Animal breeding faces one of the most significant changes of the past decades – the implementation of genomic selection. Genomic selection uses dense marker maps to predict the breeding value of animals with reported accuracies that are up to 0.31 higher than those of pedigree indexes, without the need to phenotype the animals themselves, or close relatives thereof. The basic principle is that because of the high marker density, each quantitative trait loci (QTL) is in linkage disequilibrium (LD) with at least one nearby marker. The process involves putting a reference population together of animals with known phenotypes and genotypes to estimate the marker effects. Marker effects have been estimated with several different methods that generally aim at reducing the dimensions of the marker data. Nearly all reported models only included additive effects. Once the marker effects are estimated, breeding values of young selection candidates can be predicted with reported accuracies up to 0.85. Although results from simulation studies suggest that different models may yield more accurate genomic estimated breeding values (GEBVs) for different traits, depending on the underlying QTL distribution of the trait, there is so far only little evidence from studies based on real data to support this. The accuracy of genomic predictions strongly depends on characteristics of the reference populations, such as number of animals, number of markers, and the heritability of the recorded phenotype. Another important factor is the relationship between animals in the reference population and the evaluated animals. The breakup of LD between markers and QTL across generations advocates frequent re-estimation of marker effects to maintain the accuracy of GEBVs at an acceptable level. Therefore, at low frequencies of re-estimating marker effects, it becomes more important that the model that estimates the marker effects capitalizes on LD information that is persistent across generations.

Microarray technology is a powerful tool for animal functional genomics studies, with applications spanning from gene identification and mapping, to function and control of gene expression. Microarray assays, however, are complex and costly, and hence generally performed with relatively small number of animals. Nevertheless, they generate data sets of unprecedented complexity and dimensionality. Therefore, such trials require careful planning and experimental design, in addition to tailored statistical and computational tools for their appropriate data mining. In this review, we discuss experimental design and data analysis strategies, which incorporate prior genomic and biological knowledge, such as genotypes and gene function and pathway membership. We focus the discussion on the design of genetical genomics studies, and on significance testing for detection of differential expression. It is shown that the use of prior biological information can improve the efficiency of microarray experiments.

The objective of this study was to investigate genetic merit of return over feed (ROF), which is a herd profit index defined by CanWest Dairy Herd Improvement as a difference between milk income and feed cost. A multiple-trait (MT) model and random regression model (RRM) were used. The traits analyzed in MT were rearing cost and ROF of the first three lactations. In RRM, a cumulative ROF was fitted as function of age and rearing cost was treated as a correlated trait. Variance components were estimated within a Bayesian framework by Gibbs sampling using a subsample of data. Breeding values were then estimated for 3 041 078 animals using records of 1 951 893 cows. Estimates of heritability for rearing cost from MT and RRM were 0.23 and 0.22, respectively. ROF per lactation and cumulative ROF were negatively correlated with rearing cost. Estimates of heritability of ROF through the first, second and third lactation from MT were 0.27, 0.10 and 0.08, respectively. Estimates of heritability of ROF from RRM increased with age and ranged from 0.08 through 0.31. Estimated breeding values (EBVs) for ROF from MT and RRM were moderately correlated with official EBV for production traits and the Canadian selection index (Lifetime Profit Index). Herd life EBV had −0.07 and 0.19 correlations with EBVs for ROF from MT and RRM, respectively. From both MT and RRM, small favorable correlations were reported between EBVs for ROF and for bone quality and angularity, whereas low unfavorable correlations were reported with EBV for udder depth, front end and chest width. Majority of correlations between EBVs for ROF and for reproduction traits were near 0, with the exception of EBV for gestation length, calf size and calving ease, where small favorable correlations were reported. The ROF is a good indicator of cow profitability despite the fact that it is a simplified profit index that does not account for animal-specific health and reproductive cost. However, because ROF does not account for differences in heritabilities between components of profit, ROF is not recommended to be used for direct selection for profit.

Mink skin size in Finland, as well as in other countries, has increased considerably during last decade. However, there are signs that selection for large body size has a negative impact on litter size (LS) and also for survival of kits. Therefore, it is important to study the genetic relationships among fertility traits and animal size (AS). The variance components for age at first mating (AFM) and first three parity LS and AS were estimated using multi-trait restricted maximum likelihood animal model. Data included 82 945 animals born during 1990 to 2004, originating from nine farms. Heritability estimates for the fertility traits were from 0.10 to 0.15. For AS, heritability was estimated to be 0.18. Genetic correlation between AS and all fertility traits was estimated to be negative (varying from −0.004 to −0.38). It is important to recognize this antagonistic relationship and include the reproductive traits into breeding goals to maintain good reproductive performance when selecting for increased body size and hence larger pelts in fur animals. Genetic correlations between the traits should be accounted in breeding value evaluations by using a multi-trait model. Including AFM into breeding value estimation would also improve the accuracy of breeding value estimation for fertility, because females missing the first LS still have record on AFM.

The objective of this study was to quantify the genetic association of body energy assessed throughout lactation with a cow’s fertility. Nine direct and indirect body energy traits were defined at different stages of lactation. Four were daily records of energy balance, energy content, cumulative effective energy (CEE) and body condition score (BCS) calculated between lactation days 4 and 311. The other five traits included duration of negative energy balance (DNEB), rate of recovery during DNEB (RNEB), sum of negative energy balance (SNEB), nadir of energy content (NEC) and number of days from calving to NEC. Of these traits, energy balance, DNEB, RNEB and SNEB were primarily based on individual cow feed intake and milk yield, and considered direct measures of body energy. The other traits were calculated from body lipid and protein changes, predicted from BCS and live weight profiles, and were considered indirect measures of body energy. Fertility was defined by number of days between calving and commencement of luteal activity (DLA), first observed oestrus (DH) and conception (DC), and number of services per conception. A total of 957 cows in their first four lactations were considered in the study. Genetic models fitted cubic splines to define longitudinal traits (energy balance, energy content, CEE and BCS) and calculate heritability and genetic correlation with fertility. Daily heritability estimate ranges were 0.10 to 0.34, 0.35 to 0.61, 0.32 to 0.53 and 0.24 to 0.56 for energy balance, energy content, CEE and BCS, respectively, and, in most cases, tended to increase towards the middle of lactation and remain relatively stable thereafter. Of the other body energy traits, heritability of NEC (0.44) was the most notable. Statistically significant (P < 0.05) genetic correlations of DH with daily energy balance, energy content, CEE and BCS ranged from −0.16 to −0.28, −0.35 to −0.48, −0.16 to −0.26 and −0.37 to −0.44, respectively. For DC, respective estimates were −0.28 to −0.64, −0.37 to −0.60, −0.30 to −0.48 and −0.29 to −0.53. For DLA, they ranged from −0.47 to −0.56 with energy content and from −0.50 to −0.74 with BCS. Of special interest was the genetic correlation of NEC with DH (−0.54) and DC (−0.48). Results suggest that indirect measures of body energy have the strongest genetic association with cow fertility. NEC and early lactation (circa day 50) BCS and energy content are the most useful traits for selection in terms of the correlated improvement in a cow’s capacity to resume her reproductive activity post partum.

The study was conducted to evaluate the effects of dietary zinc addition (0 or 15 mg/kg of Zn as inorganic or organic zinc) to three maize–soybean meal basal diets varying in their native Zn, phytic P contents and phytase activity (expressed in kg of feed: P− with 25 mg Zn and 1.3 g phytic P, P+ with 38 mg Zn and 2.3 g phytic P or P+/ENZ being P+ including 500 units (FTU) of microbial phytase per kg) in two monogastric species (piglets, broilers). Measured parameters were growth performance, zinc status (plasma, and bone zinc) and soluble zinc in digesta (stomach, gizzard and intestine). The nine experimental diets were fed for 20 days either to weaned piglets (six replicates per treatment) or to 1-day-old broilers (10 replicates per treatment). Animal performance was not affected by dietary treatments (P > 0.05) except that all P− diets improved body weight gain and feed conversion ratio in piglets (P < 0.05). Piglets fed P− diets had a better Zn status than those fed P+ diets (P < 0.05). In both species, Zn status was improved with supplemental Zn (P < 0.05), irrespective of Zn source. Phytase supplementation improved piglet Zn status to a higher extent than adding dietary Zn, whereas in broilers, phytase was less efficient than supplemental Zn. Digestive Zn concentrations reflected the quantity of ingested Zn. Soluble Zn (mg/kg dry matter) and Zn solubility (% of total Zn content) were highest in gizzard contents, which also presented lower pH values than stomach or intestines. The intestinal Zn solubility was higher in piglet fed organic Zn than those fed inorganic Zn (P < 0.01). Phytase increased soluble Zn in piglet stomach (P < 0.001) and intestine (P = 0.1), but not in broiler gizzard and intestinal contents. These results demonstrate (i) that dietary zinc was used more efficiently by broilers than by piglets, most probably due to the lower gizzard pH and its related higher zinc solubility; (ii) that zinc supplementation, irrespective of zinc source, was successful in improving animal’s zinc status; and (iii) suggest that supplemented Zn availability was independent from the diet formulation. Finally, the present data confirm that phytase was efficient in increasing digestive soluble Zn and improving zinc status in piglets. However, the magnitude of these effects was lower in broilers probably due to the naturally higher Zn availability in poultry than in swine.

The correlation between rumen chemical and bacterial changes was investigated during a four periodical stepwise adaptation to a high-concentrate diet (concentrate level at 0%, 30%, 50% and 70% for diet I to IV, respectively) in goats. The results showed that ruminal pH decreased from 6.7 to 5.5 after switching from diet I to II, and was maintained at about 5.5 on diet III. Denaturing gradient gel electrophoresis results showed that the rumen bacterial community was relatively stable during the initial three feeding periods, except for the appearance of three bands when diet changed from I to II, suggesting that an appropriate concentrate level can promote the proliferation of some bacteria. After 12 days of feeding diet III, total volatile fatty acid (VFA) concentration and butyrate proportion decreased. At days 2 and 3 of feeding diet IV, ruminal pH declined sharply to 5.3 and 4.7, respectively, and total VFA concentration decreased further while lactic acid concentration increased markedly, suggesting a relation between lactic acid accumulation and ruminal pH decline. At the same time, many bacteria disappeared, including most fibrolytic-related bacteria while Streptococcus bovis and Prevotella-like species dominated. Interestingly, Succinivibrio dextrinosolvens-like species maintained throughout the experiment, suggesting its tolerance to low pH. In conclusion, rumen bacterial community was relatively stable feeding 0% to 50% concentrate diets, and it was observed that appropriate concentrate levels in the diet could increase the diversity of rumen bacteria. However, concentrate-rich diets caused lactic acid accumulation and low ruminal pH that caused the disappearance of most fibrolytic-related bacteria sensitive to low pH while S. bovis and genus Prevotella persisted.

The influence of the cloned-cattle meat diets upon reproduction in mammals was rarely studied. This study was performed to analyze the effects of the diets containing cloned-cattle (Korean native beef, Hanwoo) meat on the reproductive physiology in rats. The male and female rats were fed with the diets containing 5% or 10% of normal- (N-5 or N-10) or cloned- (C-5 or C-10) cattle meat during test periods. The rats fed with commercial pellets were used as control. Lower food consumption in normal- and cloned-cattle meat diet groups is detected in both male and female rats compared with that of control (P < 0.05, 0.01 and 0.001). No signs of cloned-cattle meat diets on male reproductive parameters are found in all groups, except for lower sperm deformity in C-5 group (P < 0.05) and higher testosterone concentration in C-10 group (P < 0.05), respectively. There are no significant test substance-related differences of Caesarean section and delivery in dams and external examination and physiological development test in neonate compared with control and normal meat groups. Based on these results, it can be postulated that there are no obvious negative effects on the reproductive physiology in rats fed with cloned-cattle meat diets compared to their comparators.

The 3-hydroxy-3-methylglutaryl-CoA reductase (HMGCR) is the rate-limiting enzyme in the biosynthesis of cholesterol. We have studied the role of the HMGCR gene in pig lipid metabolism by means of expression and structural analysis. We describe here the complete coding region of this gene in pigs and report two synonymous single nucleotide polymorphisms in the coding region. We have, additionally, studied the association of one of these polymorphisms (HMGCR:c.807A>C) with several lipid deposition- and cholesterol-related traits in a half-sib population generated from a commercial Duroc line, showing in some families a positive relationship of HMGCR:c.807A allele with serum low-density lipoprotein (LDL)-bound cholesterol and triglyceride levels, and also with intramuscular fat (IMF) content of gluteus medius muscle. We have also assessed the expression levels in muscle and in liver from 68 Duroc individuals corresponding to the most extreme animals for the analysed traits. Liver HMGCR expression correlated negatively with the serum high-density lipoprotein (HDL) levels, carcass lean percentage and stearic acid content, while muscle expression correlated also negatively with the carcass lean percentage, stearic and linoleic acids content, but showed a positive correlation with the serum lipid cholesterol (HDL, LDL and total cholesterol), IMF and muscle oleic and palmitic fatty acid content. With this information, we have performed an association analysis of expression data with lipid metabolism phenotypic levels and the HMGCR genotype. The results indicate that HMGCR expression levels in muscle are different in the two groups of pigs with extreme values for fat deposition and total cholesterol levels, and also between animals with the different HMGCR genotypes.

Equations for predicting the meat, fat and bone proportions in beef carcasses using the European Union carcass classification scores for conformation and fatness, and hindquarter composition were developed and their accuracy was tested using data from 662 cattle. The animals included bulls, steers and heifers, and comprised of Holstein–Friesian, early- and late-maturing breeds × Holstein–Friesian, early-maturing × early-maturing, late-maturing × early-maturing and genotypes with 0.75 or greater late-maturing ancestry. Bulls, heifers and steers were slaughtered at 15, 20 and 24 months of age, respectively. The diet offered before slaughter includes grass silage only, grass or maize silage plus supplementary concentrates, or concentrates offered ad libitum plus 1 kg of roughage dry matter per head daily. Following the slaughter, carcasses were classified mechanically for conformation and fatness (scale 1 to 15), and the right side of each carcass was dissected into meat, fat and bone. Carcass conformation score ranged from 4.7 to 14.4, 5.4 to 10.9 and 2.0 to 12.0 for bulls, heifers and steers, respectively; the corresponding ranges for fat score were 2.7 to 11.5, 3.2 to 11.3 and 2.8 to 13.3. Prediction equations for carcass meat, fat and bone proportions were developed using multiple regression, with carcass conformation and fat score both included as continuous independent variables. In a separate series of analyses, the independent variable in the model was the proportion of the trait under investigation (meat, fat or bone) in the hindquarter. In both analyses, interactions between the independent variables and gender were tested. The predictive ability of the developed equations was assed using cross-validation on all 662 animals. Carcass classification scores accounted for 0.73, 0.67 and 0.71 of the total variation in carcass meat, fat and bone proportions, respectively, across all 662 animals. The corresponding values using hindquarter meat, fat and bone in the model were 0.93, 0.87 and 0.89, respectively. The bias of the prediction equations when applied across all animals was not different from zero, but bias did exist among some of the genotypes of animals present. In conclusion, carcass classification scores and hindquarter composition are accurate and efficient predictors of carcass meat, fat and bone proportions.

Effects of environmental enrichment at different stages of life on stress physiology of pigs were investigated in a trial with 63 groups, each of four siblings. In each of the three growing phases (suckling 0 to 4 weeks of age, nursery 5 to 9 weeks, fattening 10 to 24 weeks) pens either were (=E) or were not (=0) enriched. Accordingly, the treatments were (i) 000, (ii) E00, (iii) EE0, (iv) 00E, (v) 0EE and (vi) EEE. The enrichment material, renewed twice daily to leave a thin layer, consisted of wood shavings and chopped straw. Salivary cortisol was sampled hourly from 0700 to 1900 h at the age of 9 and 21 weeks. The presence of a circadian secretion rhythm was evaluated by an intra-assay coefficient of variation-based method. An adrenocorticotropic hormone test was performed at 21 weeks. Treatment effects on the odds of a physiological cortisol rhythm were assessed by logistic regression, and effects on cortisol concentrations with a repeated measures GLM. Substrate-enrichment from 0 to 9 weeks of age increased the odds of a rhythm as compared to barren housing (odds ratio (OR) = 30.0, P < 0.01). A flat cortisol secretion pattern may indicate chronic stress and/or delayed maturation of the rhythm. Barren as compared to enriched rearing (0 to 4 weeks of age) seemed to cause a blunted secretion rhythm at 21 weeks of age. Although behavioural and tail lesion observations provided support to the assumption that a blunted rhythm indicates chronic stress, the biological significance of these cortisol results needs confirmation in future studies.

To evaluate the effect of stocking density and transport time on physiological responses and meat quality, 72 male suckling lambs were transported by road to the slaughterhouse at three different stocking densities (0.12, 0.20 or 0.25 m2/lamb) and two transport times (5 h or 30 min). Blood samples were collected pre-transport at the farm and after unloading in the slaughterhouse to measure levels of cortisol, creatine kinase (CK) and lactate dehydrogenase (LDH). After slaughter, the weights of the hot carcass, liver and spleen were recorded and pH in Musculuslongisimus thoracisetlumborum (L), Musculussemitendinosus (ST) and Musculuspsoas major (PM) were determined. Colour, water-holding capacity (WHC), texture and thiobarbituric acid-reactive substances (TBARS) values were measured in samples of L, at 24 h post mortem and after 5 days of ageing. Cortisol and LDH were higher in suckling lambs transported for 30 min than those transported for 5 h. Stocking density did not affect blood parameters studied. Transport time significantly affected some carcass quality parameters, but stocking density had no significant effect. Suckling lambs transported for 5 h had lower liver weights and dressing percentages than those transported for 30 min. Transport time influenced pH values, with lambs subjected to the longer journey showing the lowest pH at 0 h in the three muscles studied, with the lowest final pH in L and PM. The PM lambs transported at high density (0.12 m2/lamb) had the lowest pH at 24 h. Transport time and stocking density did not greatly affect colour and texture parameters. The meat from lambs transported for 30 min had higher WHC than meat from lambs transported for 5 h. Animals transported for longer journeys showed higher lipid oxidation after 5 days of ageing than those transported for 30 min. Loading and initial transport caused significant stress response in suckling lambs, that stress response was reduced over the time course of the journey.

This review provides an assessment of research findings into the current practices and standards and the principles and aspirations for organic dairy production, with respect to the health and welfare of the dairy cow. The relationships between the four main factors: management, environment, genetics and nutrition and their impact on the health and welfare status of organic dairy cows are considered. The concept that good animal health and welfare is more than merely the absence of disease, with behavioural aspects of health and welfare such as physiological and psychological needs, is also discussed. These factors are inter-related and important in all dairy systems, irrespective of whether the system is organic, low-input or intensive. Incidences of individual clinical and sub-clinical diseases that are recorded in conventional dairy systems also occur in organic dairy systems, with infertility, lameness and mastitis being the major problems. However, the magnitude of the incidence of many of these diseases may be either lower or higher in organic systems due to different management practices and the standards defined for organic milk production that, for example, prohibit the routine use of conventional medicines and require the feeding of high-forage diets. In relation to different systems, it is important to note that contrary to a common assumption, good welfare does not necessarily occur with more extensive systems. The type of organic system (self-sufficient, purchased-feed) also has the potential to have a major influence on the incidence of health problems and the reproductive status of organic dairy herds. Health status is also influenced by environmental and welfare factors, including the method of rearing replacement animals, type of housing and the geographical and climatic conditions of individual farms. Overall, this review identifies where conflicts arise between current practice and the organic principles and standards, and aims to provide suggestions to bring about further improvement in organic dairy health and welfare.

This research compared three wood-chip out-wintering pad (OWP; an unsheltered OWP; a sheltered OWP (both with a concrete feed apron); and an unsheltered OWP with silage provided directly on top of the wood-chip bedding (self-feed OWP)) designs and cubicle housing with regard to dairy cow performance during the pre-partum period, and for 8 weeks post partum. Data were compared during 2 years. In Year 1, the unsheltered (space allowance = 12 m2 per cow) and sheltered (6 m2 per cow) OWPs were compared with cubicle housing (n = 49 cows per treatment). In Year 2, all three OWP designs (12 m2 per cow) were compared with cubicle housing (n = 24 cows per treatment, split into two replicates). Animals were dried off and assigned to treatment in the autumn, and remained there until calving in spring. Subsequently, they were managed at pasture during lactation. Outcome measures for analysis during the pre-partum period were feed intake, live weight, body condition score (BCS), heat production and heat loss, and post-partum were live weight, BCS, milk yield and milk composition. In Year 1, all cows had a similar live weight, but both pre-partum and at calving cows on the unsheltered OWP had a lower BCS than cows in cubicles (P < 0.05). However, in Year 2, there were no differences in either live weight or BCS. In Year 1, cows in the unsheltered OWP produced less heat than in cubicles (P < 0.05), but in Year 2, there was no treatment effect. In both years, cows in unsheltered OWPs lost more heat than cows in the sheltered OWP (P < 0.001). Treatment had no effect on milk composition either year. However, in Year 2, cows in the self-feed OWP had higher milk yields than the other treatments (P < 0.05). The lower BCS and heat production values in unsheltered treatments during Year 1 were probably because of higher rainfall and wind-speed values of that year. However, in both years, live weight in all treatments increased pre partum, and BCS did not decrease, indicating that unsheltered cows did not need to mobilise body reserves. Thus, OWPs could be a suitable pre-partum alternative to cubicle housing for dry dairy cows with regard to some aspects of dairy cow productive performance. However, further research should be carried out to investigate longer-term effects.

Disagreement exists within the scientific community with regards to the level of competition for feed between sheep and kangaroos in the Australian rangelands. The greatest challenge to solving this debate is finding effective means of determining the composition of the diets of these potential grazing competitors. An option is to adopt a non-invasive approach that combines faecal collection and molecular techniques that focus on faecal DNA as the primary source of dietary information. As proof-of-concept, we show that a DNA reference data bank on plant species can be established. This DNA reference data bank was then used as a library to identify plant species in kangaroo faeces collected in the southern rangelands of Western Australia. To enhance the method development and to begin the investigation of competitive grazing between sheep and kangaroos, 16 plant species known to be palatable to sheep were initially targeted for collection. To ensure that only plant sequences were studied, PCR amplification was performed using a universal primer pair previously shown to be specific to the chloroplast transfer RNA leucine (trnL) UAA gene intron. Overall, genus-specific, single and differently sized amplicons were reliably and reproducibly generated; enabling the differentiation of reference plants by PCR product length heterogeneity. However, there were a few plants that could not be clearly differentiated on the basis of size alone. This prompted the adoption of a post-PCR step that enabled further differentiation according to base sequence variation. Restriction endonucleases make sequence-specific cleavages on DNA to produce discrete and reproducible fragments having unique sizes and base compositions. Their availability, affordability and simplicity-of-use put restriction enzyme sequence (RES) profiling as a logical post-PCR step for confirming plant species identity. We demonstrate that PCR–RES profiling of plant and faecal matter is useful for the identification of plants included in the diet of kangaroos. The limitations, potential and the opportunities created for researchers interested in investigating the diet of competing herbivores in the rangelands are discussed.

A total of 120 Iberian pigs of the Lampiña line that grew under outdoor conditions were used to study the effect of the age at the beginning of Montanera period (AM) on meat characteristics and fatty acid (FA) profile of subcutaneous fat. AM period is a free-range fattening phase from November to February in which pigs ate mainly acorns and grass. There were two treatments with two AM (20 pigs per treatment); 18 (P18) and 12 months (P12). Barrows and gilts were in the same proportion within each treatment. All the animals were slaughtered at the same time (at the end of Montanera period) reaching an average 160 kg of body weight. Meat from P18 had less protein and was more red (a*) (P < 0.05), but tended to show higher intramuscular fat content (P < 0.10) than meat from P12. Loin from P18 had lower thawing (P < 0.001) and cooking losses (P < 0.10) than loin from P12. The fat from P18 had higher monounsaturated FA content than fat from P12 pigs (P < 0.01) due to the higher level of C18:1 (P < 0.01) and C20:1 (P < 0.001). However, fat from P12 had higher polyunsaturated FA content than fat from P18 pigs (P < 0.01) because of the higher level of C18:2 (P < 0.001). It is concluded that both 12 and 18 months are adequate AM for purebred Iberian pigs from the commercial point of view. However, if the aim is to produce high-quality dry-cured Iberian products, the P18 pigs would be more advisable because had better meat and fat characteristics than the P12 pigs.

Carcass traits and meat quality of rabbits reared in conventional cages (0.385 m2), small pens (0.662 m2) or large pens (4.052 m2) at a similar stock density of 15 rabbits/m2 were compared (n = 30 per group). Pens contained an elevated platform. Slaughter weight (SW; P < 0.01) and cold carcass weight (P < 0.05) decreased in the order of Cage < Small pen < Large pen groups. SW and cold carcass weight were 7% lower in rabbits housed in large pens than in cages. Dressing out and meat-to-bone ratio were not influenced by the housing system. Percentage of fat deposits was highest in caged rabbits (+0.15 point for scapular fat and +0.26 point for perirenal fat compared to rabbits reared in large pens P < 0.05). Rabbits housed in large pens had a bigger proportion of hind part (+1 point), and meat colour was shifted towards greater a* values (P < 0.01) compared to caged rabbits. Water holding capacity and shear test parameters in longissimus lumborum muscle, lipid content and shear test parameters of abductor cruralis cranialis, biceps femoris and semitendinosus muscles were not affected by the housing system. Tibia and femur bone moment of inertia increased in the order of Cage < Small pen < Large pen groups (P < 0.05), whereas elastic modulus, which is a measure of intrinsic stiffness, was highest in caged rabbits. This study showed that large pen housing altered carcass traits independently and increased meat redness and fracture resistance of tibia and femur.

Intramuscular fat (IMF) content plays a key role in various quality traits of meat. IMF content varies between species, between breeds and between muscle types in the same breed. Other factors are involved in the variation of IMF content in animals, including gender, age and feeding. Variability in IMF content is mainly linked to the number and size of intramuscular adipocytes. The accretion rate of IMF depends on the muscle growth rate. For instance, animals having a high muscularity with a high glycolytic activity display a reduced development of IMF. This suggests that muscle cells and adipocytes interplay during growth. In addition, early events that influence adipogenesis inside the muscle (i.e proliferation and differentiation of adipose cells, the connective structure embedding adipocytes) might be involved in interindividual differences in IMF content. Increasing muscularity will also dilute the final fat content of muscle. At the metabolic level, IMF content results from the balance between uptake, synthesis and degradation of triacylglycerols, which involve many metabolic pathways in both adipocytes and myofibres. Various experiments revealed an association between IMF level and the muscle content in adipocyte-type fatty acid-binding protein, the activities of oxidative enzymes, or the delta-6-desaturase level; however, other studies failed to confirm such relationships. This might be due to the importance of fatty acid fluxes that is likely to be responsible for variability in IMF content during the postnatal period rather than the control of one single pathway. This is evident in the muscle of most fish species in which triacylglycerol synthesis is almost zero. Genetic approaches for increasing IMF have been focused on live animal ultrasound to derive estimated breeding values. More recently, efforts have concentrated on discovering DNA markers that change the distribution of fat in the body (i.e. towards IMF at the expense of the carcass fatness). Thanks to the exhaustive nature of genomics (transcriptomics and proteomics), our knowledge on fat accumulation in muscles is now being underpinned. Metabolic specificities of intramuscular adipocytes have also been demonstrated, as compared to other depots. Nutritional manipulation of IMF independently from body fat depots has proved to be more difficult to achieve than genetic strategies to have lipid deposition dependent of adipose tissue location. In addition, the biological mechanisms that explain the variability of IMF content differ between genetic and nutritional factors. The nutritional regulation of IMF also differs between ruminants, monogastrics and fish due to their digestive and nutritional particularities.