The genetic and phenotypic associations between sow body composition, early piglet growth and lactation feed intake (LFI) recorded during the first lactation were estimated using data collected from two maternal lines (N~2500). Heritability estimates for lactation feed intake, average piglet birth weight (ABW) and total born (TB) were 0.16±0.04, 0.27±0.03 and 0.10±0.04; genetic correlations between LFI and ABW or TB were positive but not significantly different to zero. Heritabilities for sow weight and fat depths prior to farrowing and at weaning ranged from 0.27 to 0.37 (±0.05) and within trait genetic correlations between these time points were less than one. Positive genetic (ra) and phenotypic (rp) correlations show that increased LFI is associated with higher sow weaning weight and fat depths (ra: 0.52±0.13 and 0.21±0.16; rp: 0.38±0.02 and 0.15±0.03) and higher litter gain (ra: 0.10±0.24, rp: 0.20±0.02). While correlations are not antagonistic between LFI and TB, ABW or litter gain, any correlated response in LFI to selection on these traits would be low.

Two studies were undertaken at Grafton, NSW, to determine the effects of supplementing a subtropical hay diet with a mixture of non-protein nitrogen (urea) and protein (protected casein), on the feed intake and growth of 20 steers of four genotypes (Study I), and on the digestive and metabolic functions of 16 of the steers that were fistulated in the rumen (Study 2). All steers were reared in the one subtropical environment. They consisted of backcross Hereford (H) (H × BH), backcross F1 (BH × BH) and backcross Brahman (B × BH), all of 50% heterosis, and a first-cross F1 of 100% heterosis (BxH). Steers in both studies were confined in pens and offered a basal diet of chaffed pasture hay (digestibility 52f 1.4% and nitrogen [N] content of 6.1 ± 0.2 g/kg dry matter [DM]) supplemented with minerals only (low N diet; 8 steers) or with urea or formaldehyde-treated casein and cottonseed meal (high N diet; 12 steers) for 49 days. There were eight steers, for each of the two diets in Study 2, which were fed for 30 days. There was a diet × genotype interaction (P < 0-05) in the daily DM intake (DMI) of hay by steers in Study 1. The mixed N supplement increased (P < 0.05) DM1 (per kg liveweight) by 14% in HxBH and by 13% in BxBH steers, but there was no significant effect of the supplement on the DM1 of BxH and BHxBH steers. Daily liveweight change was increased (P < 0.05) by the supplement from-30 to 250 (s.e.d ± 40) g/steer and there was no significant difference between genotypes. N supplementation increased (P < 0.05) rumen volume (63 to 87 ± 7.6 L) and fluid residence time (491 to 822 ± 76.9 min) (P < 0.05) in BHxBH steers, but the increases in other genotypes were not significant. Rumen ammonia concentration (30 to 61 ± 3 7 mg N/L) and plasma urea concentration (56 to 94 ± 6-0 g N/L) were increased (P < 0.05) by supplementation. Total protozoa density in rumen fluid was greater (P < 0.05) in BxBH than HxBH steers but did not differ significantly between supplemented and unsupplemented steers. The HxBH steers had the lowest density of small entodiniomorph protozoa when N-supplemented, which was less (P < 0.05) than that in BxBH steers which had the greatest density. Supplementation increased (P < 0.05) N retention but only B × BH steers had a positive N balance. These experiments indicated that there are some physiological differences between genotypes. The BxH genotype with the high hybrid vigour had a high DM1 on the low digestibility hay diet without the N supplements and it transferred more urea from the plasma pool to the gut. The backcross steers (HxBH and BxBH) had low DM1 which increased when supplemented. The high content B. indicus steers (BxBH) had positive net retentions of N, but the results indicated that rumen protected proteins may be more usefully fed to steers with a lower B. indicus content.

Carcasses from 56 lambs representing male progeny of 3 sires selected for muscling (M sire-type), 3 sires selected for postweaning weight (G sire-type), and 3 control sires (C sire-type) were evaluated. Lambs had been raised on low (LOW) or high (HIGH) planes of available nutrition from 10 days of age to approximately 8 months when they were slaughtered at an average cold carcass weight (CCW) of 21.4 kg. When adjusted for CCW, M lambs had more lean tissue in the loin, a greater depth and width of the 'M. longissimus thoracis et lumborum' at the 12th rib, and a greater weight of major hindlimb muscles than did G or C lambs. Although there was no difference in GR tissue depth due to sire-type at an adjusted CCW, there was less total fat in the carcass of M lambs and the amount of fat in the carcass of M lambs on HIGH nutrition was not greater than that on LOW nutrition, as it was for C and G lambs. This reduced propensity of M lambs to deposit fat in the carcass in response to HIGH nutrition was particularly evident in the loin, with fat-trim from the loin decreasing for M lambs in response to HIGH nutrition, whereas fat trim increased for C and G lambs compared at an adjusted CCW.

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.

Two experiments were conducted assessing the effects of presence or absence of rumen protozoa and dietary nitrate addition on rumen fermentation characteristics and in vitro methane production in Brahman heifers. The first experiment assessed changes in rumen fermentation pattern and in vitro methane production post-refaunation and the second experiment investigated whether addition of nitrate to the incubation would give rise to methane mitigation additional to that contributed by defaunation. Ten Brahman heifers were progressively adapted to a diet containing 4.5% coconut oil distillate for 18 d and then all heifers were defaunated using sodium 1-(2-sulfonatooxyethoxy) dodecane (Empicol). After 15 d, the heifers were given a second dose of Empicol. Fifteen days after the second dosing, all heifers were allocated to defaunated or refaunated groups by stratified randomisation, and the experiment commenced (d 0). On d 0, an oral dose of rumen fluid collected from unrelated faunated cattle was used to inoculate 5 heifers and form a refaunated group so that the effects of re-establishment of protozoa on fermentation characteristics could be investigated. Samples of rumen fluid collected from each animal using oesophageal intubation before feeding on d 0, 7, 14, and 21 were incubated for in vitro methane production. On d 35, 2% nitrate (as NaNO₃) was included in in vitro incubations to test for additivity of nitrate and absence of protozoa effects on fermentation and methane production. It was concluded that increasing protozoal numbers were associated with increased methane production in refaunated heifers 7, 14, and 21 d after refaunation. Methane production rate was significantly higher from refaunated heifers than from defaunated heifers 35 d after refaunation. Concentration and proportions of major volatile fatty acids, however, were not affected by protozoal treatments. There is scope for further reducing methane output through combining defaunation and dietary nitrate as the addition of nitrate in the defaunated heifers resulted in 86% reduction in methane production in vitro.

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.

The relationship between rumen microbial ecology and the host is regulated by multiple factors including diet, the microbial inoculum entering the gut, and host genetics. Two hypotheses associated with this statement were developed and tested during this project. The first focused on the relationship between diet, early life microbial inoculum and rumen microbiota and the second concentrated on the association between host genetics and gut microbial ecology. Hypothesis one was that the rumen microbiome of lambs could be altered by post-natal diet and by early-life microbial intervention, to achieve differences in rumen fermentation, development and animal performance that persist beyond weaning. Secondly, it was hypothesized that sheep with different genetic merit for wool growth harbour differences in their rumen microbiome that are associated with differences in gut morphology, physiology, digesta retention time and microbial protein outflow which underpin their wool phenotypes.

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.

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).

Body composition and energy expenditure were investigated in Angus heifers divergently selected for residual feed intake. Differences in fat deposition at rib and rump sites were observed between the lines but there was no difference in protein deposition, weight gain or energy expenditure. Most of the variation in energy expenditure could be accounted for by the metabolisable energy consumed by the animal. The implications of this observation on the biological consequences of selection for residual feed intake are discussed. These are preliminary observations and further work on the biological basis of the trait is required to provide definitive answers.

The combined effects of age and genetics and Poll Dorset sire and growth path were studied in two separate experiments (n = 595 and 627, respectively). In the first experiment, containing genotype crosses typically used in Australia (Merino, Poll Dorset, Border Leicester) and sires selected for growth or muscling, sheep were slaughtered at 4, 8, 14 and 22 months. The second experiment used Poll Dorset sires selected for high muscling, fat or growth with progeny having two levels of nutrition postweaning. Border Leicesters expressed higher levels of carcass fat percentage and intramuscular fat and produced the heaviest carcass. Merinos had the lowest subcutaneous fat depth and highest carcass lean percentage when compared at the same age. The progeny of Poll Dorset sires selected for high muscling (PDm) expressed a shift toward glycolytic fibres relative to those from Merino sires, and PDm sires produced progeny with reduced spine and limb length and higher carcass muscle : mineral ratios, suggesting skeletal stunting. Genotype meat quality differences were minimal except that PDm sire topsides were tougher and Merinos produced higher pH meat. With age (4-22 months), lambs became heavier and fatter, fibres shifted towards oxidative and away from glycolytic, muscle myoglobin increased, the meat became darker and redder and tenderness declined. Early weaning had no effect on the time to reach slaughter weight, provided nutrition was not restricted. The sire genetics influence on the carcass composition far outweighed the effect of nutrition postweaning. Lambs on a restricted diet tended to have less acceptable meat quality but this was not evident in lambs from sires selected for high fatness. Sensory tenderness was improved and intramuscular fat was higher in lamb progeny from sires selected for high fatness.

Concentration of indigestible markers in feces is routinely used to estimate the digestibility or rate of passage of feed through the gut. Current procedure for measuring fecal marker concentrations is an acid digest before analysis using inductively coupled plasma optical emission spectroscopy (ICP). Portable X-ray fluorescence (pXRF) spectroscopy uses short wavelength X-rays to excite sample material and generate characteristic elemental emissions proportional to the concentration of the element present in ground fecal material. The aim of this study was to measure fecal concentrations of Co, Cr, Ti, and Yb digesta marker by both ICP and pXRF and determine any correlation between the two methods, thereby assessing the potential of using pXRF as a marker analysis method. Silica (Si) concentrations in fecal and feed samples were also measured using both methods. Cattle and sheep feces and various feed samples collect from four separate studies were analyzed for concentrations of Co (CoEDTA), Cr (Cr mordanted fibre), Ti (TiO2), Yb (Yb(III)acetate), and Si using ICP and pXRF. Regression analysis used to assess the relationship between ICP and pXRF determined fecal concentrations indicated strong linear relationships (P<0.01) between pXRF and ICP estimates of Co (r2=1.00), Cr (r2=0.95), Ti (r2=0.97), Yb (r2=0.94), and Si (r2=0.88). All curves were validated using a second set of independent fecal samples. A full set of total collection fecal samples for six sheep were also analyzed by pXRF for Co and Cr (digesta kinetics), and Si (digestion) marker concentrations. These fecal Co and Cr concentrations were used to estimate digesta mean retention times (MRT) and compared to estimated digesta MRT from the same sheep using Co and Cr marker concentrations determined by ICP analysis. No differences in estimated MRT were found when using either analytical method. Silica concentrations from the same fecal samples as determined by pXRF were used to determine the rate of DMD for each animal. When compared to apparent DMD for the same animals as determined using feed DM intake and fecal DM output collected during the total collection, no differences were again found using either analytical method. The results indicate that pXRF can be used as an alternative to standard ICP procedure, obviating the need for acid digestion, reducing cost and time; and may also offer an alternative analytical method for determining livestock DM digestibility.