The mapping of complete sets of genes, transcripts and proteins from many organisms has prompted the development of new ‘-omic’ technologies for collecting and analysing very large amounts of data. Now that the tools to generate and interrogate such complete data sets are widely used, much of the focus of biological research has begun to turn towards understanding systems as a whole, rather than studying their components in isolation. This very broadly defined systems approach is being deployed across a range of problems and scales of organisation, including many aspects of the animal sciences. Here I review selected examples of this systems approach as applied to poultry and livestock production, product quality and welfare.

We studied the ontogenetic growth of goat wethers (castrated male goats) of the Saanen and Swiss Alpine breeds based on a large range of intraspecific body mass (BM). The body parts and the chemical constituents of the empty body were described by the allometric function by using BM and the empty body mass (EBM) as the predictors for morphological traits and chemical composition, respectively. We fitted the allometric scaling function by applying the SAS NLMIXED procedure, but to evaluate assumptions regarding variances in morphological and compositional traits, we combined the scaling function with homoscedastic (MOD1), and the heteroscedastic exponential (MOD2) and power-of-the-mean (MOD3) variance functions. We also predicted the ontogenetic growth by using the traditional log-log transformation and back-transformed results into the arithmetic scale (MOD4). We obtained predictions from MOD4 in the arithmetic scale by a two-step process, and evaluated MOD1, MOD2 and MOD3 by a model selection framework, and compared MOD4 with MOD1, MOD2 and MOD3 based on goodness-of-fit measures. Based on information criteria for model selection, heterogeneous variance functions were more likely to describe 10 over 36 traits with a low level of model selection uncertainty. One trait was predicted by averaging the MOD1 and MOD2 variance functions; and nine traits were better described by averaging the MOD2 and MOD3 variance functions. The predictions for other 16 traits were averaged from MOD1, MOD2 and MOD3. However, MOD4 better described 11 traits according to the goodness-of-fit measures. Depending on the variable being analyzed, the body parts and the chemical amounts exhibited the three types of allometric behavior with respect to BM and EBM, that is, positive, negative and isometric ontogenetic growth. Reference BMs, that is, 20, 27, 35 and 45 kg, were used to compute the net protein and energy requirements based on the first derivative of the scaling function, and the results were presented in reference to the EBM and EBM0.75. Both the net protein and energy requirements scaled to EBM0.75 increased from 20 to 45 kg of BM.

Research on the causes of sheep death in sea voyages from Australia to the Middle East is limited, in particular little is known about the influence of climatic factors. Mortality data from 417 shipments of sheep exported over an 11-year period (November 2004 to June 2015) were modelled retrospectively to determine associated climatic factors. The statistical analysis were performed for both the full data set with 417 voyages based on actual and estimated departure and arrival dates and a restricted data set with 71 voyages based on actual dates. The results of the full data set demonstrated a seasonal mortality pattern, with more deaths occurring on sea voyages leaving Australia in the southern hemisphere winter or spring than those departing in Australian summer or autumn. Heat stress and inadequate fat mobilisation for energy supply when sheep are inappetant on shipments may explain this seasonality. Based on these two models, the voyage and weather factors associated with sheep mortalities included departure year, autumn departure in the southern hemisphere, voyage duration, single or multiple loading port(s), weekly mean dry bulb temperature and wind speed at departure ports, and humidity at destination ports. Significant correlations were observed between weather variables at the departure ports in the Australian winter and a high sheep mortality rate during voyages. This, together with the anticipated increased heat stress risk as a result of climate change, suggests that there could be review of the trade from Australia in the southern hemisphere winter. The influence of weather at the departure ports should be considered in sheep mortality prediction models, especially Australia’s heat stress risk assessment model.

According to EU legislation, group-housed gestating sows must have a minimum of 2.25 m2 floor area per sow with at least 1.3 m2 of continuous solid floor of which a maximum of 15% is reserved for drainage openings. The aim of the experiment was to quantify the impact of different drainage openings on ammonia and greenhouse gas emissions. Three successive batches of 10 gestating sows were used. Each batch was divided into two groups kept separately in two identical rooms with similar volume and surface. The solid part of the floor presented 15% drainage openings in the first room and 2.5% in the second room. The gas emissions (ammonia (NH3), methane (CH4), nitrous oxide (N2O), carbon dioxide (CO2) and water vapour (H2O)) were measured three times during 6 consecutive days. Gaseous emissions were significantly lower with 15% drainage openings with reductions of 19% for NH3 (12.77 v. 15.83 g/day per sow), 15% for CH4 (10.15 v. 11.91 g/day per sow), 10% for N2O (0.47 v. 0.52 g/day per sow), 9% for CO2 (2.41 v. 2.66 kg/day per sow) and 13% for H2O (3.25 v. 3.75 kg/day per sow). This trial showed the advantage, in an environmental point of view, to use 15% drainage openings on the solid part of partly slatted floors in pens for group-housed gestating sows.

Genetic and phenotypic parameters were estimated for farmed red deer (Cervus elaphus) in an upland environment in the north-east of Scotland. Genetic parameters were estimated using restricted maximum likelihood analyses. Heritabilities of pre-weaning traits associated with growth were moderate for birth weight (0·27 (s.e. 0·04)), weaning weight, generally in September at 3 months of age (0·21 (s.e. 0·06)) and growth rate from birth to weaning (0·15 (s.e. 0·03)). Heritabilities for post-weaning traits were 0·10 (s.e. 0·05) for turn-out weight in April/May, 0·14 (s.e. 0·06) for September weight, at 15 months of age, 0·08 (s.e. 0·05) for growth rate weaning to turn-out and 0·12 (s.e. 0·06) for growth rate turn-out to September. Correlations between weaning weight and post-weaning traits were high indicating the usefulness of weaning weight as a selection criterion for red deer on upland farms. While Wapiti (Cervus elaphus canadensis) crosses grew faster than pure red deer they also tended to have higher mortality rates pre-weaning. Older dams were more likely to have a successful pregnancy and also tended to calve earlier. Date of calving was found to show no heritable variation in this study.

An experiment was conducted to determine the effect of time of uptake of colostrum on blood gamma-globulin concentrations, lamb survival and subsequent growth rate. Seventy-six Greyface ewes and their lambs were housed throughout the experiment. After lambing, the lambs were either allowed to suck their dams immediately or restricted from sucking for 6 or 18 hr after birth. The gamma-globulin concentration in the lamb sera reached a peak 24 to 72 hr after the time of first suck and then gradually declined to 6 weeks. Restriction from sucking for the first 18 hr after birth did not reduce the amount of gamma-globulin absorbed compared with lambs allowed immediate access to colostrum. There was no difference between groups in lamb mortality which was low in all cases. With both single and twin lambs the best live-weight gain was achieved by lambs allowed to suck their dams from birth.

Various uses of donkeys’ milk have been recently proposed for human consumption on the basis of its nutritional characteristics. Improvements in milk fatty acid profile and animal oxidative status can be induced through dietary supplementation of phenolic compounds. The study aimed to evaluate in donkeys the effects of dietary supplementation with verbascoside (VB) on: (i) the fatty acid profile and vitamins A and E contents of milk during a whole lactation, and (ii) blood biochemical parameters and markers of oxidative status of the animals. At foaling, 12 lactating jennies were subdivided into two groups (n 6): control, without VB supplement; VB, receiving a lipid-encapsulated VB supplement. Gross composition, fatty acid profile and vitamins A and E contents in milk were assessed monthly over the 6 months of lactation. Serum total cholesterol, high-density lipoproteins cholesterol and low-density lipoproteins cholesterol, tryglicerides, non-esterified fatty acid, bilirubin, alanine aminotransferase (ALT), aspartate aminotransferase, reactive oxygen metabolites, thiobarbituric acid reactive substances (TBARs), vitamin A and vitamin E were evaluated at 8 days after foaling (D0) and then at D90, D105 and D120 of lactation. In milk, the VB supplementation decreased the saturated fatty acids (P<0.05) and increased the monounsaturated fatty acids (P<0.05), and vitamins A and E (P<0.01) values. On the serum parameters, the VB supplementation decreased total cholesterol (P<0.01), tryglicerides, bilirubin, ALT and TBARs, and increased (P<0.01) vitamin E. In conclusion, the VB dietary supplementation affects the nutritional quality of donkey’s milk with a benefit on the oxidative status and serum lipidic profile of the animals.

The effect of rate of substitution of processed, urea-treated whole-crop wheat (pWCW) for grass silage on intake, performance and whole-tract digestibility was evaluated using 44 dairy cows. Cows received 10.5 kg of concentrates per day and one of the following forage mixtures (dry matter (DM) basis): grass silage alone (W-0); 0.75 grass silage, 0.25 pWCW (W-25); 0.5 grass silage, 0.5 pWCW (W-50) or 0.25 grass silage, 0.75 pWCW (W-75). Forage DM intake increased linearly with inclusion rate of pWCW from 9.7 kg DM per day in cows fed W-0 to 14.6 kg DM per day in W-75. By contrast, milk and protein yield (kg/day) were higher (P < 0.05) in cows receiving W-25 compared with W-0, but there was no effect (P>0.05) of treatment on fat yield (kg/day). From week 11 of the experiment onwards, body condition score increased with rate of inclusion of pWCW (P < 0.05). Whole-tract apparent digestibility of organic matter (OM) and fibre (kg/kg), decreased linearly with rate of inclusion of pWCW. Assuming a constant digestibility of starch in the other diet components, the apparent digestibility of starch in pWCW was 0.95 kg/kg and was not affected by rate of inclusion (P>0.05). Four continuous culture vessels were used to determine the effect of rate of inclusion of pWCW on ruminal metabolism in four periods, each of 14 d duration with sampling conducted on days 9 to 14. Vessel ammonia concentration increased linearly (P < 0.05) with rate of inclusion of pWCW whilst mean pH tended (P = 0.06) to decrease. The ratio of acetate to propionate increased from 2.5 in vessels receiving W-0 to 3.2 in those receiving W-75 (P < 0.001). There was no effect (P>0.05) of treatment on digestibility (g/g) of OM, fibre or starch or microbial protein flow (g/day). It is concluded that forage DM intake increased linearly with rate of inclusion of pWCW, but there was no further improvement in milk yield from inclusion rates above 0.25 of the forage DM, with body condition score increasing instead. Increasing the inclusion rate of pWCW resulted in a more ketogenic volatile fatty acid profile but did not affect the efficiency of microbial protein synthesis when determined in vitro.

The aim of this study was to investigate thyroid hormone levels in horses stabled in two different locations on the island of Sicily. The study was carried out on a total of 72 clinically healthy Sanfratellano horses ranging in age from 5 to 9 years and weighing 585 ± 40 kg. The results showed higher thyroxine values (P < 0.02) in horses stabled in an endemic goitre area (group II) than those observed in horses in a non-endemic area (group I). Unexpectedly, the T4/T3 and the fT4/fT3 rations were both lower in group I than in group II. The percentages of fT4 to T4 and of fT3 to T3 were both higher in group I than the percentages for group II. On the basis of gender, comparison between the two groups showed higher T4 (P < 0.01) and fT4 levels (P < 0.001) in males, and lower fT3 (P < 0.001) and fT4 levels (P < 0.005) in females stabled in the goitre endemic area. On the basis of age, younger horses (<7 years old) showed the highest thyroid hormone levels in both groups. Results suggest a physiological adaptive response of the equine species to an endemic goitre environment. The possibility that hypothyroidism is present in these horses is thus excluded and is supported not only by the lack of clinical signs, but also by the rarity of cases previously reported.

A trial was carried out over a 7-year period (1999 to 2005 calf crops) to compare indicators of seasonality in Angus cattle, which were part of a long-term genetic selection experiment. Divergent selection was applied for early (‘AGE−’) or late (‘AGE+’) age at puberty (AP) in heifers, and selection lines differed over the 7-year period by 62 days (15% of the mean). The primary measures of seasonality studied in 629 heifer progeny (59 sire groups) were serum concentration of prolactin (PRL), and winter and summer hair growth. Serial samples were obtained for PRL from 11 to 18 months of age, and data were analysed with adjustment for cortisol concentration. Using restricted maximum likelihood procedures with an animal model, heritability estimates were: AP, 0.26 ± 0.03; logePRL concentration, 0.23 ± 0.07; logecortisol concentration, 0.22 ± 0.07; hair weight, 0.21 ± 0.04; and hair length, 0.09 ± 0.05. Corresponding repeatability estimates for the last four traits were 0.49 ± 0.03, 0.38 ± 0.03, 0.21 ± 0.04, and 0.64 ± 0.02, respectively. The genetic correlation between AP and logePRL concentration was estimated at −0.29 ± 0.13 (P < 0.05). PRL concentration in the AGE− line after passing through puberty was 11 ± 5% lower than in the AGE+ line (P < 0.05). Line effects were not significant for hair weight or hair length. It was concluded that divergent selection for AP changed PRL concentration, which may partly reflect sensitivity to changing day length.

Immunocastration provides a less invasive means of castrating lambs. Considering increasing consumer awareness, the efficacy of this technique on commercial slaughter lambs needs to be further investigated and its effects on growth and stress responses need to be established. This study compared the growth rate, testes size and stress responses of immunocastrated lambs with that of lambs physically castrated with a Burdizzo clamp, as well as intact rams. A total of 40 Dohne Merino ram lambs (average live weight = 45.4±3.68 kg) were randomly allocated to the following four treatment groups: control (intact; R), Burdizzo-castrated (on day 2; B), immunocastrated with a 4-week (ICS4), or a 6-week (ICS6) interval between the second immunocastration vaccination and slaughter. Within the immunocastration treatments, the reaction to vaccination was assessed through injection site scoring, recording the local injection site surface temperature and assigning a walking score. The response to Burdizzo castration was assessed by scoring the reaction during the procedure, testes palpation reaction, walking gait and measuring testis temperature. Additional parameters recorded included BW, serum cortisol concentration, scrotal circumference and rectal temperature. Pain behaviours were described for the short-, medium- and long-term effects after the two methods of castration. Predominantly, tissue-hardening and bruising occurred at the injection sites of immunocastrates, but little effect was observed on walking comfort and no effect on injection site temperature or rectal temperatures. After Burdizzo castration, lambs spent more time in abnormal postures, and from day 3 (D3) to D8 of the trial, discomfort was observed during testes palpation and walking in B lambs. Serum cortisol concentrations were elevated in B lambs on D3 and D15, indicating physiological stress. Thus, immunocastration improved the welfare of castrated lambs as assessed by cortisol secretion, scrotal swelling and pain behaviours, without influencing growth rate.

Despite many recent advances in single nucleotide polymorphism (SNP) genotyping technologies, there is still the need for methodologies with a reasonable throughput. In this study, we compared three PCR-based methods for SNP detection: (1) a conventional PCR-based allele detection system with fluorescent genotyping technology, (2) a SNaPshot methodology by single nucleotide primer extension and, (3) a real-time PCR-based method by allele-specific minor groove-binder probes. These three methodologies were used to analyze 104 meat samples of a particular Italian cattle breed known for producing excellent quality meat and for a characteristic increased development of muscle mass, caused by a point mutation (C313Y) in the Myostatin gene. The analysis revealed 98 samples to be homozygous (mh/mh) and five to be heterozygous (mh/+) for the mutation whereas one sample resulted to be homozygous for the wild type (+/+). The results obtained with the three different assays were consistent. Overall, all three methodologies proved to be efficient for allelic discrimination studies; however, real-time PCR was faster and allowed to genotype up to 96 samples in a single step, minimizing the number of steps required for samples manipulation.

The use of herbal plants as traditional medicines has a century long history. Plantain (Plantago lanceolata L.) is a perennial herb containing bioactive components with free radical scavenging activities. An isotope dilution technique using [U-13C]glucose was conducted to determine the effect of plantain on the responses of plasma glucose metabolism to exogenous insulin infusion in sheep. Six crossbred sheep (three wethers and three ewes; mean initial BW=40±2 kg) were fed either a mixed hay of orchardgrass (Dactylis glomerata) and reed canarygrass (Phalaris arundinacea) (MH-diet) or mixed hay and fresh plantain (1 : 1 ratio, dry matter basis, PL-diet) and exposed to a thermoneutral (TN, 20°C; 70% relative humidity (RH)) environment or a heat exposure (HE, 30°C; 70% RH) for 5 days using a crossover design for two 23-day periods. The isotope dilution was conducted on days 18 and 23 of the experimental period during TN and HE, respectively. Plasma concentration of α-tocopherol was greater (P<0.0001) for the PL-diet than the MH-diet and remained comparable between environmental treatments. Plasma glucose concentration before isotope dilution technique was reduced for sheep (P=0.05) during HE compared with TN and remained comparable between diets. Plasma glucose turnover rate during the preinfusion period of insulin did not differ (P=0.10) between dietary treatments and between environments (P=0.65). The response of plasma glucose utilization to exogenous insulin administration was lower (P=0.04) for the PL-diet than the MH-diet. Under present experimental conditions, the plantain group was found to be resistant to the effects of insulin infusion.

Research has shown both production and health benefits for the use of chicory (Cichorium intybus) within ruminant diets. Despite this, little was known about the effects of this forage, containing differing fatty acid profiles and secondary plant compounds compared with ryegrass, on beef stability, fatty acid composition or sensory properties. An experiment was conducted to investigate whether the inclusion of chicory in the diet of grazing beef steers would alter these three properties in the M. Longissimus muscle when compared with beef steers grazing perennial ryegrass (Lolium perenne). Triplicate 2 ha plots were established with a chicory (cv. Puna II)/perennial ryegrass mix or a perennial ryegrass control. A core group of 36 Belgian Blue – cross steers were used within a 2-year beef finishing experiment (n=6/replicate plot). In the 2nd grazing year, steers were slaughtered as they reached a target fat class of 3. Muscle pH was checked 2 and 48 h post-slaughter. A section of the hindloin joint containing the M. Longissimus lumborum muscle was removed and a 20 mm-thick steak was cut and muscle samples were taken for analysis of vitamin E and fatty acid analysis. The remaining section of the loin was vacuum packed in modified atmosphere packs and subjected to simulated retail display. A section of the conditioned loin was used for sensory analysis. Data on pH, vitamin E concentration and colour stability in a simulated retail display showed there were no effects of including chicory in the diet of grazing beef steers on meat stability. There were also no differences found in the fatty acid composition or the overall eating quality of the steaks from the two treatments. In conclusion, there were no substantive effects of including chicory in the swards of grazing beef cattle on meat stability, fatty acid composition or sensory properties of the M. Longissimus muscle when compared with beef steers grazing ryegrass-only swards.

The effect of feeding supplemental biotin on net absorption and metabolism of nutrients by the portal-drained viscera (PDV; the gut, pancreas, spleen and associated fat) and liver of lactating dairy cows was measured. Three cows in early to mid-lactation catheterised for measurements of net nutrient absorption and metabolism by the PDV and liver were fed a total-mixed ration with or without supplemental biotin at 20 mg/day using a switch-back design (ABA v. BAB) with three 2-week periods. There were no effects of feeding biotin on dry matter intake (22.2 kg/day), milk yield (29.5 kg/day) or milk composition. There was also no effect of feeding biotin on net release of glucose by the liver, net liver removal of glucose precursors (propionate, alanine, lactate) or net liver release of β-hydroxybutyrate. Feeding biotin increased net PDV release of ammonia. Reasons for the response are not certain, but a numerical increase in net PDV release of acetate suggests that rumen or hindgut fermentation was altered. Results of the present study do not support the hypothesis that supplemental biotin increases liver glucose production in lactating dairy cows.

This study aimed to identify and better understand management strategies that help livestock farmers adapt to changes in their production contexts, a fundamental challenge. A total of nine beef-cattle farmers were interviewed three times over 1 year to discuss 13 dimensions of livestock farming (e.g. reproduction, feeding, sales, etc.). Characterisation of management strategies rested on three main factors: (i) ranking of the dimensions according to the degree to which farmers desired to control them, (ii) reasons for the ranking and (iii) management guidelines. Although farmers agreed upon the rank of certain dimensions, such as herd management, they differed on that of others, such as sales and administration/regulations. Four motivation categories were identified: risk, pleasure, efficiency and ability to control the dimension. Three management guidelines were identified, which indicated that farmers managed for future survival of their farms at different scales (animal/herd v. whole-farm), involving different resources (biological v. financial) and based on different animal categories (reproductive cows v. animals sold). These results improve understanding of individual livestock farmers and their current management strategies by integrating the motivations behind their strategies. For this reason, they constitute methodological elements that agricultural advisors can use to provide relevant information to farmers while accommodating differences in farm management.

The effects of day length, of the daily change in day length and of heat load, together with age effect, on live-weight gain of Holstein-Friesian bull calves, were studied using 8205 gain records of 1019 calves that were maintained in the experimental herd at Newe Ya'ar during a 5-year period (1991 to 1995). The age range of the calves was 150 to 450 days. Effects of day length (h) and of day length change (min/day) were assumed to be linear and effect of age was assumed to be quadratic. Three heat load indexes were calculated, accounting for day temperatures above 27°C, or night temperatures above 18°C, or both, and their effect was assumed to be linear also. Random effect of calf and fixed effect of the year were also accounted for by the regression analysis. The mean gain was 1·274 kg/day. The effect of day length was 0·027 (s.e. 0·003) kg/day per h, and effect of day length change was 0·042 (s.e. 0·003) kg/ay per min/day both effects being highly significant (P < 0·0001). The effects of heat load according to each of the three indexes were either not significant, or tended to be positive, which implies increased gain with increasing heat load. Effect of age was positive (P = 0·0005), and of age2 was negative (P < 0·0001). Based on the regression model that did not include heat load effect, the peak gain was obtained on 19 May, 33 days before the longest day and the trough was obtained on 18 November, with a difference of 0·206 kg/day (proportionately 0·15 of the peak gain) between peak and trough gains. It was calculated by the regression coefficients for the photoperiod effects, that a calf that enters the feedlot at the age of 150 days and a live weight of 180 kg on 1 January, will be 23 kg heavier at the age of 350 days than a calf that enters the feedlot at the same age and weight on 1 July. This difference is reduced to 10 kg at the age of 450 days.

One of the major limitations to the widespread use of artificial insemination (AI) in the United Kingdom (UK) sheep industry is that with frozen-thawed semen current insemination techniques result in lowered fertility. Consequently, only fresh or liquid-chilled ram semen can be used if commercially acceptable conception rates are to be achieved.

The effects of supplementary feeding of licks containing non-protein nitrogen on the reproductive performance of beef breeding cows and on the live-weight gain of growing stock in Botswana is described. The trials involved 1375 breeding cows at five artificial insemination centres, and 360 breeding cows and 269 growing stock under ranch conditions. These licks increased the percentage of pregnancies in cows under lactation stress by up to 20%, but had no effect on the reproductive performance of dry cows or cows with a calf older than 5 mo. In growing animals the provision of rumen stimulatory licks increased live-weight gain by an average of 12%, but was of doubtful economic value.

Modern, intensive fox breeding implies a human-animal relationship but human contact causes stress in farm-bred blue foxes. Handling is a common part of routine farming practices, particularly during the breeding season. The purpose of this study was to determine how handling influences certain morphometric and hormonal parameters of adrenocortical and ovarian function and fertility in pregnant blue foxes and whether these effects are mediated through an increase in plasma concentrations of cortisol. Blue fox females were subjected to a 1-min daily-handling treatment in the last trimester of pregnancy (term = 52 days). Plasma concentrations of ACTH, cortisol, progesterone, oestradiol and testosterone, as well as the in vitro adrenal and gonadal production of steroids were measured by radio-immuno assay in control (C, no. = 6) and handled (H, no. = 7) vixens on days 47 to 48 of pregnancy. In addition, the number of viable and dead foetuses, body, adrenal and ovarian weights in pregnant foxes and body weights of their viable foetuses were recorded. Handling increased plasma concentration of cortisol (C: 6·8 (s.e. 1·6) ng/ml v. H: 22·8 (s.e. 5·9) ng/ml, P < 0·05) as well as in vitro adrenal production of cortisol. In addition, handling decreased the body (C: 7·40 (s.e. 0·48) kg v. H: 6·24 (s.e. 0·13) kg, P < 0·05) and ovarian (C: 3·45 (s.e. 0·26) g v. H: 2·73 (s.e. 0·17) g, P < 0·05) weights of pregnant vixens and also the body weight of viable foetuses (C: 59·1 (s.e. 0·9) g, no. = 73 v. H: 50·6 (s.e. 1·2) g, no. = 58, P < 0·01). Handling did not cause any changes in adrenal weight, plasma concentrations of progesterone and oestradiol or in vitro ovarian steroid production. It is concluded that persistent handling of pregnant blue foxes is a mild stressor, which results in an increase in plasma concentration and adrenal production of cortisol and reduces maternal and foetal body weights.