In the Australian sheep industry, Estimated Breeding Values (EBVs) are being increasingly used to select Merino sheep for excellence in traits such as high clean fleece weight (CFW), low fibre diameter (FD) and high yearling live weight (YLW). It has been proposed that genetic differences in CFW may be related to skin protein metabolism and that it is sensitive to the level of nutrition (Williams and Morley 1994; Liu et al. 1998). The underlying physiological responses to EBV and plane of nutrition are not well understood.

Protein metabolism in skin and muscle was studied in Merino wethers selected for high (F+, n = 10) or low (F–, n = 10) estimated breeding values for clean fleece weight, but with similar estimated breeding values for liveweight and fibre diameter, raised to 20 months of age under the same conditions, and then offered two levels of nutrition (0.8 or 1.8 × maintenance) for 37 days. Over 37 days, F+ sheep had greater rate of wool production, liveweight gain, and had greater eye-muscle and fat depth than F– sheep (P < 0.05). Fractional synthesis rates of protein (%/day) in the epidermis, dermis, whole skin and muscle were affected by both feeding level (P < 0.05) and genotype (P < 0.05). The fractional synthesis rates of protein were greater (P < 0.05) in F+ sheep at both levels of intake. There was an interaction (P < 0.01) between genotype and feeding level for the protein fractional synthesis rate in muscle, where F+ sheep were more responsive to higher feed intake. Muscle of F– sheep responded to increased amino acid supply by reducing the rate of protein degradation without altering synthesis rate; whereas muscle of F+ sheep responded by increasing the rates of both protein synthesis and degradation. The overall muscle fractional synthesis rate (1.6%/day) was ~7-times lower than the skin fractional synthesis rate (10.8%/day) in these animals (P < 0.01). F+ sheep had a higher rate of protein synthesis in dermis and whole skin to support their higher wool protein accretion at both levels of feed intake. Muscle protein synthesis rate was greater in F+ sheep offered above-maintenance metabolisable energy (ME) intake than those given below-maintenance ME intake but was unaffected by ME intake in F– sheep. The results indicate that selection for wool growth not only affects production of wool and the wool follicle, but also affects the rate of protein turnover in components of the skin and skeletal muscle.

On-farm CH₄ emissions have been identified as the largest contributors to the carbon footprint of livestock production systems. A requirement to quantify on-farm mitigation under commercial production conditions and a desire to establish the phenotype of thousands of ruminants for breeding programs, has fueled the development of techniques to estimate daily methane production (DMP) from short-term measures of methane concentration or methane flux.The accuracy, precision and applicability of these methods has been largely untested and forms the susbtance of this thesis. In assessing the accuracy of short-term emissions measures to estimate DMP, a high level of concordance was observed between DMP measured over 24h in a respiration chamber (RC) and estimated from multiple short-term measurement estimates using the GreenFeed Emission Monitoring system (GEM). Three independent experiments comparing DMP confirmed that estimates between methods differ by 5% to 8% (P>0.05). This implies that multiple short-term measures of emission rates are complementary to and consistent with respiration chamber-derived measures, providing capability to measure a greater number of animals, potentially in their production environment over extended periods of time. Methane yields (MY; g CH₄/kg DMI) were also derived based on multiple short-term emission measures, with results consistently within 10% of those calculated based on 24h RC data. The overall MY of animals consuming roughages was 21.8g CH₄/kg DMI using GEM data, in keeping with the 22.3g CH₄/kg DMI average in the literature. That implies that GEM units can not only accurately estimate DMP of cattle but also support accurate MY estimates that can be used in quantifying livestock emissions for national greenhouse inventory calculations.

Calcium nitrate and urea were fed as a supplement on an isonitrogenous basis to Angus steers and their erythrocytic methaemoglobin concentrations and NADH- and NADPH-methaemoglobin reductase levels were measured over a 54-day period. Methaemoglobin concentrations remained elevated despite increases in NADH-methaemoglobin reductase activity. In a second experiment, Brahman cross steers were fed either calcium nitrate or urea supplements for 111 days. Blood cells were then taken, washed and exposed to sodium nitrite to convert all haemoglobin to methaemoglobin. The rates of glycolysis and methaemoglobin reduction were measured following incubation of these cells in buffers containing 1, 5 or 10 mM inorganic phosphate. Glucose consumption and methaemoglobin reduction were increased by inorganic phosphate and were more rapid in those animals supplemented with nitrate. Lactate production of erythrocytes was reduced in those animals fed nitrate. It is concluded that adaptation to chronic nitrite exposure occurs in the erythron, resulting in greater methaemoglobin reduction potential and that there is competition between NADH-methaemoglobin reductase and lactate dehydrogenase for NADH.

With increasing world population, global demand for a secure and growing food supply challenges the livestock producers of today to increase output of milk and meat while reducing the environmental impact of animal production. This thesis reports a review of literature and targeted new research assessing the consequences of eliminating rumen protozoa (defaunation) on the performance, digestive function and emissions of the greenhouse gas methane, by livestock.
• Comparative studies of rumen fermentation and animal growth were conducted in growing Merino lambs, crossbred sheep and Brahman cattle. In these studies ruminants were defaunated using coconut oil distillate to suppress protozoa then dosed with sodium 1-(2-sulfonatooxyethoxy) dodecane in a protocol that suppressed feed intake for an average of 10 days but had no detrimental effects on animal health.
• Reflecting the diversity in published literature, these studies found inconsistent effects of defaunation on volatile fatty acid (VFA) concentrations and proportions. Averaged over all experiments conducted, defaunation was associated with a small (5%) reduction in total VFA concentration and an increase (5%) in the ratio of acetate to propionate in the rumen.
• While effects on VFA were not consistent, an average 30% reduction in rumen ammonia concentration and a 16% increase in microbial crude protein outflow (estimated by allantoin excretion) were apparent, suggesting substantial differences in the ruminal degradation and outflow of protein due to defaunation. These changes were associated with an 18% increase in average daily gain (ADG), but surprisingly no increase in wool growth rate.
• Defaunation was associated with a lower enteric methane emission (average 20% reduction) compared to faunated ruminants, with the first studies of daily methane production (DMP) ever made while grazing, made using GreenFeed Emission Monitoring (GEM) units, confirming a 3% lower DMP (non-significant; P > 0.05) and a 9% lower methane yield (MY; CH4/kg DMI; P = 0.06) in defaunated sheep.
• Protozoa affected the rumen response to nitrate, with the nitrate induced reduction in MY being 29% greater in faunated compared to defaunated lambs.
• With dietary coconut oil, no interaction with defaunation was apparent with both coconut oil and defaunation significantly reducing DMP and MY in cattle.
• While defaunation tended to increase average daily gain and reduced enteric methane emissions in cattle by 10%, establishing defaunated cattle proved difficult and is a major constraint to expanding defaunation into commercial herds.
• Assessment of the distribution of protozoa in the forestomaches showed that the number of entodiniomorph protozoa attached to the 'leaves' of the bovine omasum was at least as great as the number attached to the entire surface of the rumen, though all tissue-attached populations are far fewer than the population in the rumen fluid.
• It is concluded that defaunation alone or in combination with dietary supplements of nitrate is effective in decreasing methane emissions, while increasing microbial protein supply and ADG. Commercial implementation of defaunation for cattle will not be able to rely on addition of surfactants to the rumen and it is suggested a bioactive compound distributed through the blood may be needed to remove protozoa residing in the omasum.

It is unclear how nutritional conditions (below or above maintenance) affect Merino follicle characteristics in sheep with different estimated breeding values (EBVs) for wool production but with similar EBVs for fibre diameter and liveweight. This was addressed in our study. Twenty castrated male Merino sheep were selected from a commercial flock, 10 with high EBVs for wool production (F+) and 10 with low EBVs (F–). The animals were offered a diet providing 1.2 times their metabolisable energy requirement for maintenance (1.2 M) for 4 weeks. After 4 weeks’ acclimatisation, five sheep from each EBV group were offered a diet of providing 0.8 times their metabolisable energy requirement for maintenance (0.8 M), and the other five from each EBV group were offered the 1.8 M diet for 5 weeks. On Day 35, one skin biopsy was taken from a shaved area on the left mid-side of each animal under local anaesthesia (subcutaneous injection of 2 ml 2% (w/v) Lignocaine), using a trephine (1.5 cm diameter). The skin sample was stored in 37% (w/v) buffered formalin (pH = 7) for skin histology analysis. Skin samples were processed by CSIRO (Armidale, NSW). The histology methods were essentially those described by Maddocks and Jackson (1988).

Profitable and sustainable agricultural production in resource-limited crop-livestock farming systems is largely dependent on the efficiency with which essential nutrients (N, P, K, Mg and S) are conserved and recycled. Although the economic and environmental importance of N cycling in agriculture is evident, the most feasible, profitable and sustainable practices that resource-limited and financially-challenged farmers can employ to increase N conservation and N cycling efficiency remain scarce. Based on the situation in Cambodia, five studies were designed to identify strategies to improve efficiency of N cycling through livestock in smallholder crop-livestock farming systems.

The efficiency of dietary protein utilisation in broiler chickens was studied by conventional balance techniques and by digestion and metabolism of ¹⁵N-labelled protein in the diet. Between 16 and 30 days of age, male chickens tended to be heavier and to ingest more feed than female chickens: however, female chickens tended to absorb and utilize dietary protein more efficiently than male chickens. Whole-body synthesis rate did not differ between sexes and was 6.7-7.5 times the protein absorption rate. Only about 10% of the protein synthesized was deposited in tissue gain whereas 90% was degraded. Fractional protein synthesis rates were determined from the decline in enrichment in small intestinal, liver and breast muscle samples taken sequentially from birds that had earlier ingested ¹⁵N-labelled feed. FSRs declined with age but did not differ between sexes and were 44-52, 23-29 and 15-18 %/d, respectively.

In the Australian sheep industry, Estimated Breeding Values (EBVs ) are being increasingly used to select Merino sheep for excellence in traits such as high clean fleece weight (CFW), low fibre diameter (FD) and high yearling live weight (YLW). It has been proposed that genetic differences in CFW may be related to skin protein metabolism and that it is sensitive to the level of nutrition (Williams and Morley 1994; Liu et al. 1998). The underlying physiological responses to EBV and plane of nutrition are not well understood. We selected 20 wethers from a commercial flock (18 month-old weighing about 33.3 kg) with similar EBV for FD and YLW, but 10 wethers had high EBV for CFW (F+), and 10 had low EBV for CFW (F-). We used a 2 x 2 experiment (F+ and F- wethers at two levels of intake, i.e. 0.8 and 1.8 x maintenance of commercial pellets) and determined CFW and protein synthesis rates (FSR) in their skin and muscle pools using the flooding dose technique (Rocha et al. 1993, i.e. i/v injection of deuterium-labelled [L-ring-D⁵] phenylalanine). The commercial pellets contained 13.3% crude protein, 20% crude fibre, 9.5 MJ/kg ME.