MicroRNAs (miRNAs) are a class of small non-coding RNAs that negatively regulate gene expression of target messenger RNAs (mRNAs) and miRNAs have been proven to play vital roles in skeletal muscle development. The miRNA-499-5p has been reported to be negatively related with the expression of Sox6, a critical transcription factor for the maintenance of fast-twitch skeletal muscle. In this study, we amplified a length of 2012-bp mRNA that contains a 1512-bp porcine Sox6 (pSox6) 3'UTR from skeletal muscle of a Duroc×Landrace×Yorkshire pig. By luciferase reporter assay we verified that pSox6 is a target of miR-499-5p. In extensor digitorum longus and Soleus muscles of pigs, the expression levels of miR-499-5p and pSox6 mRNA were also inversely correlated. Besides, overexpression of miR-499-5p in porcine satellite cells promoted the expression of MyHC I and MyHC IIa mRNA, along with a reduction of pSox6 mRNA. Taken together, these results indicate that miR-499-5p may facilitate the oxidative myofibers formation by downregulating pSox6 expression.

The Nofence technology is a GPS-based virtual fencing system designed to keep sheep within predefined borders, without using physical fences. Sheep wearing a Nofence collar receive a sound signal when crossing the virtual border and a weak electric shock if continuing to walk out from the virtual enclosure. Two experiments testing the functionality of the Nofence system and a new learning protocol is described. In Experiment 1, nine ewes with their lambs were divided into groups of three and placed in an experimental enclosure with one Nofence border. During 2 days, there was a physical fence outside the border, during Day 3 the physical fence was removed and on Day 4, the border was moved to the other end of the enclosure. The sheep received between 6 and 20 shocks with an average of 10.9±2.0 (mean±SE) per ewe during all 4 days. The number of shocks decreased from 4.38±0.63 on Day 3 (when the physical fence was removed) to 1.5±0.71 on Day 4 (when the border was moved). The ewes spent on average 3%, 6%, 46% and 9% of their time outside the border on Days 1, 2, 3 and 4, respectively. In Experiment 2, 32 ewes, with and without lambs, were divided into groups of eight and placed in an experimental enclosure. On Day 1, the enclosure was fenced with three physical fences and one virtual border, which was then increased to two virtual borders on Day 2. To continue to Day 3, when there was supposed to be three virtual borders on the enclosure, at least 50% of the ewes in a group should have received a maximum of four shocks on Day 2. None of the groups reached this learning criterion and the experiment ended after Day 2. The sheep received 4.1±0.32 shocks on Day 1 and 4.7±0.28 shocks on Day 2. In total, 71% of the ewes received the maximum number of five shocks on Day 1 and 77% on Day 2. The individual ewes spent between 0% and 69.5% of Day 1 in the exclusion zone and between 0% and 64% on Day 2. In conclusion, it is too challenging to ensure an efficient learning and hence, animal welfare cannot be secured. There were technical challenges with the collars that may have affected the results. The Nofence prototype was unable to keep the sheep within the intended borders, and thus cannot replace physical fencing for sheep.

Pre-slaughter transportation may affect poultry welfare and mortality rates. A retrospective analysis was conducted to examine the effect of environmental, management and individual factors on the percentage of dead birds during pre-slaughter transportation (dead-on-arrival, DOA). The variables accounted for in the analyses included: environmental temperature, travel duration, genetic line, gender, crate type and crate stocking density. Among the 41 452 loads of turkeys (34 696 388 birds) and 3241 of end of lay hens (21 788 124 birds) transported to three large abattoirs in northern Italy in a 3-year period, the median DOA was 0.14% in turkeys, and 0.38% in hens. In turkeys, travel duration longer than 30 min, temperature higher than 26°C and high in-crate densities were associated with increased DOA. In winter (⩽2°C), high stocking densities did not reduce the mortality risk from cold stress; on the contrary, for stocking densities either near to or just above the maximum density in EC Reg. 1/2005, the DOA risk was greater than for loads with densities of 10 kg/m2 less than the EC maximum. Male birds and specific genetic lines also showed a higher DOA. In hens, transportation lasting longer than 2 h and the brown-feathered breed were associated with higher DOA. Dead-on-arrival progressively increased with travel duration, remaining constant between 4 and 6 h and peaking at 8 h (median: 0.57%). The maximum DOA increase was detected during winter. These results show that several species-specific factors may lead to increased risk of mortality.

Livestock farming is an essential activity in many rural areas, where it contributes to the maintenance of soil fertility and farmland biodiversity, as well as to a set of social public goods including food security, rural vitality and culture. However, livestock sustainability assessments tend to focus primarily on environmental and economic dimensions; therefore, these valuations might be limited because they do not consider the complete set of associated goods and services (GS). Hence, a need exists to recognise the multiple contributions provided by livestock to human well-being and society. The objective of this study was to analyse the provision of multiple GS derived from livestock across regions in France and empirically demonstrate sets of GS that repeatedly appeared together. We designated these multiple GS provided by livestock as contributions to productive, environmental, rural vitality and cultural benefits that human populations derive directly or indirectly from livestock agroecosystems. First, we combined expert knowledge with results of a literature review to define a bundle of GS provided by livestock. We then described indicators that quantified each good or service and screened national databases to determine the availability of supporting data. Finally, we assessed the GS and their relationships (synergies or trade-offs) on a nation-wide gradient in France at the department level (Nomenclature of Territorial Units for Statistics 3). Four main categories of GS were considered: provisioning (e.g. food quantity and quality), environmental quality (e.g. biodiversity, landscape heterogeneity, water quality), rural vitality (e.g. employment, rural dynamism) and culture (e.g. gastronomy and landscape heritage). Four major types of GS bundles were identified, which suggested strong contrasts among French rural areas in terms of the nature of the GS that occurred together and their levels of provision. GS bundles in France had a non-random spatial distribution. This study represents an initial step towards developing a methodology to consider GS bundles provided by livestock. Nonetheless, further research is needed to understand socio-economic, environmental, political and geographic determinants of the composition of GS bundles.

The effect of supplementing high-quality fresh forage, mainly based on alfalfa, to growing lambs fed with decreasing levels of total mixed ration (TMR) was studied on intake, digestion and ruminal environment. In total, 24 catheterized lambs (25.2±3.67 kg) housed in individual metabolism cages were assigned to one of four treatment diets: ‘TMR100’: TMR offered ad libitum; ‘TMR75’ and ‘TMR50’: TMR at a level of 0.75 and 0.50 of potential intake, respectively, complemented with fresh forage without restriction; ‘TMR0’: only fresh forage ad libitum. The feeding behavior, nutrient intake and digestibility, kinetics of passage and rumen environment were evaluated. As the level of TMR in the diet decreased, lambs increased the forage intake and spent more time eating and ruminating, less time resting and demonstrated a higher rate of intake. Those changes resulted in a higher nutrient intake of dry matter, organic matter, nitrogen, NDF and ADF, but a slightly lower organic matter digestibility, while no differences were detected in the output rate of particles. As a consequence, with the decrease of TMR and increase of forage intake, the ingested energy increased. Higher ruminal pH and NH3–N concentrations were observed for lower levels of TMR in the diet. The total volatile fatty acids, acetate and propionate concentrations presented a quadratic response. Total volatile fatty acids and acetate concentrations were higher and propionate concentration was lower in lambs consuming mixed diets (TMR50 and TMR75). We concluded that the inclusion of high-quality fresh forage in a combined diet with TMR in lambs had positive effects on nutrient intake without negative consequences on digestion and rumen environment.

The objectives of this study were to infer phenotypic causal networks involving gestation length (GL) and calving difficulty (CD) for the primiparity of 1850 Japanese Black heifers, and the birth weight (BWT), withers height (WH) and chest girth (CHG) of their full blood calves, and to compare the causal effects among them. The inductive causation (IC) algorithm was employed to search for causal links among these traits; it was applied to the posterior distribution of the residual (co)variance matrix of a multiple-trait sire-maternal grand sire (MGS) model. The IC algorithm implemented with 95% and 90% highest posterior density intervals detected only one structure with links between GL and BWT (WH or CHG) and between BWT (WH or CHG) and CD, although their directions were not resolved. Therefore, a possible causal structure based on the networks obtained from the IC algorithm [GL→BWT (WH or CHG)→CD] was fitted using a structural equation model to infer causal structure coefficients between the traits. The structural coefficients of GL on BWT and of BWT on GL on the observable scale showed that an extra day of GL led to a 270-g gain in BWT, and a 1-kg increase in BWT increased the risk for dystocia by 1.1%, in the causal structure. Similarly, an increase in GL by 1 day resulted in a 2.1 (2.0)-mm growth in WH (CHG), and a 1-cm increase in WH (CHG) increased the risk of dystocia by 1.2% (0.9%). The structural equation model was also fitted to alternative causal structures, which involved the addition of a directed link from GL to CD, or GL→CD to the structures described above. The inferred structural coefficients with the alternative structures were almost the same as the corresponding ones that had GL→BWT (WH or CHG)→CD. However, the direct causal effect of the extra link from GL on CD was similar to the indirect causal effect of GL through the mediating effect of BWT (WH or CHG) on CD and significant (P<0.05). This suggest that maternal genetic effects might not be removed completely from the residual variance components in the sire-MGS model, and the application of the IC algorithm to the variances from the model could detect an incorrect structure. Nonetheless, fitting the structural equation model to the causal structure provided useful information such as the magnitude of the causal effects between the traits.

Traumatic situations in animals induce responses including pain, expressed through behavioural and physiological pathways such as inflammation, oxidative stress, hypothalamic–pituitary–adrenal (HPA) axis and autonomic nervous system. As some of these systems can also be activated during excitement and situations with a positive valence, their use as a means to assess pain response is difficult. We explored (i) how these five aforementioned pathways change in sheep exposed to various degrees of invasiveness of surgical procedures despite a therapeutic regimen and (ii) whether a multiparametric analysis that combines information from these five pathways enhances the discrimination between these situations, and estimates the relative importance of these pathways in the response. We used 24 adult sheep split into four treatments: Control (C; no fasting, no anaesthesia, no surgery), Sham (S; fasting, anaesthesia, no surgery), Rumen Canulation (R; fasting, anaesthesia, rumen cannulation) and Rumen–Duodenal–Ileum cannulation (RDI; fasting, anaesthesia, cannulation of the rumen, duodenum and ileum). Sheep’ responses were measured for 5 days after surgery. When considering each behavioural or physiological pathway independently, discrimination between treatments was acceptable, its sensitivity (Se) ranging from 0% to 100%, and its specificity (Sp) ranging from 62% to 100%. The multiparametric analysis gathering information from the five pathways enhanced the effectiveness of discrimination between treatments (Se, 50% to 100%; Sp, 82% to 100%), and gave additional information on the relative contribution of each pathway to the global sheep response. Sheep global response was higher when exposed to a surgery, and increased with the surgery invasiveness. This response relied mostly on inflammation (absolute correlation for haptoglobin, 0.89), HPA (cortisol, 0.85) and behaviour (antalgic postures, 0.85). The multiparametric approach seems to be a promising tool to discriminate between different degrees of invasiveness of surgical procedures.

Rusitec fermenters are in vitro systems widely used to study ruminal fermentation, but little is known about the microbial populations establishing in them. This study was designed to assess the time evolution of microbial populations in fermenters fed medium- (MC; 50% alfalfa hay : concentrate) and high-concentrate diets (HC; 15 : 85 barley straw : concentrate). Samples from solid (SOL) and liquid (LIQ) content of fermenters were taken immediately before feeding on days 3, 8 and 14 of incubation for quantitative polymerase chain reaction and automated ribosomal intergenic spacer analysis analyses. In SOL, total bacterial DNA concentration and relative abundance of Ruminococcus flavefaciens remained unchanged over the incubation period, but protozoal DNA concentration and abundance of Fibrobacter succinogenes, Ruminococcus albus and fungi decreased and abundance of methanogenic archaea increased. In LIQ, total bacterial DNA concentration increased with time, whereas concentration of protozoal DNA and abundance of methanogens and fungi decreased. Diet×time interactions were observed for bacterial and protozoal DNA and relative abundance of F. succinogenes and R. albus in SOL, as well as for protozoal DNA in LIQ. Bacterial diversity in SOL increased with time, but no changes were observed in LIQ. The incubated diet influenced all microbial populations, with the exception of total bacteria and fungi abundance in LIQ. Bacterial diversity was higher in MC-fed than in HC-fed fermenters in SOL, but no differences were detected in LIQ. Values of pH, daily production of volatile fatty acids and CH4 and isobutyrate proportions remained stable over the incubation period, but other fermentation parameters varied with time. The relationships among microbial populations and fermentation parameters were in well agreement with those previously reported in in vivo studies. Using 15N as a microbial marker or quantifying total microbial DNA for estimating microbial protein synthesis offered similar results for diets comparison, but both methods presented contrasting results for microbial growth in SOL and LIQ phases. The study showed that fermentation parameters remained fairly stable over the commonly used sampling period (days 8 to 14), but shifts in microbial populations were detected. Moreover, microbial populations differed markedly from those in the inocula, which indicates the difficulty of directly transposing results on microbial populations developed in Rusitec fermenters to in vivo conditions.

The present study aims to assess the effects of pig’s genotype (lean v. fatty) and dietary protein level (control v. reduced) on intramuscular fat (IMF) content, fatty acid composition and fibre profile of psoas major, a representative red muscle in pig’s carcass scarcely studied relative to white longissimus lumborum. The experiment was conducted on 40 intact male pigs (20 Alentejana purebred and 20 Large White×Landrace×Pietrain crossbred) from 60 to 93 kg of live weight. Pigs were divided and allocated to four dietary groups: control protein diet equilibrated for lysine (17.5% of CP and 0.7% of lysine) and reduced protein diet (RPD) not equilibrated for lysine (13.1% of crude protein and 0.4% of lysine) within a 2×2 factorial arrangement (two genotypes and two diets). Alentejana purebred had higher IMF content (15.7%) and monounsaturated fatty acids (MUFA) (8.9%), whereas crossbred pigs had higher PM weight (46.3%) and polyunsaturated fatty acids (PUFA) (20.1%). The genotype also affected colour with higher lightness (15.1%) and yellowness (33.8%) and lower redness (9.9%) scores in crossbred pigs. In line with this, fatty pigs displayed more oxidative fibres (29.5%), whilst lean pigs had more glycolytic (54.4%). Relative to fatty acids, RPD increased MUFA (5.2%) and SFA (3.2%) but decreased PUFA (14.8%). Ultimately, RPD increased IMF content (15.7%) in the red muscle under study, with no impact on glycolytic to oxidative fibre type transformation.

Licuri (Syagrus coronate) cake is a biodiesel by-product used in ruminant feed as a beneficial energy source for supplementation in managed pastures. The objective was to evaluate the performance, digestibility, nitrogen balance, blood metabolites, ingestive behavior and diet profitability of eight crossbred Holstein (3/4)×Gyr (5/8) multiparous cows (480±25 kg BW and 100 days milking) grazing and supplemented with licuri cake partially replacing ground corn and soybean meal in concentrate (0, 200, 400 and 600 g/kg in dry matter (DM)), distributed in an experimental duplicated 4×4 Latin square design. Licuri cake partially replacing ground corn and soybean meal increased (P<0.01) the intake and digestibility of ether extract and decreased the non-fiber carbohydrates; however, there were no influences on the intakes of DM, CP, NDF and total digestible nutrients (TDN). The digestibilities of DM, CP and NDF were not influenced by licuri cake addition. There was a decrease trend on TDN digestibility (P=0.08). Licuri cake replacing ground corn and soybean meal in concentrate did not affect the intake; fecal, urinary and mammary excretions; N balance; and triglycerides concentrations. However, the blood urea nitrogen (P=0.04) concentration decreased with the licuri cakes inclusion in cow supplementation. There was an increasing trend for serum creatinine (P=0.07). Licuri cake inclusion did not affect body condition score, production, yield, protein, lactose, total solids and solid non-fat contents of milk and Minas frescal cheese. There was a linear decrease in average daily weight gain (g/day). The milk fat concentration and cheese fat production (P<0.1) presented a linear increase with partial replacement of ground corn and soybean meal with licuri cakes. The addition of licuri cake did not alter the time spent feeding, ruminating or idling. There was an increasing trend in NDF feeding efficiency (P=0.09). The replacing of ground corn and soybean meal with licuri cake up to 600 g/kg decreased the concentrate cost by US$0.45/cow per day. Licuri cake replacing corn and soybeans (400 g/kg) in concentrate promoted a profit of US$0.07/animal per day. Licuri cake is indicated to concentrate the supplementation of dairy cows with average productions of 10 kg/day at levels up to 400 g/kg in the concentrate supplement because it provides an additional profit of US$0.07/animal per day and increased milk and Minas frescal cheese fat without negative effects on productive parameters.

As the environments in which livestock are reared become more variable, animal robustness becomes an increasingly valuable attribute. Consequently, there is increasing focus on managing and breeding for it. However, robustness is a difficult phenotype to properly characterise because it is a complex trait composed of multiple components, including dynamic elements such as the rates of response to, and recovery from, environmental perturbations. In this review, the following definition of robustness is used: the ability, in the face of environmental constraints, to carry on doing the various things that the animal needs to do to favour its future ability to reproduce. The different elements of this definition are discussed to provide a clearer understanding of the components of robustness. The implications for quantifying robustness are that there is no single measure of robustness but rather that it is the combination of multiple and interacting component mechanisms whose relative value is context dependent. This context encompasses both the prevailing environment and the prevailing selection pressure. One key issue for measuring robustness is to be clear on the use to which the robustness measurements will employed. If the purpose is to identify biomarkers that may be useful for molecular phenotyping or genotyping, the measurements should focus on the physiological mechanisms underlying robustness. However, if the purpose of measuring robustness is to quantify the extent to which animals can adapt to limiting conditions then the measurements should focus on the life functions, the trade-offs between them and the animal’s capacity to increase resource acquisition. The time-related aspect of robustness also has important implications. Single time-point measurements are of limited value because they do not permit measurement of responses to (and recovery from) environmental perturbations. The exception being single measurements of the accumulated consequence of a good (or bad) adaptive capacity, such as productive longevity and lifetime efficiency. In contrast, repeated measurements over time have a high potential for quantification of the animal’s ability to cope with environmental challenges. Thus, we should be able to quantify differences in adaptive capacity from the data that are increasingly becoming available with the deployment of automated monitoring technology on farm. The challenge for future management and breeding will be how to combine various proxy measures to obtain reliable estimates of robustness components in large populations. A key aspect for achieving this is to define phenotypes from consideration of their biological properties and not just from available measures.

Reducing the dietary CP content is an efficient way to limit nitrogen excretion in broilers but, as reported in the literature, it often reduces performance, probably because of an inadequate provision in amino acids (AA). The aim of this study was to investigate the effect of decreasing the CP content in the diet on animal performance, meat quality and nitrogen utilization in growing-finishing broilers using an optimized dietary AA profile based on the ideal protein concept. Two experiments (1 and 2) were performed using 1-day-old PM3 Ross male broilers (1520 and 912 for experiments 1 and 2, respectively) using the minimum AA:Lys ratios proposed by Mack et al. with modifications for Thr and Arg. The digestible Thr (dThr): dLys ratio was increased from 63% to 68% and the dArg:dLys ratio was decreased from 112% to 108%. In experiment 1, the reduction of dietary CP from 19% to 15% (five treatments) did not alter feed intake or BW, but the feed conversion ratio was increased for the 16% and 15% CP diets (+2.4% and +3.6%, respectively), while in experiment 2 (three treatments: 19%, 17.5% and 16% CP) there was no effect of dietary CP on performance. In both experiments, dietary CP content did not affect breast meat yield. However, abdominal fat content (expressed as a percentage of BW) was increased by the decrease in CP content (up to +0.5 and +0.2 percentage point, in experiments 1 and 2, respectively). In experiment 2, meat quality traits responded to dietary CP content with a higher ultimate pH and lower lightness and drip loss values for the low CP diets. Nitrogen retention efficiency increased when reducing CP content in both experiments (+3.5 points/CP percentage point). The main consequence of this higher efficiency was a decrease in nitrogen excretion (−2.5 g N/kg BW gain) and volatilization (expressed as a percentage of excretion: −5 points/CP percentage point). In conclusion, this study demonstrates that with an adapted AA profile, it is possible to reduce dietary CP content to at least 17% in growing-finishing male broilers, without altering animal performance and meat quality. Such a feeding strategy could therefore help improving the sustainability of broiler production as it is an efficient way to reduce environmental burden associated with nitrogen excretion.

Modern research makes frequent use of animal models, that is, organisms raised and bred experimentally in order to help the understanding of biological and chemical processes affecting organisms or whole environments. The development of flexible, reprogrammable and modular systems that may help the automatic production of ‘not-easy-to-keep’ species is important for scientific purposes and for such aquaculture needs as the production of alive foods, the culture of small larvae and the test of new culture procedures. For this reason, we planned and built a programmable experimental system adaptable to the culture of various aquatic organisms, at different developmental stages. The system is based on culture cylinders contained into operational tanks connected to water conditioning tanks. A programmable central processor unit controls the operations, that is, water changes, temperature, light irradiance, the opening and closure of valves for the discharge of unused foods, water circulation and filtration and disinfection systems, according to the information received by various probes. Various devices may be set to modify water circulation and water changes to fulfil the needs of given organisms, to avoid damage of delicate structures, improve feeding performances and reduce the risk of movements over the water surface. The results obtained indicate that the system is effective in the production of shrimp larvae, being able to produce Hippolyte inermis post-larvae with low mortality as compared with the standard operation procedures followed by human operators. Therefore, the patented prototype described in the present study is a possible solution to automate and simplify the rearing of small invertebrates in the laboratory and in production plants.