Genomic selection has become increasingly important in the breeding of animals and plants. The response variable is an important factor, influencing the accuracy of genomic selection. The de-regressed proof (DRP) based on traditional estimated breeding value (EBV) is commonly used as response variable. In the current study, simulated data from 16th QTL-MAS Workshop and real data from Chinese Holstein cattle were used to compare accuracy and bias of genomic prediction with two methods of calculating DRP. Our results with simulated data showed that the correlation between genomic EBV and true breeding value achieved using the Jairath method (DRP_J) was superior to that achieved using the Garrick method (DRP_G) for simulated trait 1 but the reverse was true for simulated trait 3, and these two methods performed comparably for simulated trait 2. For all three simulated traits, DRP_J yielded larger bias of genomic prediction. However, DRP_J outperformed DRP_G in both accuracy and unbiasedness for four milk production traits in Chinese Holstein. In the estimation of genomic breeding value using genomic BLUP model, two methods for weighting diagonal elements of incidence matrix associated with residual error were also compared. With increasing the proportion of genetic variance unexplained by markers, the accuracy of genomic prediction was decreased and the bias was increased. Weighting by the reliability of DRP produced accuracy comparable to the evaluation where the proportion of genetic variance unexplained by markers was considered, but with smaller bias in general.

The identification of individuals’ breed of origin has several practical applications in livestock and is useful in different biological contexts such as conservation genetics, breeding and authentication of animal products. In this paper, penalized multinomial regression was applied to identify the minimum number of single nucleotide polymorphisms (SNPs) from high-throughput genotyping data for individual assignment to dairy sheep breeds reared in Sicily. The combined use of penalized multinomial regression and stability selection reduced the number of SNPs required to 48. A final validation step on an independent population was carried out obtaining 100% correctly classified individuals. The results using independent analysis, such as admixture, Fst, principal component analysis and random forest, confirmed the ability of these methods in selecting distinctive markers. The identified SNPs may constitute a starting point for the development of a SNP based identification test as a tool for breed assignment and traceability of animal products.

Genomic regions under high selective pressure present specific runs of homozygosity (ROH), which provide valuable information on the genetic mechanisms underlying the adaptation to environment imposed challenges. In broiler chickens, the adaptation to conventional production systems in tropical environments lead the animals with favorable genotypes to be naturally selected, increasing the frequency of these alleles in the next generations. In this study, ~1400 chickens from a paternal broiler line were genotyped with the 600 K Affymetrix® Axiom® high-density (HD) genotyping array for estimation of linkage disequilibrium (LD), effective population size (Ne), inbreeding and ROH. The average LD between adjacent single nucleotide polymorphisms (SNPs) in all autosomes was 0.37, and the LD decay was higher in microchromosomes followed by intermediate and macrochromosomes. The Ne of the ancestral population was high and declined over time maintaining a sufficient number of animals to keep the inbreeding coefficient of this population at low levels. The ROH analysis revealed genomic regions that harbor genes associated with homeostasis maintenance and immune system mechanisms, which may have been selected in response to heat stress. Our results give a comprehensive insight into the relationship between shared ROH regions and putative regions related to survival and production traits in a paternal broiler line selected for over 20 years. These findings contribute to the understanding of the effects of environmental and artificial selection in shaping the distribution of functional variants in the chicken genome.

The growing request for healthier fatty acid composition of animal products is raising the necessity of a deeper knowledge of the main factors controlling fatty acids storage in muscle and backfat. Perilipin (PLIN) 5, and the whole Perilipin family, seem to play a crucial role in the regulation of lipids deposition as code for proteins coating intracellular lipid droplets surface. Nevertheless, the knowledge of these genes in pig is still incomplete. The present research was aimed at investigating in different pig breeds the PLIN5 gene, analysing its expression level and the associations of the variability in its downstream gene region with pork meat and carcass quality traits. Moreover, the PLIN5 protein localisation in porcine skeletal muscle was investigated through immunofluorescence, resulting to be widespread in Semimembranosus muscle (SM) myofibers. The identified single nucleotide polymorphism (SNP) rs327694326 (NC_010444.4:g.74314701T>C) located in PLIN5 downstream region was analysed in different pig populations, represented by 512 Italian Large White (ILW) pigs, 300 Italian Duroc (IDU) samples, 100 Italian Landrace, 100 Pietrain and 60 pigs belonging to three Italian native breeds (20 samples of Cinta Senese, 20 Calabrese and 20 Casertana pigs). The C allele was found in ILW, IDU and Pietrain pigs. In ILW pigs this SNP showed results indicating a possible association with oleic and cis-vaccenic fatty acid contents in backfat tissue. Furthermore, as PLINs are known to regulate lipases activity, we tested if the rs327694326 SNP was associated with differences in Hormone-sensitive lipase (LIPE) gene expression levels. In SM of ILW pigs, PLIN5 C allele was associated with significantly lower LIPE transcription levels than T allele (P=0.02 for Student’s t test of TT v. CT samples, P<0.0001 for TT v. CC pigs), whereas in IDU breed no significant difference was noticed in LIPE transcription levels between TT and TC animals. The results may suggest that variations in the PLIN5 sequence may be linked to LIPE expression through a still poorly known regulative molecular process.

This study examines the impact of Lupinus angustifolius variety (C) and inclusion level (L) in broiler diets on the nutritional value, viscosity of ileal digesta and activity of gut microbiota. The experiment was conducted on 154 female 21-day-old broilers, allocated to 11 groups (kept individually). A reference lupin-free diet and 10 test diets containing one of five lupin seeds; Kadryl, Regent, Dalbor, Bojar and Tango, mixed with the reference diet at a ratio of 25 : 75 or 32 : 68 dry matter (DM) (low or high level of inclusion) were prepared. Diets were fed for 6 days, excreta were collected over last 4 days. Apparent metabolizable energy corrected to zero N balance (AMEN) of diets and AMEN of lupin seeds were calculated. Birds were sacrificed, ileal and caecal digesta were pooled by segments from two birds, and the activity of bacterial enzymes was determined. The ileal digesta viscosity was measured immediately (ileal viscosity immediate (IVI)) or after 6 days storage at −18°C (ileal viscosity frozen). AMEN of test diets were lower than the reference diet. Lupin AMEN values ranged from 6.04 MJ/kg DM for Regent at high level to 9.25 MJ/kg DM for Bojar at low level. High inclusion level numerically decreased AMEN value in all cultivars, except for Kadryl, for which it increased (significant C×L interaction). The IVI value was 2.6 mPa·s in the reference group, but ranged from 6.3 to 21.7 mPa·s in lupin-fed birds. It increased significantly with level for Regent, Dalbor and Tango but not for the other two cultivars (significant C×L interaction). There was a negative correlation between IVI and: apparent total tract N retention, fat digestibility from test diets, AMEN of diets and lupins. Ileal viscosity immediate was positively correlated with the activity of ileal α- and β-glucosidase and negatively with ileal α-galactosidase and caecal α-glucosidase. Ileal viscosity frozen ranged from 3.2 to 5 mPa·s and it was not correlated with lupins AMEN. This suggests that the digesta viscosity caused by narrow-leafed lupin is detrimental to its nutritional value and interfere with the gut microbial activity. In addition, the lupins viscosity was measured by two in vitro methods: the water extract viscosity (WEV) method and after incubation in conditions imitating in vivo digestion (enzyme-treated extract viscosity (EEV)). In vivo viscosity was weakly reflected by in vitro measurements as there was no correlation between IVI and WEV or EEV. Overall, findings suggest that the different cultivars of narrow-leafed lupin may have different value for practical application in broiler diets.

Over the past decade, in vitro methods have been developed to study intestinal fermentation in pigs and its influence on the digestive physiology and health. In these methods, ingredients are fermented by a bacterial inoculum diluted in a mineral buffer solution. Generally, a reducing agent such as Na2S or cysteine-HCl generates the required anaerobic environment by releasing metabolites similar to those produced when protein is fermented, possibly inducing a dysbiosis. An experiment was conducted to study the impact of two reducing agents on results yielded by such in vitro fermentation models. Protein (soybean proteins, casein) and carbohydrate (potato starch, cellulose) ingredients were fermented in vitro by bacteria isolated from fresh feces obtained from three sows in three carbonate-based incubation media differing in reducing agent: (i) Na2S, (ii) cysteine-HCl and (iii) control with a mere saturation with CO2 and devoid of reducing agent. The gas production during fermentation was recorded over 72 h. Short-chain fatty acids (SCFA) production after 24 and 72 h and microbial composition of the fermentation broth after 24 h were compared between ingredients and between reducing agents. The fermentation residues after 24 h were also evaluated in terms of cytotoxicity using Caco-2 cell monolayers. Results showed that the effect of the ingredient induced higher differences than the reducing agent. Among the latter, cysteine-HCl induced the strongest differences compared with the control, whereas Na2S was similar to the control for most parameters. For all ingredients, final gas produced per g of substrate was similar (P>0.10) for the three reducing agents whereas the maximum rate of gas production (Rmax) was reduced (P<0.05) when carbohydrate ingredients were fermented with cysteine-HCl in comparison to Na2S and the control. For all ingredients, total SCFA production was similar (P>0.10) after 24 h of fermentation with Na2S and in the control without reducing agent. Molar ratios of branched chain-fatty acids were higher (P<0.05) for protein (36.5% and 9.7% for casein and soybean proteins, respectively) than for carbohydrate (<4%) ingredients. Only fermentation residues of casein showed a possible cytotoxic effect regardless of the reducing agent (P<0.05). Concerning the microbial composition of the fermentation broth, most significant differences in phyla and in genera ascribable to the reducing agent were found with potato starch and casein. In conclusion, saturating the incubation media with CO2 seems sufficient to generate a suitable anaerobic environment for intestinal microbes and the use of a reducing agent can be omitted.

The effect of a calcium (Ca) and phosphorus (P) depletion and repletion strategy was studied in four consecutive feeding phases of 28 days each. In all, 60 castrated male pigs (14±1.6 kg initial BW) received 60% (low (L) diet; depletion) or 100% (control (C) diet; repletion) of their Ca and digestible P requirements according to six feeding sequences (CCCC, CCCL, CLCC, CCLC, LCLC and LLLL; subsequent letters indicate the diet received in phases 1, 2, 3 and 4, respectively). Pigs bone mineral content in whole-body (BMCb) and lumbar vertebrae L2 to L4 (BMCv) was measured in every feeding phase by dual-energy X-ray absorptiometry. Growth performance was slightly (<10%) affected by depletion, however, dietary treatments did not affect overall growth. Compared with control pigs, depletion reduced BMCb (34%, 38%, 33% and 22%) and BMCv (46%, 54%, 38% and 26%) in phases 1 to 4, respectively. Depletion increased however digestible P retention efficiency from the second to the fourth phases allowing LLLL pigs to present no differences in BMCb and BMCv gain compared with CCCC pigs in phase 4. Growth performance in repleted compared with control pigs was lower in phase 2, was no different in phase 3 and was lower in CLCC pigs in phase 4. Repletion increased body P and Ca retention efficiency when compared with control pigs (respectively, 8% and 10% for LC v. CC, P<0.01; 8% and 10% for CLC v. CCC, P<0.10; 18% and 25% for CLCC, CCLC, LCLC v. CCCC, P<0.001). Moreover, BMCv gain was higher in CLC pigs (P<0.001) and gains of body P, Ca, BMCb and BMCv in phase 4 were also higher in repleted than in CCCC pigs (respectively, 14%, 20%, 20% and 52%; P⩽0.02). Repletion reduced body P, Ca, BMCb and BMCv masses in phase 2 but no differences were found in phase 4 compared with control pigs. Lumbar vertebrae L2 to L4 bone mineral content was more sensitive to depletion and repletion sequences than BMCb especially in the first phase probably due to a higher proportion of metabolically active trabecular bone in vertebrae than in the whole skeleton. Dietary Ca was, however, oversupply in L compared with C diets (3.1 v. 2.5 Ca:digestible P ratio, respectively) suggesting that P has probably driven the regulations. Phosphorus and Ca depletion and repletion increases dietary P utilization efficiency and can help to reduce dietary P supply, but the underlying mechanisms need elucidation before its practical application.

The main limitation for determining feed efficiency of freely grazing ruminants is measurement of daily individual feed intake. This paper describes an investigation that assessed a method for estimating intake of forage based on changes in BW of ewes. A total of 24 dry and non-pregnant Romane ewes (12 hoggets, HOG; mean±SD 51.8±2.8 kg BW; body condition score (BCS) 2.6±0.2; and 12 adults, ADU; 60.4±8.5 kg BW; BCS 2.7±0.8) were selected for the study and moved from their rangeland system to a confined pen with controlled conditions and equipped with individual automatic feeders. The experiment lasted for 28 days (21 days adaptation and 7 days feed intake measurement). Ewes were fed hay and trained to use the electronic feeders (one feeding station per ewe) in which actual daily intake (H intake24) was measured. The pens were designed to maximize movement of trained ewes through an automated Walk-over-Weighing device, by using water and mineral salts as attractants. Total individual intake of hay measured in the automatic feeder at each meal (H intake) was compared with indirect estimates of feed intake determined using differences in the BW of the ewes (∆BW) before and 1 h following morning and afternoon feeding at fixed times. The BW, BCS, H intake, H intake24, as well as plasma non-esterified fatty acids (NEFA), glucose and insulin profiles were determined. The BW was higher in ADU v. HOG but BCS was not affected by parity. The H intake24 was affected by day of experiment as a consequence of reduced availability and intake of water on one day. Plasma glucose, NEFA and insulin were not affected by parity or day of experiment. The H Intake was and ∆BW tended to be higher in the morning in HOG, whereas H intake was and ∆BW tended to be higher in ADU at the afternoon meal. Irrespective of parity or feeding time, there was very strong correlation (r 2=0.93) between H intake and ∆BW. This relationship confirms that our indirect method of estimating individual forage intake was reliable within the strictly controlled conditions of the present experiment. The method appears suitable for use in short-term intensive group feeding situations, and has potential to be further developed for longer-term forage intake studies, with a view to developing a method for freely grazing ruminants.

The control of nutrient partitioning is complex and affected by many factors, among them physiological state and production potential. Therefore, the current model aims to provide for dairy cows a dynamic framework to predict a consistent set of reference performance patterns (milk component yields, body composition change, dry-matter intake) sensitive to physiological status across a range of milk production potentials (within and between breeds). Flows and partition of net energy toward maintenance, growth, gestation, body reserves and milk components are described in the model. The structure of the model is characterized by two sub-models, a regulating sub-model of homeorhetic control which sets dynamic partitioning rules along the lactation, and an operating sub-model that translates this into animal performance. The regulating sub-model describes lactation as the result of three driving forces: (1) use of previously acquired resources through mobilization, (2) acquisition of new resources with a priority of partition towards milk and (3) subsequent use of resources towards body reserves gain. The dynamics of these three driving forces were adjusted separately for fat (milk and body), protein (milk and body) and lactose (milk). Milk yield is predicted from lactose and protein yields with an empirical equation developed from literature data. The model predicts desired dry-matter intake as an outcome of net energy requirements for a given dietary net energy content. The parameters controlling milk component yields and body composition changes were calibrated using two data sets in which the diet was the same for all animals. Weekly data from Holstein dairy cows was used to calibrate the model within-breed across milk production potentials. A second data set was used to evaluate the model and to calibrate it for breed differences (Holstein, Danish Red and Jersey) on the mobilization/reconstitution of body composition and on the yield of individual milk components. These calibrations showed that the model framework was able to adequately simulate milk yield, milk component yields, body composition changes and dry-matter intake throughout lactation for primiparous and multiparous cows differing in their production level.

Negative energy balance (NEB) is an altered metabolic state in modern high-yielding dairy cows. This metabolic state occurs in the early postpartum period when energy demands for milk production and maintenance exceed that of energy intake. Negative energy balance or poor adaptation to this metabolic state has important effects on the liver and can lead to metabolic disorders and reduced fertility. The roles of regulatory factors, including transcription factors (TFs) and micro RNAs (miRNAs) have often been separately studied for evaluating of NEB. However, adaptive response to NEB is controlled by complex gene networks and still not fully understood. In this study, we aimed to discover the integrated gene regulatory networks involved in NEB development in liver tissue. We downloaded data sets including mRNA and miRNA expression profiles related to three and four cows with severe and moderate NEB, respectively. Our method integrated two independent types of information: module inference network by TFs, miRNAs and mRNA expression profiles (RNA-seq data) and computational target predictions. In total, 176 modules were predicted by using gene expression data and 64 miRNAs and 63 TFs were assigned to these modules. By using our integrated computational approach, we identified 13 TF-module and 19 miRNA-module interactions. Most of these modules were associated with liver metabolic processes as well as immune and stress responses, which might play crucial roles in NEB development. Literature survey results also showed that several regulators and gene targets have already been characterized as important factors in liver metabolic processes. These results provided novel insights into regulatory mechanisms at the TF and miRNA levels during NEB. In addition, the method described in this study seems to be applicable to construct integrated regulatory networks for different diseases or disorders.

Previous studies showed that spermine could protect the organism from oxidative damage in vivo. However, in vivo information on the antioxidant-related underlying molecular mechanism of spermine is limited. In this experiment, we further evaluated the effects of spermine supplementation and extended spermine administration on the antioxidant status and antioxidant-related signaling molecules gene expression in the liver and longissimus dorsi of piglets. A total of 80 piglets were randomly distributed to two groups, that is, those with adequate nutrient intake administrated with spermine (0.4 mmol/kg BW) or those with restricted nutrient intake supplemented by saline. The piglets were fed in pairs for 7 h or 3, 6, or 9 days. The results are as follows: (1) spermine can promote the antioxidant capacity by increasing enzymatic antioxidant capacity, glutathione content and clearance of oxygen radicals; (2) spermine significantly increased the mRNA levels of enzymatic antioxidant substances, NF-E2-related nuclear factor 2, Kelch-like ECH-associated protein 1, and the mammalian target of rapamycin but decreased the mRNA levels of ribosomal p70 S6 kinase in the liver and longissimus dorsi of the piglets.

Intramuscular fat (IMF) has a large effect in the sensory properties of meat because it affects tenderness, juiciness and flavour. A divergent selection experiment for IMF in longissimus dorsi (LD) muscle was performed in rabbits. Since liver is the major site of lipogenesis in rabbits, the objective of this work is to study the liver metabolism in the lines of the divergent selection experiment. Intramuscular fat content, perirenal fat weight, liver weight, liver lipogenic activities and plasma metabolites related to liver metabolism were measured in the eighth generation of selection. Direct response on IMF was 0.34 g/100 g of LD, which represented 2.7 SD of the trait, and selection showed a positive correlated response in the perirenal fat weight. High-IMF line showed greater liver size and greater liver lipogenic activities of enzymes glucose-6-phosphate dehydrogenase and malic enzyme. We did not find differences between lines for fatty acid synthase lipogenic activity. With regard to plasma metabolites, low-IMF line showed greater plasma concentration of triglycerides, cholesterol, bilirubin and alkaline phosphatase than high-IMF line, whereas high-IMF line showed greater albumin and alanine transaminase concentrations than low-IMF line. We did not observe differences between lines for glucose, total protein and plasma concentrations. Phenotypic correlations between fat (IMF and perirenal fat weight) and liver traits showed that liver lipogenesis affects fat deposition in both, muscle and carcass. However, the mechanisms whereby liver lipogenesis affected IMF content remain to be clarified.

Broiler eggs were either incubated at 37.8°C during the whole incubation period (control), or at higher (38.8°C, group H) and lower temperatures (36.8°C, group L) from embryonic day (ED) 7 up to ED 10 (ED 7 to 10) or from ED 10 up to ED 13 (ED 10 to 13). Before and after this temperature treatment the eggs were incubated at 37.8°C. The day-old chicks were weighted, sexed and fed up to day 35. On days 1 and 35 samples were taken from the breast and leg muscles for analyzing of the mitochondrial respiratory activity (MRA) and from the breast muscles for analysis of the cross-sectional areas (CSA) and the glycogen phosphorylase (GP), phosphofructokinase (PFK), lactate dehydrogenase (LDH), citrate synthase (CS) and cytochrome oxidase (COX) activities. Statistical analysis showed that treatment (control, group H, group L), sex and their interaction, but not the treatment period (ED 7 to 10; ED 10 to 13), significantly influenced the results. Group H chicks had lower (P⩽0.05) body and heart weights but higher (P⩽0.05) liver weights, CSA values, leg MRA as well as PFK, LDH, CS, GP and COX activities compared with the group L chicks. The results of the control chicks differ (P⩽0.05) from those of the group H (body, heart weight, COX), the group L chicks (liver weight, PFK, LDH, CS, GP) or the birds of both other groups (CSA). The group H broiler had higher (P⩽0.05) body and leg weights as well as LDH, CS, COX and GP activities than the group L broilers. The BWs and the LDH and GP results of the control broiler differ (P⩽0.05) from those of both other groups or from the results of the group H (CS) and group L broiler (COX). Female broilers had lower (P⩽0.05) body, breast and leg weights, but higher (P⩽0.05) CSA, LDH, CS and GP activities than the male animals. Analysis of treatment×sex interaction showed that group H hens had higher (P⩽0.05) body and breast weights, LDH and GP activities compared with the group L hens, whereas in the male broiler no effect of the interaction could be found, except for the lower (P⩽0.05) CSA values in the group H than group L cocks. The treatment effects are probably due to altered embryonic activity and related molecular mechanisms. The sex-related differences in the broiler indicate that these alterations already occur in the embryos and chicks, but become significant with the sexual dimorphism after hatch.

The effects of obesity on reproduction have been widely reported in humans and mice. The present study was designed to compare the reproductive performance of lean and fat chicken lines, divergently selected for abdominal fat content. The following parameters were determined and analyzed in the two lines: (1) reproductive traits, including age at first egg and total egg numbers from generations 14 to 18, absolute and relative testicular weights at 7, 14, 25, 30, 45 and 56 weeks of age, semen quality at 30, 45 and 56 weeks of age in generation 18, and fertility and hatchability from generations 14 to 18; (2) reproductive hormones at 7, 14, 25, 30, 45 and 56 weeks of age in generation 18; (3) and the relative mRNA abundance of genes involved in reproduction at 7, 14, 25, 30, 45 and 56 weeks of age in generation 18. In females, birds in the lean line laid more eggs from the first egg to 40 weeks of age than the birds in the fat line. In male broilers, the birds in the lean line had higher absolute and relative testicular weights at 7, 14 and 25 weeks of age, but lower absolute and relative testicular weights at 56 weeks of age than the birds in the fat line. Male birds in the lean line had greater sperm concentrations and larger numbers of motile and morphologically normal sperms at 30, 45 and 56 weeks of age than the birds in the fat line. Fertility and hatchability were also higher in the lean line than in the fat line. Significant differences in the plasma levels of reproductive hormones and the expression of reproduction-associated genes were also found at different ages in the lean and fat birds, in both males and females. These results suggest that reproductive performance is better in lean birds than in fat birds. In view of the unique divergent lines used in this study, these results imply that selecting for abdominal fat deposition negatively affects the reproductive performance of birds.

The present study investigated whether dietary turmeric (Curcuma longa L.) can improve rabbit reproduction, ovarian function, growth, or viability. Female New Zealand White rabbits were either fed a standard diet (n=15) or a diet enriched with 5 g (group E1) or 20 g (group E2) turmeric powder per 100 kg feed mixture (n=16 or 15, respectively). After 295 days, weight gain, conception and kindling rates, pup and mother viability, ovarian macro- and micro-morphometric indices, release of leptin in response to the addition LH, and the release of progesterone, testosterone and leptin by isolated ovarian fragments were analyzed. Dietary turmeric failed to affect ovarian length and weight but did increase the number of primary follicles (E2: 32.5% greater than control group), as well as the diameter of primary (E1: +19.4%, E2: +21.1%), secondary (E2: +41.4%), and tertiary (E1: +97.1%, E2: +205.1%) follicles. Turmeric also increased the number of liveborn (E1: +21.0%) and weaned (E1: +25.0%) pups and decreased the number of stillborn pups (E2: −87.5%) but did not affect weight gain, conception, or kindling rate. Furthermore, dietary turmeric decreased doe mortality during the first reproductive cycle (13.3% in control; 0% in E1; and 6.7% in E2) but not during the second cycle. In vitro, the ovaries of the turmeric-treated rabbits released more progesterone (E1: +85.7%, E2: +90.0%) and less testosterone (E2: −87.0%) and leptin (E2: −29.0%) than the ovaries of control rabbits. Moreover, LH decreased the leptin output of control rabbits but increased that of experimental rabbits. Therefore, it is likely that dietary turmeric improves pup viability and that it could promote rabbit fecundity by either (1) promoting the production of primary ovarian follicles or (2) stimulating the growth of follicles at all stages of folliculogenesis.

Vocalisations are commonly expressed by gregarious animals, including cattle, as a form of short- and long-distance communication. They can provide conspecifics with meaningful information about the physiology, affective state and physical attributes of the caller. In cattle, calls are individually distinct meaning they assist animals to identify specific individuals in the herd. Consequently, there is potential for these vocalisations to be acoustically analysed to make inferences about how individual animals or herds are coping with their external surroundings, and then act on these signals to improve feed conversion efficiency, reproductive efficiency and welfare. In the case of dairy farming, where herd sizes are expanding and farmers are becoming more reliant on technologies to assist in the monitoring of cattle, the study of vocal behaviour could provide an objective, cost effective and non-invasive alternative to traditional measures of welfare. The vocalisations of cattle in response to calf separation, social isolation and painful husbandry procedures, alongside changes to feeding and oestrous activity are here reviewed. For future application of sound technology, research is first necessary to analyse the acoustic structure of cattle vocalisations and determine the specific information they encode. This review draws together the latest research in field of cattle bioacoustics highlighting how the source–filter theory and affective state dimensional approach can be adopted to decode this information and improve on-farm management.

One challenge of intensive pig production is tail damage caused by tail biting, and farmers often decrease the prevalence of tail damage through tail docking. However, tail docking is not an optimal preventive measure against tail damage and thus, it would be preferable to replace it. The aim of the current study was to investigate the relative effect of three possible preventive measures against tail damage. The study included 112 pens with 1624 finisher pigs divided between four batches. Pens were randomly assigned to one level of each of three treatments: (1) tail-docked (n=60 pens) v. undocked (n=52 pens), (2) 150 g of straw provided per pig per day on the solid floor (n=56 pens) v. no straw provided (n=56 pens), (3) stocking density of 1.21 m2/pig (11 pig/pen; n=56 pens) v. 0.73 m2/pig (18 pigs/pen; n=56 pens). Tail damage was recorded three times per week throughout the finisher period by scoring the tail of each individual pig. A pen was recorded as a tail damage pen and no longer included in the study if at least one pig in a pen had a bleeding tail wound; thus, only the first incidence of tail damage on pen level was recorded. Data were analysed by a Cox regression for survival analysis assuming proportional hazards. Results are presented as hazards, and a higher hazard means that a pen has a higher risk of tail damage and of it happening earlier in the finisher period. Pens with undocked pigs had a 4.32-fold higher hazard of tail damage compared with pens with docked pigs (P<0.001). Pens with no straw provided had a 2.22-fold higher hazard of tail damage compared with pens with straw provided (P<0.01). No interactions was seen between the treatments, but the effect of tail docking was higher than the effect of straw provision (P<0.001). Stocking density did not have a significant effect on the hazard of tail damage (hazard rate ratios (HRR)=1.67; P=0.064). However, a combination of straw provision and lowered stocking density showed a similar hazard of tail damage as seen with only tail docking (HRR=1.58; P=0.39). In conclusion, tail docking and straw provision were preventive measures against tail damage, and tail docking reduced the risk more than straw provision. A combination of other preventive measures is necessary to reduce the risk of tail damage in undocked pigs to the same level as in docked pigs.

Previous cafeteria studies suggested that a moderate natural gastrointestinal nematode (GIN) infection did not modify the resource selection of adult Criollo goats towards tannin-rich plants compared with worm-free goats. A higher infection with Haemonchus contortus could trigger a change in the resource selection behaviour towards tannin-rich foliage. Alternatively, goats might select plant species solely to meet their nutritional requirements. A cafeteria study investigated the effect of a high artificial infection with H. contortus on the feed resource selection of goats. Adult Criollo goats (37.5±4.8 kg BW) with browsing experience were distributed in two groups: the infected group (IG) with six animals artificially infected with H. contortus (6000 L3/animal); and the non-infected group (NIG) with six animals maintained worm-free. The experiment included two 5-day periods with additional 5-day adaptation period. In the first period, animals were offered foliage of five plant species with a decreasing gradient of condensed tannins (CT) (Mimosa bahamensis, Gymnopodium floribundum, Havardia albicans, Acacia pennatula, Lysiloma latisiliqum), and three plant species with negligible CT content (Leucaena leucocephala, Piscidia piscipula and Brosimum alicastrum). In the second period the foliage of B. alicastrum was withdrawn. A grain-based concentrate feed was offered daily at 1% BW in DM basis. Dry matter and nutrient intake was determined. Foliage selection of each experimental group was determined using the Chesson selection index. The H. contortus egg count per gram of faeces (EPG) was determined for infected goats twice daily. Chesson index showed a similar pattern of foliage selection on periods 1 and 2. Mean EPG of goats in IG was 2028±259 EPG during period 1 and 1 293±198 EPG during period 2 (P>0.05). During period 1, the selection pattern was highest for B. alicastrum (tannin-free), followed by a tannin-rich plant (M. bahamensis). These two plants remained as highly selected during period 2. The Chesson index showed that both experimental groups (IG and NIG) selected the same plant species in both periods. Thus, a high H. contortus infection did not affect selection of goats fed with CT-rich plants. Apparently, goats balanced their nutrient intake with the plants selected, showing evidence of nutritional wisdom. This balance may have helped to prevent excess protein in the diet and also to maintain a low GIN infection, both considered as examples of prophylactic self-medication.

European pig production continues to encounter economic and environmental challenges. To address these issues, methods have been developed to assess performances of pig production systems. Recent studies indicate that considering variability in performances among pigs improves the accuracy and reliability of results compared with modelling an average animal. Our objective was to develop a pig fattening unit model able to (i) simulate individual pig performances, including their variability in interaction with farmers’ practices and management, and (ii) assess their effects on technical, economic and environmental performances. Farmer practices included in the model were chosen from a typology generated from on-farm surveys focused on batch management, pig allocation to pens, pig feeding practices, practices of shipping to the slaughterhouse, and management of the remaining pigs. Pigs are represented using an individual-based model adapted from the InraPorc® model. To illustrate the model’s abilities, four scenarios were simulated that combine two feed rationing plans (ad libitum, restricted to 2.5 kg/day) and two feed sequence plans (two-phase, 10-phase). Analysis of variance was performed on the simulated technical, economic and environmental indicators (calculated via Life Cycle Assessment). The feed rationing plan and feed sequence plan significantly affected all indicators except for the premium per pig, for which the feed sequence plan did not have a significant effect. The ‘restricted 10-phase’ scenario maximised gross margin of the fattening unit (14.2 €/pig) and minimised environmental impacts per kg of pig produced. In contrast, the ‘ad libitum two-phase’ scenario generated the lowest margin (8.20 €/pig) and the highest environmental impacts. The model appears to be a promising tool to assess effects of farmers’ practices, pig characteristics and farm infrastructure on technical, economic and environmental performances of the fattening unit, and to investigate the potential of improvement. However, further work is needed, based on virtual experiments, in order to evaluate the effects of a larger diversity of practices.