Genetic evaluation based on information from phenotypes, pedigree and markers can be implemented using a recently developed single-step method. In this paper we compare accuracies of predicted breeding values for daily gain and feed conversion ratio (FCR) in Danish Duroc pigs obtained from different versions of single-step methods, the traditional pedigree-based method and the genomic BLUP (GBLUP) method. In particular, we present a single-step method with an adjustment of the genomic relationship matrix so that it is compatible to the pedigree-based relationship matrix. Comparisons are made for both genotyped and non-genotyped animals and univariate and bivariate models. The results show that the three methods with marker information (two single-step methods and GBLUP) produce more accurate predictions of genotyped animals than the pedigree-based method. In addition, single-step methods provide more accurate predictions for non-genotyped animals. The results also show that the single-step method with adjusted genomic relationship matrix produce more accurate predictions than the original single-step method. Finally, the results for the bivariate analyses show a somewhat improved accuracy and reduced inflation of predictions for FCR for the two single-step methods compared with the univariate analyses. The conclusions are: first, the methods with marker information improve prediction compared with the pedigree-based method; second, a single-step method, contrary to GBLUP, provides improved predictions for all animals compared to the pedigree-based method; and third, a single-step method should be used with an adjustment of the genomic relationship matrix.

The presence of the fermentable sugar d-mannitol in the diet improves nitrogen (N) utilization in rabbits. To clarify the mechanism by which d-mannitol improves N utilization, we studied the effect of d-mannitol on the fate of blood urea N in growing rabbits. Growing rabbits received a control diet or a diet containing d-mannitol, which were formulated by adding 80 g/kg glucose or d-mannitol to timothy hay. After 9 days of feeding of the experimental diets, 15N-urea was administrated intravenously under anesthesia 1 h before slaughter. The blood urea level (concentration of both urea N (43.6% of the control group (CG), P < 0.05) and 15N (95% of the CG, P < 0.05) in blood serum) was reduced in the mannitol group. The concentration and amount of N, and 15N atom % excess in the contents of the cecum and colon were higher (P < 0.05) in the rabbits fed the mannitol diet than in rabbits fed the control diet, especially in the cecum. The consumption of mannitol caused bacterial proliferation in the cecum characterized by marked short-chain fatty acid production (165% of the CG, P < 0.05), decreased cecal ammonia N (73% of the CG, P < 0.05) and elevated cecal bacterial N (150% of the CG, P < 0.05). On the other hand, addition of d-mannitol to the diet decreased N (80% of the CG, P < 0.05) and 15N (77% of the CG, P < 0.05) excretion in the urine. These results indicate that d-mannitol increases the transfer of blood urea N to the large intestine, where it is used for bacterial N synthesis.

Horses are often stabled in individual boxes, a method that does not meet their natural needs and may cause psychical and musculoskeletal diseases. This problem is particularly evident in Iceland, where horses often spend the long winter periods in cramped boxes. The aim of this study was to analyze the suitability of a group housing system in Iceland, but the results are also applicable to horses of other regions. Eight Icelandic horses were observed in an active stable system, and their behavior and time budget were recorded. Movement and lying behavior were studied with ALT (Activity, Lying, Temperature detection) pedometers. The effect of an automatic concentrate feeding station (CFS) on the horses’ behavior was examined. In the first period of investigation, the horses were fed concentrates manually, and in the second period, they were fed with the CFS. Additional behavioral observations and a determination of social hierarchy occurred directly or by video surveillance. The physical condition of the horses was recorded by body weight (BW) measurement and body condition scoring (BCS). The results showed a significant increase between the first and second trial periods in both the activity (P < 0.001) and the lying time (P = 0.003) of the horses with use of the CFS. However, there was no significant change in BW during the first period without the CFS (P = 0.884) or during the second period with the CFS (P = 0.540). The BCS of the horses was constant at a very good level during both trial periods, and the horses showed a low level of aggression, a firm social hierarchy and behavioral synchronization. This study concludes that group housing according to the active stable principle is a welfare-friendly option for keeping horses and is a suitable alternative to conventional individual boxes.

In order to describe the temporal evolution of milk yield (MY) and composition in extended lactations, 21 658 lactations of Italian Holstein cows were analyzed. Six empirical mathematical models currently used to fit 305 standard lactations (Wood, Wilmink, Legendre, Ali and Schaeffer, quadratic and cubic splines) and one function developed specifically for extended lactations (a modification of the Dijkstra model) were tested to identify a suitable function for describing patterns until 1000 days in milk (DIM). Comparison was performed on individual patterns and on average curves grouped according to parity (primiparous and multiparous) and lactation length (standard ⩽305 days, and extended from 600 to 1000 days). For average patterns, polynomial models showed better fitting performances when compared with the three or four parameters models. However, LEG and spline regression, showed poor prediction ability at the extremes of the lactation trajectory. The Ali and Schaeffer polynomial and Dijkstra function were effective in modelling average curves for MY and protein percentage, whereas a reduced fitting ability was observed for fat percentage and somatic cell score. When individual patterns were fitted, polynomial models outperformed nonlinear functions. No detectable differences were observed between standard and extended patterns in the initial phase of lactation, with similar values of peak production and time at peak. A considerable difference in persistency was observed between 200 and 305 DIM. Such a difference resulted in an estimated difference between standard and extended cycle of about 7 and 9 kg/day for daily yield at 305 DIM and of 463 and 677 kg of cumulated milk production at 305 DIM for the first- and second-parity groups, respectively. For first and later lactation animals, peak yield estimates were nearly 31 and 38 kg, respectively, and occurred at around 65 and 40 days. The asymptotic level of production was around 9 kg for multiparous cows, whereas the estimate was negative for first parity.

The current study was conducted to determine the effect of different α-tocopherol (vitamin E) inclusion levels on trans(t)-18:1 and conjugated linoleic acid (CLA) profiles in subcutaneous and intramuscular fat of steers fed a barley-based diet. Fifty-six feedlot steers were offered a barley-based finisher diet (73% steam rolled barley, 22% barley silage and 5% supplement as-fed basis) with four levels of supplementary dl-α-tocopheryl acetate (340, 690, 1040 or 1740 IU/steer per day) for 120 days. Adding vitamin E to the diet had little effect on the overall fatty acid composition of intramuscular fat. The proportion of individual and total t,t- and cis(c),t-CLA, n-3 fatty acids, total polyunsaturated fatty acids (PUFA), mono-unsaturated fatty acids and saturated fatty acids to PUFA ratio in subcutaneous fat were not influenced (P > 0.05) by dietary vitamin E supplementation. Increasing levels of vitamin E led to linear reductions in t6-/t7-/t8-18:1 and t10-18:1 (P < 0.05), and linear increase in t11-/t10-18:1 ratio (P < 0.05) in subcutaneous fat. The content of 20:3n-6 and total n-6 in subcutaneous fat decreased (P < 0.05) linearly with increasing amounts of vitamin E. The subcutaneous fat n-6:n-3 ratio showed a quadratic (P < 0.05) response to vitamin E. In conclusion, although vitamin E supplementation has some potential to reduce t10-18:1 formation and increase t11-/t10-18:1 ratio in subcutaneous fat of cattle fed barley-based diets, the changes in the present study were limited and may not have been sufficient to impact on human health.

The objective of this study was to quantify the genetic associations between a range of carcass-related traits including wholesale cut weights predicted from video image analysis (VIA) technology, and a range of pre-slaughter performance traits in commercial Irish cattle. Predicted carcass cut weights comprised of cut weights based on retail value: lower value cuts (LVC), medium value cuts (MVC), high value cuts (HVC) and very high value cuts (VHVC), as well as total meat, fat and bone weights. Four main sources of data were used in the genetic analyses: price data of live animals collected from livestock auctions, live-weight data and linear type collected from both commercial and pedigree farms as well as from livestock auctions and weanling quality recorded on-farm. Heritability of carcass cut weights ranged from 0.21 to 0.39. Genetic correlations between the cut traits and the other performance traits were estimated using a series of bivariate sire linear mixed models where carcass cut weights were phenotypically adjusted to a constant carcass weight. Strongest positive genetic correlations were obtained between predicted carcass cut weights and carcass value (min r g(MVC) = 0.35; max r g(VHVC) = 0.69), and animal price at both weaning (min r g(MVC) = 0.37; max r g(VHVC) = 0.66) and post weaning (min r g(MVC) = 0.50; max r g(VHVC) = 0.67). Moderate genetic correlations were obtained between carcass cut weights and calf price (min r g(HVC) = 0.34; max r g(LVC) = 0.45), weanling quality (min r g(MVC) = 0.12; max r g(VHVC) = 0.49), linear scores for muscularity at both weaning (hindquarter development: min r g(MVC) = −0.06; max r g(VHVC) = 0.46), post weaning (hindquarter development: min r g(MVC) = 0.23; max r g(VHVC) = 0.44). The genetic correlations between total meat weight were consistent with those observed with the predicted wholesale cut weights. Total fat and total bone weights were generally negatively correlated with carcass value, auction prices and weanling quality. Total bone weight was, however, positively correlated with skeletal scores at weaning and post weaning. These results indicate that some traits collected early in life are moderate-to-strongly correlated with carcass cut weights predicted from VIA technology. This information can be used to improve the accuracy of selection for carcass cut weights in national genetic evaluations.

Stochastic simulation was used for studying the impacts of sexed semen on genetic progress and reproductive performance of dairy cows. Three strategies were compared: WSS (use unsexed semen in cows and heifers), SSH (use sexed semen in heifers and unsexed semen in cows) and SSCH (use sexed semen in both cows and heifers). Conception rate (CR) of unsexed semen was considered to be 35% and 65% in cows and heifers, respectively. CR of sexed semen was considered to be 15 (20% in cows and 50% in heifers), 10, 5 and 0 percentage points lower than unsexed semen. Thus, four subschemes were compared under SSCH (SSCH15, SSCH10, SSCH5, SSCH0) and SSH (SSH15, SSH10, SSH5, SSH0). Moreover, the effect was studied in four distinct paths of selection: active sires (AS), young bulls (YB), bull dams (BD) and milking cows (CW). The average genetic superiority of CW was 12% and 9.5% in SSCH15 and SSH15 strategies relative to a base scheme, respectively. The average genetic superiority of CW was 19% and 10.5% in SSCH0 and SSH0, respectively. Regression analysis showed that genetic superiority of CW increased significantly, that is, 0.5% and 0.1% per every 1% increase in CR in SSCH and SSH, respectively. The result showed that there is a significant difference between genetic superiority of cows in SSCH and SSH schemes. Widespread and limited use of sexed semen in commercial dairy herds resulted in a large genetic advantage in CW. The genetic advantage of gender control was minimal in the selection paths of AS, YB and BD. Open days and services per conception reached to 153 v. 125 days and 5 v. 2.86 under SSCH15 compared with WSS. The age at first calving increased from 774 to 790 days in SSH15 and SSCH15 strategies. Mean of parities decreased to 2.26 v. 2.42 by using sexed semen. The widespread use of sexed semen increased the age average of cows in all parities. Sexed semen increased selection intensity in the CW path, and this contributed to the genetic merit of future cows. On the other hand, sexed semen had a negative effect on the reproductive performance of dairy cows. Generally, although the effect of widespread use of sexed semen (SSCH) on genetic progress is significantly more than limited use of sexed semen (SSH), SSCH decreased reproductive performance of dairy herds dramatically, and this suggests that SSH scenarios might be more appropriate in animal breeding programs. Finally, to make a decision of which schemes are more convenient, it is necessary to compare the economic aspects of schemes.

Intensification and specialisation of agriculture in developed countries enabled productivity to be improved but had detrimental impacts on the environment and threatened the economic viability of a huge number of farms. The combination of livestock and crops, which was very common in the past, is assumed to be a viable alternative to specialised livestock or cropping systems. Mixed crop-livestock systems can improve nutrient cycling while reducing chemical inputs and generate economies of scope at farm level. Most assumptions underlying these views are based on theoretical and experimental evidence. Very few assessments of their environmental and economic advantages have nevertheless been undertaken in real-world farming conditions. In this paper, we present a comparative assessment of the environmental and economic performances of mixed crop-livestock farms v. specialised farms among the farm population of the French ‘Coteaux de Gascogne’. In this hilly region, half of the farms currently use a mixed crop-livestock system including beef cattle and cash crops, the remaining farms being specialised in either crops or cattle. Data were collected through an exhaustive survey of farms located in our study area. The economic performances of farming systems were assessed on 48 farms on the basis of (i) overall gross margin, (ii) production costs and (iii) analysis of the sensitivity of gross margins to fluctuations in the price of inputs and outputs. The environmental dimension was analysed through (i) characterisation of farmers’ crop management practices, (ii) analysis of farm land use diversity and (iii) nitrogen farm-gate balance. Local mixed crop-livestock farms did not have significantly higher overall gross margins than specialised farms but were less sensitive than dairy and crop farms to fluctuations in the price of inputs and outputs considered. Mixed crop-livestock farms had lower costs than crop farms, while beef farms had the lowest costs as they are grass-based systems. Concerning crop management practices, our results revealed an intensification gradient from low to high input farming systems. Beyond some general trends, a wide range of management practices and levels of intensification were observed among farms with a similar production system. Mixed crop-livestock farms were very heterogeneous with respect to the use of inputs. Nevertheless, our study revealed a lower potential for nitrogen pollution in mixed crop-livestock and beef production systems than in dairy and crop farming systems. Even if a wide variability exists within system, mixed crop-livestock systems appear to be a way for an environmental and economical sustainable agriculture.

The benefits of using white clover in pastures have been widely recognised for many years. However, clover is perceived as being unreliable because of its typically low content, which is spatially and temporally variable, in mixed pastures. One proposed solution to increase the proportion of clover in the diet of grazing animals and composition in the pasture is to spatially separate clover from grass within the same field. In a field experiment ryegrass and white clover were grown in fine mixtures, and in pure alternating strips of ryegrass and clover of 1.5 m, 3 m or 18 m width within a field. Pastures were grazed for two grazing periods of 9 and 12 weeks, and measurements of sward surface height (SSH), herbage mass and composition and clover morphology were taken. Grazing behaviour was also observed. Results showed that spatial separation in the long term, when compared with a fine mixture, increased clover availability (18% to 30% v. 9%, based on standing dry matter) and was not grazed to extinction. Ewes maintained their preference for clover throughout the experiment (selection coefficient 2 to 5), which resulted in a reduction in the SSH of clover in monocultures to <3 cm and significant changes to the morphology of clover (smaller leaves, shorter petioles and thicker stolon), at the expense of maximising their intake. Spatial separation in the short term may therefore allow grazing animals to select their preferred diet; however, in the long term in continuously grazed pasture, their preference for clover depletes its availability.

In regions of intensive pig and dairy farming, nutrient losses to the environment at farm level are a source of concern for water and air quality. Dynamic models are useful tools to evaluate the effects of production strategies on nutrient flows and losses to the environment. This paper presents the development of a new whole-farm model upscaling dynamic models developed at the field or animal scale. The model, called MELODIE, is based on an original structure with interacting biotechnical and decisional modules. Indeed, it is supported by an ontology of production systems and the associated programming platform DIESE. The biotechnical module simulates the nutrient flows in the different animal, soil and crops and manure sub-models. The decision module relies on an annual optimization of cropping and spreading allocation plans, and on the flexible execution of activity plans for each simulated year. These plans are examined every day by an operational management sub-model and their application is context dependent. As a result, MELODIE dynamically simulates the flows of carbon, nitrogen, phosphorus, copper, zinc and water within the whole farm over the short and long-term considering both the farming system and its adaptation to climatic conditions. Therefore, it is possible to study both the spatial and temporal heterogeneity of the environmental risks, and to test changes of practices and innovative scenarios. This is illustrated with one example of simulation plan on dairy farms to interpret the Nitrogen farm-gate budget indicator. It shows that this indicator is able to reflect small differences in Nitrogen losses between different systems, but it can only be interpreted using a mobile average, not on a yearly basis. This example illustrates how MELODIE could be used to study the dynamic behaviour of the system and the dynamic of nutrient flows. Finally, MELODIE can also be used for comprehensive multi-criterion assessments, and it also constitutes a generic and evolving framework for virtual experimentation on animal farming systems.

Alpine forages are assumed to have specific effects on ruminal digestion when fed to cattle. These effects were investigated in an experiment from two perspectives, either by using such forages as a substrate for incubation or as feed for a rumen fluid donor cow. In total, six 24-h in vitro batch culture runs were performed. Rumen fluid was collected from a non-lactating donor cow after having grazed pastures at ∼2000 m above sea level for 2, 6 and 10 weeks. These ‘alpine runs’ were compared with three lowland samplings from before and 2 and 6 weeks after the alpine grazing where a silage–concentrate mix was fed. In each run, nine replicates of four forages each were incubated. These forages differed in type and origin (alpine hay, lowland ryegrass hay, grass–maize silage mix, pure hemicellulose) as well as in the content of nutrients. Concentrations of phenolic compounds in the incubated forages were (g/kg dry matter (DM)): 20 (tannin proportion: 0.47), 8 (0.27), 15 (0.52) and 0 (0), respectively. Crude protein was highest in the silage mix and lowest with hemicellulose, whereas the opposite was the case for fiber. The total phenol contents (g/kg DM) for the high altitude and the lowland diet of the donor cow were 27 (tannins: 0.50 of phenols) and 12 (0.27), respectively. Independent of the origin of the rumen fluid, the incubation with alpine hay decreased (P < 0.05) bacterial counts, fermentation gas amount, volatile fatty acid (VFA) production as well as ammonia and methane concentrations in fermentation gas (the latter two being not lower when compared with hemicellulose). Alpine grazing of the cow in turn increased (P < 0.001) bacterial counts and, to a lesser extent, acetate proportion compared with lowland feeding. Further, alpine grazing decreased protozoal count (P < 0.05) and VFA production (P < 0.001) to a small extent, whereas methane remained widely unchanged. There were interactions (P < 0.05) between forage type incubated and feeding period of the donor cow in protozoal counts, acetate:propionate ratio, fermentation gas production and its content of methane, in vitro organic matter digestibility and metabolizable energy. Although increased phenolic compounds were the most consistent common property of the applied alpine forages, a clear attribution to certain effects was not possible in this study. As a further result, adaptation (long-term for donor cow, short term for 24 h incubations) appears to influence the expression of alpine forage effects in ruminal fermentation.

Combinations of two high-energy forage finishing diets and two initial body condition scores (BCSs) in a 2 × 2 factorial experimental design were evaluated on cull Holstein–Friesian (HF) cows to improve animal performance and carcass characteristics, aimed at achieving proper fatness and conformation scores (a minimum of ‘4’ and ‘O’, respectively) required for the marketing of high-value loin steaks. The two finishing diets were (i) conventional maize silage complemented with concentrate diet and (ii) wet maize ear silage (pastone) complemented with dry-herbage diet. The two initial body condition levels were (i) low BCS < 5 (LBCS) and (ii) high BCS > 5 (HBCS). The HBCS animals had the greatest potential to respond to the finishing diets. They needed a smaller total feed intake (TFI) and a shorter finishing period (FP) to meet the marketing requirements. The average feed budgets necessary to finish cull dairy cows and to achieve the minimum scores ‘4’ and ‘O’ of carcass classification were 2.31 and 3.61 t of dry matter (DM)/cow for HBCS and LBCS animals, respectively, while the FP lasted an average of 143 and 224 days for HBCS and LBCS animals, respectively. With regard to the two feeding diets, we found no differences for TFI, carcass characteristics and loin muscle features, such as weight, diameter and intramuscular fat.

The quality of day old chicks is crucial for profitable broiler production, but a difficult trait to define. In research, both qualitative and quantitative measures are used with variable predictive value for subsequent performance. In hatchery practice, chick quality is judged on a binomial scale, as chicks are divided into first grade (Q1-saleable) and second grade (Q2) chicks right after hatch. Incidences and reasons for classifying chicks as Q2, and potential of these chicks for survival and post-hatch performance have hardly been investigated, but may provide information for flock performance. We conducted an experiment to investigate (1) the quality of a broiler flock and the relation with post-hatch flock performance based on a qualitative score (Pasgar©score) of Q1 chicks and based on the incidence of Q2 chicks and (2) the reasons for classifying chicks as Q2, and the potential of these chicks for survival and post-hatch growth. The performance was followed of Q1 and Q2 chicks obtained from two breeder flocks that hatched in two different hatching systems (a traditional hatcher or a combined hatching and brooding system, named Patio). Eggs were incubated until embryo day 18, when they were transferred to one of the two hatching systems. At embryo day 21/post-hatch day 0, all chicks from the hatcher (including Q2 chicks) were brought to Patio, where the hatchery manager marked the Q2 chicks from both flocks and hatching systems and registered apparent reasons for classifying these chicks as Q2. Chick quality was assessed of 100 Q1 chicks from each flock and hatching system. Weights of all chicks were determined at days 0, 7, 21 and 42. There were no correlations between mean Pasgar©score and post-hatch growth or mortality, and suboptimal navel quality was the only quality trait associated with lower post-hatch growth. Growth was clearly affected by breeder flock and hatching system, which could not be linked to mean Pasgar©score or incidence of Q2 chicks. Q2 chicks showed lower post-hatch growth compared to Q1 chicks but effects on flock performance at slaughter weight were limited because early mortality in Q2 chicks was high (62.50% at 7 days). We concluded that chick qualitative scores and the incidence of Q2 chicks may be informative for the quality of incubation, but are not predictive for post-hatch flock performance. Culling Q2 chicks after hatch is well-founded in terms of both animal welfare and profitability.