at the SORN, which accounted for Nitrate pollution in tank water, would help to maintain water quality. The shift from EORN to SORN, which is associated with different amounts of Nitrogen fertiliser reduction, was sensitive to Nitrogen prices. The greatest reduction in Nitrogen fertiliser was needed at highly subsidised prices. At the actual market price the reduction in Nitrogen fertiliser from EORN to SORN was less than 10 kg Nitrogen / ha in any season, soil or yield outcome combination. Operating at SORN would reduce the Nitrate transported into water and improve the water quality in the Cascade. When the marginal private profitability of Nitrogen application very small (at EORN), the yield response curve to Nitrogen applied becomes relatively flat, and a small decrease in Nitrogen application from EORN to SORN has little effect on the yield and change in farmer's welfare. The findings of this simulation study have shown that blanket Nitrogen fertiliser applications (the current Department of Agriculture recommendation) are not economically profitable based on the yield response functions and the prices for fertiliser and rice. The Nitrogen rates applied in rice fields should include considerations in the variability of soil, season, and climate.
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ItemEconomic Impact of Government Policy of Banning Glyphosate in Sri Lanka: The Case of the Tea Industry( 2022)Tea is an important agricultural industry in Sri Lanka that supports the economy by contributing to the Gross Domestic Production, earning foreign exchange and providing livelihoods for many people. The sustainability and production capacity of the tea industry in Sri Lanka has been challenged by some government policy decisions. The island-wide ban on Glyphosate that was in place from 2015 till 2018 adversely affected the tea industry and participants in it. In this study, the economic impact of the Government policy of banning Glyphosate on the tea industry in Sri Lanka is evaluated by investigating how the ban affected the farm sector and other key market levels in the whole tea industry. The study was conducted by gathering detailed information about the effects of the ban from tea industry participants and stakeholders using primary and secondary data collection methods. An Equilibrium Displacement Model on the tea industry was developed to measure the economic losses of the ban on main market levels in the value chain. The withdrawal of Glyphosate from tea producers’ farm management decision choices has directly affected weed management; essential in commercial tea cultivation for sustained high yields, quality and profit. Tea grower groups, regardless of the size of their operation have experienced quantitative and qualitative losses with increasing weeding costs, costs of production and narrowed gross margins as they have substituted for Glyphosate with alternative weed management methods. Moreover, the ban has also resulted in an unintended consequence, a decline of tea exports in the international tea market. An annual loss of Rs. 3.5 billion on the tea industry was estimated as the direct impact of the Glyphosate ban while the unintended consequence was estimated to have led to a loss of Rs 0.35 billion. The findings of the study have implications for policy makers, decision makers at the farm level, key participants in the value chain of the tea industry and other researchers. Policies introduced to minimize suspected and actual adverse impacts resulting from market failures ought to be executed with full attention given to the scientific, economic, social and political realities of the case at hand, and the likely consequences for the affected parties and their responses.
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ItemThe role of skilled migration in Australian dairy farming and implications for agricultural workforce development( 2020)Employment of a migrant workforce is a key strategy for both the Australian Government and employers to address workforce labour and skill shortages. In the Australian dairy farm sector, structural change has increased the demand for employees with management and technical skills. This led some employers to employ skilled migrants under Temporary Work (Skilled) visas (subclass 457). The 457 visa was introduced by the Australian government in 1996 and abolished in 2017. In March 2018, a new subclass 482 visa was introduced but restricted skilled migrants’ eligibility pathways to obtain Australian permanent residency visas. Focusing on the 457 visa, this thesis examines the research question: "How does the attraction and retention of skilled migrants contribute to development of the dairy workforce?" While skilled migration has been an option for employers in agriculture, the use of the 457 visa in dairy farming in Australia has not been investigated until now. In particular, that involves how the 457 visa has supported a long-term workforce development strategy by sourcing skilled labour from the international labour market. The conceptual framework for this study integrates psychological contract theory, relating to the employment relationship between skilled migrants and farm employers, with theories of workforce development systems, relating to the sectoral and institutional arrangements governing the workforce. The conceptual framework was applied in the design of the research and in the analysis and interpretation of data. A qualitative case study research design was implemented involving semi-structured interviews with 20 case study farm employers and nine of their skilled migrant employees. A focus group was conducted with 10 industry stakeholders, and three government policy makers and three migration agents took part in semi-structured interviews. The qualitative data analysis tools of grounded theory, including coding, categorisation, conceptualisation and constant comparison of data were applied to derive the findings. The primary motivation of case study farmers in seeking skilled migrant employees under visa 457 was the limited availability of skills in the domestic workforce that were aligned to their current and future skill requirements. These skills requirements were significantly broader than qualifications and experience and were found to include attributes associated with organisational commitment and job involvement. Skill requirements were also contingent on the business stage of the farm. The case study farm employers were able to align the skills of the 457 visa employee with their future business goals, irrespective of whether the business life cycle was in a growth, mature or decline stage. Skilled migrant employees under 457 visas choose Australian dairy farm employment to meet their future needs, such as becoming an Australian permanent resident, and to access Australian dairy industry skills and knowledge. Both the employer and skilled migrant played critical roles in determining the quality of the employment relationship, which, in turn, influenced skilled migrant retention. At the pre-employment phase, a shared understanding between the employer and skilled migrant of each other’s future needs from the employment was significant in both the execution of the formal employment contract and in establishing mutual expectations for the employment relationship. A skilled migrant employee’s awareness of an employer’s provision of socio-cultural support was also found to be key in their decision to accept a job offer and in the quality of the subsequent employment relationship. Significantly, perceived strong employer support to the skilled migrant in accessing permanent residency was found to be a key component of mutuality in the psychological contract between the skilled migrant and their farm employer and was associated with both the retention of the skilled migrant and achievement of farm business outcomes. The workforce governance actors of government, community, industry, and employers play different roles in attracting and retaining skilled migrants on dairy farms. The effectiveness of the agricultural workforce development system is constrained when there is a lack of alignment between these actors with respect to supporting pathways for skilled migrants to achieve permanent residency, and recognition of the critical intermediary role of migration agents during the pre-employment phase. Such systemic misalignment impacts on how successfully skilled migrants and their farm employers achieve mutuality with respect to the psychological contract between them. In turn a misalignment of mutuality can undermine achievement of the farm business goals and skilled migrants’ personal aspirations. The findings of this research highlight how the policies and strategies that support agricultural workforce development strongly influence opportunities and constraints at the business enterprise. This study highlights the need for coordination and alignment across all stakeholders within the dairy workforce development to ensure that policies such as Visa 457 deliver benefit.
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ItemFunctional genomics to discover biologically relevant regulatory variation( 2022)Genomic prediction aims to predict the breeding value of animals based on their genotypes. It does this by looking for associations between genotypes and the phenotype in a training population. Animals which share these genotypes are then predicted to share the same phenotype. However, the association between a genotype and phenotype could be based on linkage disequilibrium (LD) between the variant identified and the causal mutation which is directly affecting the phenotype. Therefore, in populations where LD is different to the training population, such as other breeds or in subsequent generations, the association between genotype and phenotype would not occur, and genomic predictions are less accurate. It would therefore be advantageous to use the genetic variant which is directly affecting the phenotype (the causal variant) in our predictions. Identifying causal variants in cattle is difficult as there are millions of variants in the bovine genome. Work in humans shows that most variants affecting complex traits lie in non-coding functional regions, where it is thought they alter regulation of gene expression. However, functional regions are not well annotated in non-model organisms. This project annotated functional regions directly in dairy cows using a laboratory technique called ChIP-seq (Chromatin Immunoprecipitation followed by sequencing) to assay for histone modifications and a transcription factor, which are thought to mark functional regions. This was done in two ways, (1) across multiple tissues in three lactating dairy cows and (2) across multiple individuals in a single tissue (the mammary gland). Using this dataset, I annotated putative functional regions in dairy cows across a wide variety of tissues and individuals, and by doing so substantially increased the functional annotation of the bovine genome. As seen in other species, causal variants for gene expression and other complex traits were enriched in these functional regions, particularly at regions correlating with gene expression and thus identified as putative regulatory regions. Additionally, genetic sources of functional variation across 100 animals were identified by associating variation in peak height, across and within individuals, with genetic variation. These are also potential causal variants, which overlapped with eQTL and were found in putative transcription factor binding sites. The results of this study confirm that functional regions are involved in regulating gene expression, and that functional data can help to identify causal variants for complex traits. This work also provides an invaluable dataset of putative functional regions in the bovine genome. Future work will investigate whether the potential causal variants identified here improve genomic predictions.
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ItemApplication of extrusion technology for hempseed (Cannabis sativa L.) processing by-products( 2022)The seed of low-tetrahydrocannabinol (THC) hemp (Cannabis sativa L.) is an emerging food source with its recent legalization for cultivation and consumption in Australia from 2017. Industrial processing of hempseed generates oil cake and hull as by-products. These by-products are rich in protein, fiber and amide-containing phenolic compounds. Processing has the potential to further improve their nutritional value, functionality and applicability in the food industry. Extrusion is versatile food processing technology that combines multiple mixing, cooking and compressing processes, and has been utilised to prepare wide range of food products with high nutritional values as well as textural appeals. Considering the potential of extrusion, this thesis comprehensively investigated the effects of extrusion technology on the three major nutrients (protein, polyphenol, fiber) in hempseed by-products, specifically covering the: (i) proteome, structure and functionality of hempseed oil cake protein (Chapter 3), (ii) identification, quantification and biological activities of cake (Chapter 4) and hull (Chapter 5) phenolic fractions, (iii) absorption and cellular antioxidative effect of hempseed hull phenolic amides (Chapter 6), and (iv) the physical, functional and microbiota-modulating properties of hull fiber (Chapter 7). A full factorial design was used to complete the extrusion runs in the chapters of this thesis, allowing relative contribution of each individual parameter (i.e. moisture, screw speed, temperature), and their two- and three-way interactions to be determined. Extrusion, at selected combinations of parameters, improved the free-form and total amino acid content, protein solubility, water and oil binding capacity, emulsion capacity and in vitro digestibility of hempseed oil cake protein fractions (Chapter 3). The proteome-functionality correlational relationship was explored for the first time to identify protein groups or peptides with superior-inferior functionality. In addition to protein, hempseed oil cake contains a high concentration of unique amide-containing phenolics (phenylpropionamides), known as lignanamides and hydroxycinnamic acid amides. The proportion of free phenolics, flavonoids, phenylpropionamides, in vitro alpha-glucosidase and acetylcholinesterase inhibitory activities were enhanced in cake extruded at relatively lower moisture (30 %) and higher screw speed (300 rpm) (Chapter 4). At least 26 phenylpropionamides, such as N-trans-caffeoyltyramine and cannabisin A/B, were identified using LC/MS-MS, with the possibility of novel compounds and biological activities that are yet to be characterised. The hull of hempseed is richer in phenolic amides and fiber compared to the oil cake. Extrusion, at all parameters, increased the total phenolic, free in vitro antioxidant (DPPH/ABTS) activities, and total phenylpropionamides (Chapter 5). A novel absorption trial of phenylpropionamides and follow-up cellular antioxidant assay were performed in Chapter 6 using the intestinal Caco-2 cell culture. Significantly improved absorption of major phenylpropionamides, such as cannabisin B, was observed after extrusion and extraction of free phenolics fraction. The free fraction of extruded hempseed hull showed promising cellular antioxidative properties, protection of Caco-2 cells challenged by t-BOOH, and altered the transcriptome of the cells as indicated from RNA-Seq findings. In addition, extrusion improved the properties of hempseed hull fiber in terms of its solubility and content of total dietary fiber, water and oil binding capacity, viscosity in oil dispersions, inhibition of starch retrogradation (Chapter 7). 16 rRNA gene sequencing and metaproteomics further demonstrated the microbiota-modulating properties of hempseed hull fiber, with the increase in Megasphaera elsdenii and Lactobacillus spp. population, and their expressed protein of ferredoxin and enolases, respectively. Overall, this research could facilitate industrial utilization of hempseed by-products by extrusion.
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ItemFactors influencing consumer response to wet and dry-aged mutton( 2021)Mutton is the term used to describe the meat from older ovines (older than 2 years); this meat is considered to have inferior eating quality when compared to lamb and as a result returns to producers are reduced for mutton animals. The sheepmeat industry seeks to improve returns for mutton, and the application of dry ageing to mutton is proposed as a post mortem intervention that will add value. As dry aged mutton is a novel product, the consumer response to this product is largely unknown. To assess the viability and feasibility of dry aged mutton products, this thesis investigated the retail opportunity for dry aged mutton from the perspective of the consumer, producer and foodservice. The thesis also developed understanding of the influence of ageing method and meat quality factors on consumer eating quality assessment and liking, as well as the extrinsic consumer related factors affecting consumer response to dry aged mutton. These investigations leveraged both qualitative and quantitative consumer methodologies, with the overarching aim of developing insights that would address knowledge gaps in the developing dry aged mutton supply chain. A cross cultural study comparing responses to sheepmeat from Asians (export market consumers) and Australians (domestic market consumers) found these groups assess meat quality differently; Australians rely on labels, are sceptical of provenance stories and prefer Australian product. Asian consumers make quality assessments based on visual attributes and find provenance stories compelling, but they were not particularly compelled by the “Australian made” label. These findings indicate different marketing strategies are required for the two markets. For both consumer groups the recommended channel for dry aged mutton products would be foodservice or retail butchers as these outlets take away the uncertainty associated with purchasing and preparing an unfamiliar product. The development of dry aged mutton dishes in collaboration with chefs followed by consumer assessment of the dishes for liking, premiumness and fit to foodservice outlet demonstrated that these products were well liked by consumers, could be considered premium, and that dry aged mutton was a versatile product that suited a wide range of foodservice outlets ranging from casual to fine dining. An ageing trial lasting 8 weeks and comparing wet and dry aged mutton leg and loin found that yield was reduced in the dry aged treatment as opposed to the wet aged, and that these losses increased with ageing period. There was opportunity to mitigate yield losses by selecting carcases that were heavier, had increased levels of subcutaneous fat, and by fabrication of retail cuts from dry aged primals. Consumers (n=540) assessed the eating quality (tenderness, juiciness, liking of flavour and overall liking) of the longissimus thoracis et lumborum (LTL) and semimembranosus (SM) derived from the ageing trial according to MSA sensory protocols (total sample n = 3240). No differences in consumer ratings were found due to ageing method but extending the ageing period beyond 14 days improved eating quality for both muscles. Consumers most often graded LTL as “better than every day quality” and they were willing to pay (WTP) 36.60 AUD/Kg for this grade, SM was most often graded as “good everyday day quality” and WTP was 26.90 AUD/Kg. These prices were similar to current Australian retail pricing for lamb, and if mutton can achieve these prices, it would be a significant price uplift. The ageing trial result of “no effect of ageing method on eating quality” was unexpected. A check all that apply (CATA) investigation into the consumer characterised flavour profile of wet and dry aged mutton confirmed that consumers can differentiate ageing treatments; dry aged mutton was associated with increased caramel and roasted flavours while the wet aged mutton was associated with increased sheepy and metallic flavours. Further subsequent investigations into the consumer related factors affecting the eating quality assessments of the MSA ageing trial indicated that consumers could be segmented according to their liking for mutton. Agglomerative hierarchical cluster analysis revealed 3 consumer clusters; Cluster 1 (n = 219) appreciated mutton and rated it highly, Cluster 2 (n = 235) found mutton acceptable and Cluster 3 (n =79) did not like mutton. Preference maps were prepared for the three clusters; all three clusters were found to prefer LTL over SM, but Cluster 1 demonstrated a preference for dry aged mutton over wet aged, Cluster 2 had no ageing method preference and Cluster 3 preferred wet aged mutton over dry aged mutton. Characterisation of these clusters indicate that consumer familiarity with mutton and ethnicity has a role to play in the observed preference patterns. The thesis concludes that dry aged mutton has value as a premium niche product targeted at those consumers who appreciate mutton, and that there is an opportunity for mutton in local and export markets (not dry aged) that warrants further industry exploration, especially for the LTL which has good eating quality.
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ItemUsing data mining to improve the prediction of key nitrogen loss from terrestrial ecosystems( 2021)Nitrogen (N) losses through nitrification, denitrification and nitrate leaching in terrestrial ecosystems reduce fertiliser N use efficiency (NUE), affect environmental quality and human health. In the past 50 years, many individual studies both on-site and in laboratories have been carried out to investigate N loss from different pathways. However, field measurements of N dynamics are generally time-consuming, expensive and some of the processes are quite difficult to measure. Process-based models have been developed to better understand the complex, multivariate and unpredictable N cycling by integrating soil, environmental and management factors. However, the performances of these models are restricted by data availability, inconsistent responses of N loss to key drivers, difficulty of parameter derivation and limited capacity of larger scale simulation. To address the limitations of process-based models, improve the prediction and simulation of N losses, increase NUE and environmental quality, comprehensive databases of N loss from different pathways were compiled by data mining, advanced machine learning models were developed to reflect the linkage between N loss pathways and soil, environmental and climatic conditions on global scale. The research reported in this thesis quantified the nitrification rate (Rnit) and the fraction of nitrous oxide (N2O) from nitrification (fN2O_nit), denitrification and associated N2O, dinitrogen (N2) production, the contribution of N2O from autotrophic nitrification, heterotrophic nitrification and denitrification and nitrate (NO3-) leaching, investigated the key drivers of N loss from each pathway, performed global performed accurate global prediction of nitrification rate and the fraction of N2O from nitrification, NO3-N leaching with fewer input variables using data mining, machine learning models and 15N tracing experiment. Findings include: Data mining and machine learning were integrated to predict R_nit and fN2O_nit. According to the compiled global database on Rnit and fN2O_nit, the average potential Rnit in the topsoil was 1.4 kg N ha-1 d-1, and fN2O_nit was from 0.004 to 9.19% (average 0.46%). The machine-learning based stochastic gradient boosting (SGB) model outperformed three widely used process-based models in estimating R_nit and N2O emission from nitrification by using the same input variables. SGB technique was then applied for global prediction of Rnit and fN2O_nit with only a few input variables (R2 = 0.76 and 0.55, respectively). The potential Rnit was driven by long-term mean annual temperature, soil C/N ratio and soil pH, whereas fN2O_nit by mean annual precipitation, soil clay content, soil pH, soil total N. The global fN2O_nit varied by over 200 times (0.006-1.2%), it should be adjusted according to edaphic and environmental conditions when used in process-based models or global climate models in projecting N2O emissions. A global assessment of soil denitrification rate, N2O/(N2O+N2), and their driving factors and mitigation strategies was conducted based on 225 studies (3367 observations). N loss through denitrification varied greatly across land uses and climatic regions with an average of 0.25 kg N ha-1d-1. The average emission factor of denitrification (EFD) was 4.8%. The wide range of N2O/(N2O+N2) (mean: 0.33) demonstrated that the adoption of a fixed ratio in some process-based models for estimating N2 emissions from denitrification is not suitable. N2 loss accounted for 67% of total denitrification. N loss as N2, although harmless to the environment, deserves more attention from the perspective of improving NUE. Soil denitrification rate was significantly related to soil WFPS, NO3- content and soil temperature and soil oxygen (O2) content. N2 emissions were significantly correlated with latitude, WFPS, soil mineral N and soil oxygen content. Soil oxygen content, NO3- content, organic C, C/N ratio and WFPS were the key drivers of N2O/(N2O+N2) ratio. The meta-analysis showed that optimizing N application rates, using ammonium-based fertilizers compared to nitrate-based fertilizers, biochar amendment and application of nitrification inhibitors could effectively reduce soil denitrification rate and associated N2 emissions by 34-219% and 15-226%, respectively. These findings highlight that N loss via soil denitrification and N2 emissions cannot be neglected, and that mitigation strategies should be adopted to reduce N loss and improve N use efficiency. Our study provides a solid foundation to large-scale estimations of denitrification and the refinement of relevant parameters used in the submodels of denitrification in process-based models. The contribution of N2O production pathways and its driving factors in forest soils were investigated by global data analysis and an incubation experiment with 15N tracing technique in both Australia and worldwide. Based on 13 forest soils sampled within Australia, forest soils in temperate areas had the highest N2O emission rate (19.5 ug N kg-1 soil d-1), followed by subtropical and arid soils (3.84 and 3.80 ug N kg-1 soil d-1, respectively). Heterotrophic nitrification dominated N2O production in Australian forest soils; its contribution followed the order of arid (78%) > subtropical (69%) > temperate (59%). N2O from heterotrophic nitrification was negatively related to MAT and the contribution of heterotrophic nitrification to N2O production was negatively related to soil TN and TC. These results partially agreed with the global literature data synthesis, which showed that in addition to heterotrophic nitrification (42%), denitrification (43.5%) was also a key pathway of N2O production in global forest soils. Globally, soil pH, moisture content, total N content, total C content and MAT contributed to heterotrophic nitrification and denitrification to N2O production. A machine learning model (NLNO3 model) was developed based on a global literature-based database of NO3-N leaching from field experiments (1818 observations) to predict NO3-N leaching from agroecosystems. The NLNO3 model can reliably predict NO3-N leaching using a few easily accessible input variables (R2=0.75). According to the model estimation of NO3-N leaching, the global spatiotemporal pattern and hotspots were identified. The total NO3-N leaching in agroecosystems increased from 23.2 Tg N yr-1 in 1961 to 32.8 Tg N yr-1 in 2000 and 39.7 Tg N yr-1 in 2010. Hotspots of NO3-N leaching in agroecosystems expanded from Europe in 1961 to China, South Asia and Brazil in 2000 and 2010. The high spatiotemporal heterogeneity of NO3-N leaching was mainly driven by soil properties (soil TN, soil pH, soil texture), aridity index and farming practices (N fertilization and irrigation). Results of the present research demonstrate that the capacities of data mining in better understanding the complex N cycling in terrestrial ecosystems and informing potential mitigation strategies to reduce N loss. Data mining coupled with advanced machine learning methods could not only address the limitations of process-based models and improve model simulation performances, but also provide an alternative approach in predicting N dynamics at a larger scale.
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