Availability of high-density single nucleotide polymorphism (SNP) genotyping platforms provided unprecedented opportunities to enhance breeding programmes in livestock, poultry and plant species, and to better understand the genetic basis of complex traits. Using this genomic information, genomic breeding values (GEBVs), which are more accurate than conventional breeding values. The superiority of genomic selection is possible only when high-density SNP panels are used to track genes and QTLs affecting the trait. Unfortunately, even with the continuous decrease in genotyping costs, only a small fraction of the population has been genotyped with these high-density panels. It is often the case that a larger portion of the population is genotyped with low-density and low-cost SNP panels and then imputed to a higher density. Accuracy of SNP genotype imputation tends to be high when minimum requirements are met. Nevertheless, a certain rate of genotype imputation errors is unavoidable. Thus, it is reasonable to assume that the accuracy of GEBVs will be affected by imputation errors; especially, their cumulative effects over time. To evaluate the impact of multi-generational selection on the accuracy of SNP genotypes imputation and the reliability of resulting GEBVs, a simulation was carried out under varying updating of the reference population, distance between the reference and testing sets, and the approach used for the estimation of GEBVs. Using fixed reference populations, imputation accuracy decayed by about 0.5% per generation. In fact, after 25 generations, the accuracy was only 7% lower than the first generation. When the reference population was updated by either 1% or 5% of the top animals in the previous generations, decay of imputation accuracy was substantially reduced. These results indicate that low-density panels are useful, especially when the generational interval between reference and testing population is small. As the generational interval increases, the imputation accuracies decay, although not at an alarming rate. In absence of updating of the reference population, accuracy of GEBVs decays substantially in one or two generations at the rate of 20% to 25% per generation. When the reference population is updated by 1% or 5% every generation, the decay in accuracy was 8% to 11% after seven generations using true and imputed genotypes. These results indicate that imputed genotypes provide a viable alternative, even after several generations, as long the reference and training populations are appropriately updated to reflect the genetic change in the population.

A 3 to 4 week feed restriction of about 20% to 25% of the free intake is widely applied in rabbit breeding systems to reduce post-weaning digestive disorders. However, a short intensive feed restriction is described in few studies and can be beneficial for growing rabbits due to a longer re-alimentation period. The aim of this study was to evaluate the effect of ad libitum (AL) and two restriction levels of feeding (50 and 65 g/rabbit per day) applied for 1 week on performance, gastrointestinal morphology and physiological parameters during the restriction and during the re-alimentation period. Rabbits were divided into three experimental groups: AL rabbits were fed AL, R1 rabbits were restricted from 42 to 49 days of age and received 50 g daily (29% of AL) and R2 rabbits were restricted at the same age and were fed 65 g of feed daily (37% of AL). In the 1st week after weaning and in the weeks after restriction, all the groups were fed AL. During the restriction period, daily weight gain (DWG) in R1 significantly dropped to 11% (experiment 1) and 5% (experiment 2) compared with rabbits in the AL group, although they were fed 29% of AL, whereas in the R2 group it decreased to 20% (experiment 1) and 10% (experiment 2). In the week following feed restriction, DWG in the restricted groups increased (P<0.001) to 166% and 148% in R1 and to 128% and 145% in R2. Restricted rabbits in both the experiments reached up to 90% to 93% of the final live weight (70 days) of the AL group. Over the entire experimental period, feed restriction significantly decreased feed intake to 85% to 88% of the AL group; however, the feed conversion ratio was lower (P<0.05) only in experiment 1 (−6% in R1 and −4% in R2). Digestibilities of CP and fat were not significantly higher during the restriction period and during the 1st week of re-alimentation compared with the AL group. Significant interactions between feeding regime and age revealed the shortest large intestine in the AL group at 49 days of age and the longest at 70 days in the AL and R1 groups. Small intestinal villi were significantly higher and the crypts were significantly deeper in the restricted groups. It could be concluded that short intensive feed restriction increased digestible area in the small and large intestines, including the height of villi and depth of crypts, which might be involved in the compensatory growth and defence mechanism.

Aggression at regrouping is a common issue in pig farming. Skin lesions are genetically and phenotypically correlated with aggression and have been shown to have a significant heritable component. This study predicts the magnitude of reduction in complex aggressive behavioural traits when using lesion numbers on different body regions at two different time points as selection criteria, to identify the optimum skin lesion trait for selection purposes. In total, 1146 pigs were mixed into new social groups, and skin lesions were counted 24 h (SL24h) and 3 weeks (SL3wk) post-mixing, on the anterior, centre and posterior regions of the body. An animal model was used to estimate genetic parameters for skin lesion traits and 14 aggressive behavioural traits. Estimated breeding values (EBVs) and phenotypic values were scaled and standardised to allow direct comparison across multiple traits. Individuals with SL24h and SL3wk EBVs in the least aggressive 10% of the population were compared with the population mean to predict the expected genetic and phenotypic response in aggressive behaviour to selection. At mixing, selection for low anterior lesions was predicted to affect substantially more behavioural traits of aggressiveness than lesions obtained on other body parts, with EBVs between −0.21 and −1.17 SD below the population mean. Individuals with low central SL24h EBVs also had low EBVs for aggressive traits (−0.33 to −0.55). Individuals with high SL3wk EBVs had low EBVs for aggression at mixing (between −0.24 and −0.53 SD below the population mean), although this was predicted to affect fewer traits than selection against SL24h. These results suggest that selection against anterior SL24h would result in the greatest genetic and phenotypic reduction in aggressive behaviour recorded at mixing. Selection for increased SL3wk was predicted to reduce aggression at mixing; however, current understanding about aggressive behaviour under stable social conditions is insufficient to recommend using this trait for selection purposes.

Agroecology uses natural processes and local resources rather than chemical inputs to ensure production while limiting the environmental footprint of livestock and crop production systems. Selecting to achieve a maximization of target production criteria has long proved detrimental to fitness traits. However, since the 1990s, developments in animal breeding have also focussed on animal robustness by balancing production and functional traits within overall breeding goals. We discuss here how an agroecological perspective should further shift breeding goals towards functional traits rather than production traits. Breeding for robustness aims to promote individual adaptive capacities by considering diverse selection criteria which include reproduction, animal health and welfare, and adaptation to rough feed resources, a warm climate or fluctuating environmental conditions. It requires the consideration of genotype×environment interactions in the prediction of breeding values. Animal performance must be evaluated in low-input systems in order to select those animals that are adapted to limiting conditions, including feed and water availability, climate variations and diseases. Finally, we argue that there is no single agroecological animal type, but animals with a variety of profiles that can meet the expectations of agroecology. The standardization of both animals and breeding conditions indeed appears contradictory to the agroecological paradigm that calls for an adaptation of animals to local opportunities and constraints in weakly artificialized systems tied to their physical environment.

This paper studies the genetic importance of growth curve parameters and their relevance as selection criteria in breeding programmes of Segureño sheep. Logistic and Verhulst growth functions were chosen for their best fit to BW/age in this breed; the first showed the best general fit and the second the best individual fit. Live weights of 41 330 individuals from the historical archives of the National Association of Segureña Sheep Breeders were used in the analysis. The progeny of 1464 rams and 27 048 ewes were used to study the genetic and phenotypic parameters of growth curve parameters and derived traits. Reproductive management in the population consists in controlled natural mating inside every herd, with a minimum of 15% of the females fertilized by artificial insemination with fresh semen; with the purpose being the herd genetic connections, all herd genealogies are screened with DNA markers. Estimates of growth curve parameters from birth to 80 days were obtained for each individual and each function by the non-linear regression procedure using IBM SPSS statistics (version 21) with the Levenberg–Marquart estimation method. (Co)variance components and genetic parameters were estimated by using the REML/Animal model methodology. The heritability of mature weight was estimated as 0.41±0.042 and 0.38±0.021 with the logistic and Verhulst models, respectively, and the heritability of other parameters ranged from 0.41 to 0.62 and 0.37 to 0.61, with the models, respectively. A negative genetic correlation between mature weight and rate of maturing was found.

Age at first lambing (AFL) plays a key role on the reproductive performance of sheep flocks, although there are no genetic selection programs accounting for this trait in the sheep industry. This could be due to the non-Gaussian distribution pattern of AFL data, which must be properly accounted for by the analytical model. In this manuscript, two different parameterizations were implemented to analyze AFL in the Ripollesa sheep breed, that is, the skew-Gaussian mixed linear model (sGML) and the piecewise Weibull proportional hazards model (PWPH). Data were available from 10 235 ewes born between 1972 and 2013 in 14 purebred Ripollesa flocks located in the north-east region of Spain. On average, ewes gave their first lambing short after their first year and a half of life (590.9 days), and within-flock averages ranged between 523.4 days and 696.6 days. Model fit was compared using the deviance information criterion (DIC; the smaller the DIC statistic, the better the model fit). Model sGML was clearly penalized (DIC=200 059), whereas model PWPH provided smaller estimates and reached the minimum DIC when one cut point was added to the initial Weibull model (DIC=132 545). The pure Weibull baseline and parameterizations with two or more cut points were discarded due to larger DIC estimates (>134 200). The only systematic effect influencing AFL was the season of birth, where summer- and fall-born ewes showed a remarkable shortening of their AFL, whereas neither birth type nor birth weight had a relevant impact on this reproductive trait. On the other hand, heritability on the original scale derived from model PWPH was high, with a model estimate place at 0.114 and its highest posterior density region ranging from 0.079 and 0.143. As conclusion, Gaussian-related mixed linear models should be avoided when analyzing AFL, whereas model PWPH must be viewed as better alternative with superior goodness of fit; moreover, the additive genetic background underlying this reproductive trait supports its inclusion into current genetic selection programs given its economic importance.

The intensification of livestock have increased the emission of pollutants to the environment, leading to a growing interest in seeking strategies that minimise these emissions. Studies have shown that it is possible to manipulate diets by reducing CP levels and thus reducing nitrogen (N) excretion, without compromising performance. However, there is no knowledge of any study that has focused on reducing N excretion and relating this reduction to individual amino acids. This study investigated the effect of dietary methionine+cysteine (MC) and threonine (THR), the two most limiting amino acids for broiler production, on nitrogen excretion (NE) and nitrogen deposition (ND) and determined the efficiency of utilisation of both amino acids for protein deposition. Six trials were conducted to measure the NE and ND in broiler chickens during three rearing phases in response to dietary amino acid. The efficiency of utilisation of the amino acids was calculated by linear regression of body protein deposition and the amino acid intake. Despite the differences between sexes and phases, the efficiency of utilisation was the same, being 0.60 and 0.59 for MC and THR, respectively. The rate of NE behaved exponentially, increasing with amino acid intake, and can exceed 50% of N intake, being higher than ND. On average, for a reduction in intake of each unit of MC or THR (mg) there is a reduction of 0.5% of NE. Although this reduction seems low, considering that it corresponds to changes in one amino acid only, the impact on a large scale would be significant. Knowledge of how animals respond to NE and ND/protein deposition according to amino acid dietary content may represent new efforts towards reducing the impact on environment.

Delayed feed and water access is known to impair growth performance of day old broiler chickens. Although effects of feed access on growth performance and immune function of broilers have been examined before, effects of dietary composition and its potential interaction with feed access are hardly investigated. This experiment aimed to determine whether moment of first feed and water access after hatch and pre-starter composition (0 to 7 days) affect growth rate and humoral immune function in broiler chickens. Direct fed chickens received feed and water directly after placement in the grow-out facility, whilst delayed fed chickens only after 48 h. Direct and delayed fed chickens received a control pre-starter diet, or a diet containing medium chain fatty acids (MCFA) or fish oil. At 21 days, chickens were immunized by injection of sheep red blood cells. The mortality rate depended on an interaction between feed access and pre-starter composition (P=0.014). Chickens with direct feed access fed the control pre-starter diet had a higher risk for mortality than chickens with delayed feed access fed the control pre-starter diet (16.4% v. 4.2%) whereas the other treatment groups were in-between. BW gain and feed intake till 25 days in direct fed chickens were higher compared with delayed fed chickens, whilst gain to feed ratio was lower. Within the direct fed chickens, the control pre-starter diet resulted in the highest BW at 28 days and the MCFA pre-starter diet the lowest (Δ=2.4%), whereas this was opposite for delayed fed chickens (Δ=3.0%; P=0.033). Provision of MCFA resulted in a 4.6% higher BW gain and a higher gain to feed ratio compared with other pre-starter diets, but only during the period it was provided (2 to 7 days). Minor treatment effects were found for humoral immune response by measuring immunoglobulins, agglutination titers, interferon gamma (IFN- γ ), and complement activity. Concluding, current inclusion levels of fish oil (5 g/kg) and MCFA (30 g/kg) in the pre-starter diet appear to have limited (carryover) effects on growth and development, as well as on humoral immune function.

Given the capacity of ruminants to modify diet selection based on metabolic needs, we hypothesised that, when given a choice, lambs experiencing a vitamin E deficiency would consume more of a vitamin E-enriched feed than lambs not deficient in vitamin E. Fifty-six Dohne Merino lambs were divided into two groups and fed either a vitamin E-deficient diet over 40 days to induce low plasma vitamin E or a vitamin E-enriched diet to induce high plasma vitamin E. The lambs were then offered a choice of vitamin E-enriched and vitamin E-deficient pellets. For half of the animals, the enriched diet was paired with strawberry flavour and the deficient diet was paired with orange flavour, while the reverse pairings were offered to the others. Lamb preference for the diets was measured daily for the following 15 days. There was a three-way interaction between the high and low vitamin E treatment groups×vitamin E content and type of flavour in the feed×time (days). The lambs preferred pellets flavoured with strawberry but this preference changed to orange flavour in vitamin E-deficient lambs if the orange flavour was paired with high vitamin E. Lambs without a deficiency continued to prefer strawberry-flavoured pellets, regardless of the vitamin E concentrations in the pellets. It is possible that self-learning contributed to the low vitamin E group of lambs changing preference to orange flavour in order to consume more vitamin E, presumably to remediate the deficiency.

Dairy cows are high value farm animals requiring careful management to achieve the best results. Since the advent of robotic and high throughput milking, the traditional few minutes available for individual human attention daily has disappeared and new automated technologies have been applied to improve monitoring of dairy cow production, nutrition, fertility, health and welfare. Cows milked by robots must meet legal requirements to detect healthy milk. This review focuses on emerging technical approaches in those areas of high cost to the farmer (fertility, metabolic disorders, mastitis, lameness and calving). The availability of low cost tri-axial accelerometers and wireless telemetry has allowed accurate models of behaviour to be developed and sometimes combined with rumination activity detected by acoustic sensors to detect oestrus; other measures (milk and skin temperature, electronic noses, milk yield) have been abandoned. In-line biosensors have been developed to detect markers for ovulation, pregnancy, lactose, mastitis and metabolic changes. Wireless telemetry has been applied to develop boluses for monitoring the rumen pH and temperature to detect metabolic disorders. Udder health requires a multisensing approach due to the varying inflammatory responses collectively described as mastitis. Lameness can be detected by walk over weigh cells, but also by various types of video image analysis and speed measurement. Prediction and detection of calving time is an area of active research mostly focused on behavioural change.

In order to expand with validated scientific data the limited knowledge regarding the potential application of insects as innovative feed ingredients for poultry, the present study tested a partial substitution of soya bean meal and soya bean oil with defatted black soldier fly (Hermetia illucens) larvae meal (H) in the diet for growing broiler quails (Coturnix coturnix japonica) on growth performance, mortality, nutrients apparent digestibility, microbiological composition of excreta, feed choice, carcass and meat traits. With this purpose, a total of 450 10-day-old birds were allocated to 15 cages (30 birds/cage) and received three dietary treatments: a Control diet (C) and two diets (H1 and H2) corresponding to 10% and 15% H inclusion levels, respectively (H substituted 28.4% soya bean oil and 16.1% soya bean meal for H1, and 100% soya bean oil and 24.8% soya bean meal for H2, respectively). At 28 days of age, quails were slaughtered, carcasses were weighed, breast muscles were then excised from 50 quails/treatment, weighed, and ultimate pH (pHu) and L*, a*, b* colour values were measured. Breast muscles were then cooked to assess cooking loss and meat toughness. For the digestibility trial, a total of 15 28-day-old quails were assigned to the three feeding groups. The excreta samples were subjected to chemical and microbiological analysis. The same 15 quails were then simultaneously provided with C and H2 diets for a 10-day feed choice trial. Productive performance, mortality and carcass traits were in line with commercial standards and similar in all experimental groups. With the exception of ether extract digestibility, which was lower in H1 group compared with C and H2 (P=0.0001), apparent digestibility of dry matter, CP, starch and energy did not differ among treatments. Microbial composition of excreta was also comparable among the three groups. Feed choice trial showed that quails did not express a preference toward C or H2 diets. Breast meat weight and yield did not differ among C, H1 and H2 quails. Differently, the inclusion of H meal reduced meat pHu compared with C. In conclusion, this study demonstrated that H. illucens larvae meal can partially replace conventional soya bean meal and soya bean oil in the diet for growing broiler quails, thus confirming to be a promising insect protein source for the feed industry. Further research to assess the impact of H meal on intestinal morphology as well as on meat quality and sensory profile would be of utmost importance.

Rapid assessment of the nutritional quality of diets ingested by grazing animals is pivotal for successful cow–calf management in east Mediterranean rangelands, which receive unpredictable rainfall and are subject to hot-spells. Clipped vegetation samples are seldom representative of diets consumed, as cows locate and graze selectively. In contrast, faeces are easily sampled and their near-IR spectra contain information about nutrients and their utilization. However, a pre-requisite for successful faecal near-infrared reflectance spectroscopy (FNIRS) is that the calibration database encompass the spectral variability of samples to be analyzed. Using confined beef cows in Northern and Southern Israel, we calibrated prediction equations based on individual pairs of known dietary attributes and the NIR spectra of associated faeces (n=125). Diets were composed of fresh-cut green fodder of monocots (wheat and barley), dicots (safflower and garden pea) and natural pasture collected at various phenological states over 2 consecutive years, and, optionally, supplements of barley grain and dried poultry litter. A total of 48 additional pairs of faeces and diets sourced from cows fed six complete mixed rations covering a wide range of energy and CP concentrations. Precision (linearity of calibration, R2cal, and of cross-validation, R2cv) and accuracy (standard error of cross-validation, SEcv) were criteria for calibration quality. The calibrations for dietary ash, CP, NDF and in vitro dry matter digestibility yielded R2cal values >0.87, R2cv of 0.81 to 0.89 and SEcv values of 16, 13, 39 and 31 g/kg dry matter, respectively. Equations for nutrient intake were of low quality, with the exception of CP. Evaluation of FNIRS predictions was carried out with grazing animals supplemented or not with poultry litter, and implementation of the method in one herd over 2 years is presented. The potential usefulness of equations was also established by calculating the Mahalanobis (H) distance to the spectral centroid of a calibration population of 796 faecal samples collected throughout 2 years in four herds. Seasonal trends in pasture quality and responses to management practices were identified adequately and H<3.0 for 98% of faecal samples collected. We conclude that the development of FNIRS equations with confined animals is not only unexpensive and ethically acceptable, but their predictions are also sufficiently accurate to monitor dietary composition (but not intake) of beef cattle in east Mediterranean rangelands.

Litter size is essential for an efficient production of rabbit meat. A diallel cross between four maternal lines was carried out and the analysis of the components of litter size has been already done. This paper presents the analysis of litter size traits themselves (total born (TB), number born alive (NBA), number weaned (NW)) and kindling interval (KI), that complete the analysis of the reproductive performance. The 16 genetic groups were distributed in four Spanish farms. The V line was present in all farms in order to be used as reference group. A total of 34 546 parities from 7111 does, were analysed. The crossbreeding parameters were estimated according to Dickerson model. The differences between lines performance were of low magnitude and not significant for litter size traits. The LP line showed the shortest KI followed by H respect to lines A and V. These differences reflected the differences between direct and maternal genetic effects. The differences between the average of all crosses and line V were found to be significant and seemed to be important, being 0.46 for TB, 0.56 for NBA, 0.75 for NW and −2.21 days for KI. The differences between reciprocal crosses for litter size were of low magnitude and non-significant, which indicate that the maternal effects are not important between these lines. In general, the lines did not show significant differences in direct and maternal genetic effects for TB, NBA and NW but there were some significant differences for KI, which ranged from 1.54 to 6.85 days in direct effects and from 0.63 to 3.38 days for maternal effects. A positive and, in some cases, relevant heterosis was found. The largest heterosis was for TB in the HV cross (1.05 rabbits), followed by the AH (0.74 rabbits), AV (0.57 rabbits) and LH (0.55 rabbits) crosses. For NBA, significant heterosis was found in HV (1.11 rabbits) and AV (0.49 rabbits) and for NW in AV (0.90 rabbits), LH (0.70 rabbits) and LV (0.58 rabbits). Favourable and significant heterosis for KI was found in AV and LV crosses, whereas it was unfavourable in AL and in LH. The more recommended crosses were AV and LH, showing the greatest performances on NW, while the cross HV, which shows the greatest performances an NBA, could be highly recommended when cross-fostering is practised to equalise litter sizes after birth, in this situation the lower NW performance observed could be improved.

Canola co-products are sources of amino acid and energy in pig feeds, but their fermentation characteristics in the pig intestine are unknown. Thus, we determined the in vitro fermentation characteristics of the canola co-products Brassica juncea solvent-extracted canola meal (JSECM), Brassica napus solvent-extracted canola meal (NSECM), B. napus expeller-pressed canola meal (NEPCM) and B. napus cold-pressed canola cake (NCPCC) in comparison with soybean meal (SBM). Samples were hydrolysed in two steps using pepsin and pancreatin. Subsequently, residues were incubated in a buffer solution with fresh pig faeces as inocula for 72 h to measure gas production. Concentration of volatile fatty acids (VFA) per gram of dry matter (DM) of feedstuff was measured in fermented solutions. Apparent ileal digestibility (AID) and apparent hindgut fermentation (AHF) of gross energy (GE) for feedstuffs were obtained from pigs fed the same feedstuffs. On DM basis, SBM, JSECM, NSECM, NEPCM and NCPCC contained 15, 19, 22, 117 and 231 g/kg ether extract; and 85, 223, 306, 208 and 176 g/kg NDF, respectively. In vitro digestibility of DM (IVDDM) of SBM (82.3%) was greater (P<0.05) than that of JSECM (68.5%), NSECM (63.4%), NEPCM (67.5%) or NCPCC (69.8%). The JSECM had greater (P<0.05) IVDDM than NSECM. The IVDDM for NSECM was lower (P<0.05) than that for NEPCM, which was lower (P<0.05) than that for NCPCC. Similarly, AID of GE was greatest for SBM followed by NCPCC, JSECM, NEPCM and then NSECM. Total VFA production for SBM (0.73 mmol/g) was lower (P<0.05) than that of JSECM (1.38 mmol/g) or NSECM (1.05 mmol/g), but not different from that of NEPCM (0.80 mmol/g) and NCPCC (0.62 mmol/g). Total VFA production of JSECM was greater (P<0.05) than that of NSECM. Total VFA production of NSECM was greater (P<0.05) than that of NEPCM or NCPCC, which differed (P<0.05). The ranking of feedstuffs for total VFA production was similar to AHF of GE. In conclusion, in vitro fermentation characteristics of canola co-products and SBM simulated their fermentation in the small and large intestine of pigs, respectively. The 30% greater VFA production for JSECM than NSECM due to lower lignified fibre of JSECM indicates that fermentation characteristics differ between canola species. The NSECM had the highest fermentability followed by NEPCM and then NCPCC, indicating that fat in canola co-products can limit their fermentability in the hindgut.

In this study, 160 Hycole weaned rabbits (35 days old) were randomly divided into four groups of 40. The rabbits were studied throughout a 54-day experimentation period in order to determine the impact of dietary supplementation from herbs composed of 0.2%, 0.4% dry ground Lythrum salicaria leaves (LS) and 0.3% Cunirel® (CR; a commercial herb mixture containing LS as the main ingredient) on performance, digestibility, health and meat quality. The basal diet was given to the control group. No significant differences were found in performance, 10 rabbits from each group were selected for evaluation regarding apparent digestibility. The rabbits fed the control diet and the diet with the low level of LS had a higher level of CP digestibility than did the animals that were supplemented with the high LS levels and CR (85.7% and 84.9% v. 84.0% and 84.0%, respectively; P<0.05). The ether extract digestibility was lower in the treatment group with 0.4%LS addition and CR as compared with the control group (52.2% and 54.5% v. 62.6%, respectively; P<0.05). The slaughter process was performed on 89-day-old rabbits to study the carcass characteristics, meat quality, blood parameters, caecal contents and gut histology. The total leukocyte counts in the control animals were lower than they were in the rabbits fed 0.2%, 0.4%LS and CR (4.06 v. 8.25, 8.63 and 8.21×109/l, respectively; P<0.05). For caecal fermentation, the caecal contents of the rabbits fed 0.4% of LS, showed higher concentrations of total volatile fatty acid (VFA; 24.1 v. 18.9 mg/kg dry matter (DM); P<0.05) and acetic acid (18.3 v. 14.4 mg/kg DM; P<0.05), but lower ammonia levels (594 v. 892 mg/kg DM; P<0.05) as compared with the control group. PCR-denaturing gradient gel electrophoresis analyses were performed to evaluate the microbial community in hard faeces, collected at days 35, 42, 49, 56, 70 and 89, whereas the caecal contents were taken after slaughtering. The results demonstrated that between the treatment groups, the similarity of the microbial communities was higher as compared with the control group. Moreover, only age was shown to influence microbiota diversity. In conclusion, the results of this study indicated that supplementation of LS in rabbit diets leads to an increase in the total white blood cells, total VFA and acetic acid concentration, and a decrease in the ammonia levels, as well as the digestibility when CR and high level of LS were supplemented, without causing any adverse effects on other parameters.

Factor analysis was applied to individual type traits (TT) scored in primiparous cows belonging to two dual purpose Italian breeds, Rendena (REN; 20 individual type traits evaluated on 11 399 first parity cows), and Aosta Red Pied (ARP; 22 individual type traits evaluated on 36 168 primiparous cows). Six common latent factors (F1 to F6; eigenvalues ⩾1) which explained 63% (REN) and 58% (ARP) of the total variance were obtained. F1 included TT mainly related to muscularity, and F2 to body size. The F3 and F4 accounted for udder size and conformation, respectively. F5 included rear legs and feet. Biological significance for F6 was not readily obtained. Moderate to low heritability were estimated through REML single-trait analysis from factor scores (from 0.22 to 0.52 in REN, and from 0.08 to 0.37 in ARP). The greatest heritability values were estimated for body size and muscularity (0.52 and 0.37 for body size; and 0.40 and 0.32 for muscularity in REN and ARP, respectively). As expected, rank correlations, obtained considering estimated breeding values derived from best linear unbiased prediction analysis on the individual TT and factor score, showed similar coefficients to those observed in the factor analysis following loading of TT within each latent factor. These results suggest the possibility to implement the factor analysis in the morphological evaluation, simplifying the information given by the type traits into new variables useful for the genetic improvement of dual purpose cattle.

The increased demand for animal-derived protein and energy for human consumption will have to be achieved through a combination of improved animal genetic merit and better management strategies. The objective of the present study was to quantify whether differences in genetic merit among animals materialised into phenotypic differences in commercial herds. Carcass phenotypes on 156 864 animals from 7301 finishing herds were used, which included carcass weight (kg), carcass conformation score (scale 1 to 15), carcass fat score (scale 1 to 15) at slaughter as well as carcass price. The price per kilogram and the total carcass value that the producer received for the animal at slaughter was also used. A terminal index, calculated in the national genetic evaluations, was obtained for each animal. The index was based on pedigree index for calving performance, feed intake and carcass traits from the national genetic evaluations. Animals were categorised into four terminal index groups on the basis of genetic merit estimates that were derived before the expression of the phenotypic information by the validation animals. The association between terminal index and phenotypic performance at slaughter was undertaken using mixed models; whether the association differed by gender (i.e. young bulls, steers and heifers) or by early life experiences (animals born in a dairy herd or beef herd) was also investigated. The regression coefficient of phenotypic carcass weight, carcass conformation and carcass fat on their respective estimated breeding values (EBVs) was 0.92 kg, 1.08 units and 0.79 units, respectively, which is close to the expectation of one. Relative to animals in the lowest genetic merit group, animals in the highest genetic merit group had, on average, a 38.7 kg heavier carcass, with 2.21 units greater carcass conformation, and 0.82 units less fat. The superior genetic merit animals were, on average, slaughtered 6 days younger than their inferior genetic merit contemporaries. The superior carcass characteristics of the genetically elite animals materialised in carcasses worth €187 more than those of the lowest genetic merit animals. Although the phenotypic difference in carcass traits of animals divergent in terminal index differed statistically by animal gender and early life experience, the detected interactions were generally biologically small. This study clearly indicates that selection on an appropriate terminal index will produce higher performing animals and this was consistent across all production systems investigated.

Scrapie is a naturally occurring transmissible spongiform encephalopathy in sheep and goat. It has been known for ~250 years and is characterised by the accumulation of an abnormal isoform of a host-encoded prion protein that leads to progressive neurodegeneration and death. Scrapie is recognised in two forms, classical and atypical scrapie. The susceptibility to both types of scrapie is influenced by polymorphisms of the prion protein gene (PRNP). Sheep susceptibility or resistance to classical scrapie is strongly regulated by the polymorphisms at codons 136, 154 and 171 of the PRNP. The genetic role in atypical scrapie in sheep has been defined by polymorphisms at codons 141, 154 and 171, which are associated with different degrees of risk in the occurrence of the ovine disease. Progress has been achieved in the prevention of scrapie in sheep due to efficient genetic breeding programmes based on eradication and control of the disease. In Europe, the success of these programmes has been verified by applying eradication and genetic selection plans. In general terms, the ovine selection plans aim to eliminate and reduce the susceptible allele and to enrich the resistant allele ARR. During outbreaks all susceptible animals are slaughtered, only ARR/ARR resistant rams and sheep and semi-resistant females are preserved. In the occurrence of scrapie positive goats a complete cull of the flock (stamping out) is performed with great economic loss and severe risk of extinction for the endangered breeds. The ability to select scrapie-resistant animals allows to define new breeding strategies aimed to boost genetic progress while reducing costs during scrapie outbreaks. Allelic variants of PRNP can be protective for caprine scrapie, and the knowledge of their distribution in goats has become very important. Over the past few years, the integration of genetic information on goat populations could be used to make selection decisions, commonly referred to as genetic selection. The objective of this review was to summarise the main findings of polymorphisms of the caprine prion protein (PrP) gene and to discuss the possible application of goat breeding schemes integrating genetic selection, with their relative advantages and limitations.

Agroecology uses ecological processes and local resources rather than chemical inputs to develop productive and resilient livestock and crop production systems. In this context, breeding innovations are necessary to obtain animals that are both productive and adapted to a broad range of local contexts and diversity of systems. Breeding strategies to promote agroecological systems are similar for different animal species. However, current practices differ regarding the breeding of ruminants, pigs and poultry. Ruminant breeding is still an open system where farmers continue to choose their own breeds and strategies. Conversely, pig and poultry breeding is more or less the exclusive domain of international breeding companies which supply farmers with hybrid animals. Innovations in breeding strategies must therefore be adapted to the different species. In developed countries, reorienting current breeding programmes seems to be more effective than developing programmes dedicated to agroecological systems that will struggle to be really effective because of the small size of the populations currently concerned by such systems. Particular attention needs to be paid to determining the respective usefulness of cross-breeding v. straight breeding strategies of well-adapted local breeds. While cross-breeding may offer some immediate benefits in terms of improving certain traits that enable the animals to adapt well to local environmental conditions, it may be difficult to sustain these benefits in the longer term and could also induce an important loss of genetic diversity if the initial pure-bred populations are no longer produced. As well as supporting the value of within-breed diversity, we must preserve between-breed diversity in order to maintain numerous options for adaptation to a variety of production environments and contexts. This may involve specific public policies to maintain and characterize local breeds (in terms of both phenotypes and genotypes), which could be used more effectively if they benefited from the scientific and technical resources currently available for more common breeds. Last but not least, public policies need to enable improved information concerning the genetic resources and breeding tools available for the agroecological management of livestock production systems, and facilitate its assimilation by farmers and farm technicians.