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.

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.

The continued growth in biofuel production has led to a search for alternative value-added applications of its main by-product, crude glycerin. The surplus glycerin production and a higher cost of feedstuffs have increased the emphasis on evaluating its nutritive value for animal feeding. The aim of this research was to evaluate the effect of the dietary addition of crude glycerin on sow and litter performance, and to determine the serum concentrations of hormones related to energy metabolism and feed intake in sows during gestation and lactation. A total of 63 sows were assigned randomly to one of three dietary treatments, containing 0, 3 or 6% crude glycerin (G0, G3 and G6, respectively) added to a barley-soybean meal-based diet. During gestation, none of the dietary treatments had an effect on performance, while during lactation, glycerin-fed sows consumed less feed than those fed the control diet (3.8 v. 4.2kg DM/day; P=0.007). Although lactating sows fed the G3 diet had a higher BW loss than those fed the control diet (−20.6 v. −8.7 kg; P=0.002), this difference was not reflected in litter performance. In gestation, the inclusion of glycerin did not affect blood concentrations of insulin or cortisol. However, pregnant sows fed diets supplemented with glycerin showed lower concentrations of acyl-ghrelin and higher concentrations of leptin (−55 and +68%, respectively; P<0.001). In lactating sows, there were no differences between dietary treatments for any of the hormones measured. Pre-prandial acyl-ghrelin concentrations were positively correlated with cortisol concentrations during gestation (r=0.81; P=0.001) and lactation (r=0.61; P=0.015). In conclusion, the inclusion of up to 6% crude glycerin did not affect the performance of sows during the gestation period; however it had a negative effect on the feed intake and weight loss of lactating sows. Moreover, further research is needed to elucidate the potential relationship between glycerin inclusion levels in the diet and the serum concentrations of hormones related to feed intake and energy balance control.

Among several potential animal models that can be used for adipogenic studies, Wagyu cattle is the one that presents unique molecular mechanisms underlying the deposit of substantial amounts of intramuscular fat. As such, this review is focused on current knowledge of such mechanisms related to adipose tissue deposition using Wagyu cattle as model. So abundant is the lipid accumulation in the skeletal muscles of these animals that in many cases, the muscle cross-sectional area appears more white (adipose tissue) than red (muscle fibers). This enhanced marbling accumulation is morphologically similar to that seen in numerous skeletal muscle dysfunctions, disease states and myopathies; this might indicate cross-similar mechanisms between such dysfunctions and fat deposition in Wagyu breed. Animal models can be used not only for a better understanding of fat deposition in livestock, but also as models to an increased comprehension on molecular mechanisms behind human conditions. This revision underlies some of the complex molecular processes of fat deposition in animals.

Nutritional stressors may cause negative effects on animal health and growth and lead to significant economic impact. Adipose tissue is an endocrine organ producing, mediators and hormones, called adipokines. They play a dynamic role in body homeostasis and in the regulation of energy expenditure, interacting with feeding behavior, hormones and growth factors. This in vitro study aimed to investigate how nutritional conditions and growth hormone (GH) can influence nitric oxide (NO) production and the expression and secretion of three important adipokines, that is leptin, interleukin-6 (IL-6) and tumor necrosis factor-α (TNF-α), by swine adipocytes. In our experimental model, mesenchymal stem cells from omental adipose tissue were induced to adipogenic differentiation. After differentiation, adipocytes were incubated for 24 h (T0) with DMEM/Ham’s F12 (group A) or DMEM/Ham’s F12 salts (group B), a DMEM/Ham’s F12 formulation deprived of nutritional components. Primary adipocyte cells were also co-cultured for 4 h (T+4) or 12 h (T+12) with or without anterior pituitary slices. To stimulate GH secretion by pituitary cells, growth hormone releasing hormone at 10−8 M was added at the start of the incubation times (4 or 12 h). At T0, T+4 and T+12, NO production, leptin, IL-6 and TNF-α expression and secretion were measured. NO increased (P<0.05) up to twofold in restricted culture conditions. Deprived medium and coincubation with anterior pituitary positively influenced leptin secretion and expression. TNF-α was expressed and secreted only in deprived culture condition groups (B, B1 and B2). Nutrients availability and pituitary co-culture did not affect IL-6 expression and secretion. Our study shows an endocrine function for porcine adipocytes. In our model, adipocytes readily responded to nutritional inputs by secretion of molecules affecting energy balance. This secretion capacity was modulated by GH. Improving our knowledge of the role of adipocyte in the endocrine system, may lead to a more complete understanding of regulating energy balance in swine.

Diet influences animal body and tissue composition due to direct deposition and to the nutrients effects on metabolism. The influence of specific nutrients on the molecular regulation of lipogenesis is not well characterized and is known to be influenced by many factors including timing and physiological status. A trial was performed to study the effects of different dietary energy sources on lipogenic genes transcription in ham adipose tissue of Iberian pigs, at different growth periods and on feeding/fasting situations. A total of 27 Iberian male pigs of 28 kg BW were allocated to two separate groups and fed with different isocaloric feeding regimens: standard diet with carbohydrates as energy source (CH) or diet enriched with high oleic sunflower oil (HO). Ham subcutaneous adipose tissue was sampled by biopsy at growing (44 kg mean BW) and finishing (100 kg mean BW) periods. The first sampling was performed on fasted animals, while the last sampling was performed twice, with animals fasted overnight and 3 h after refeeding. Effects of diet, growth period and feeding/fasting status on gene expression were explored quantifying the expression of a panel of key genes implicated in lipogenesis and lipid metabolism processes. Quantitative PCR revealed several differentially expressed genes according to diet, with similar results at both timings: RXRG, LEP and FABP5 genes were upregulated in HO group while ME1, FASN, ACACA and ELOVL6 were upregulated in CH. The diet effect on ME1 gene expression was conditional on feeding/fasting status, with the higher ME1 gene expression in CH than HO groups, observed only in fasting samples. Results are compatible with a higher de novo endogenous synthesis of fatty acids (FA) in the carbohydrate-supplemented group and a higher FA transport in the oleic acid-supplemented group. Growth period significantly affected the expression of most of the studied genes, with all but PPARG showing higher expression in finishing pigs according to a pattern dissimilar from the usual in cosmopolitan pig breeds. Feeding/fasting status only influenced PPARG gene transcription. The lack of effects of feeding/fasting status on lipogenic gene expression and the higher ME1 response to diet in fasting samples than in postprandial sampling, suggest the persistence of de novo lipogenesis during fasting. Overall results improve the understanding of the influence of different factors on lipid metabolism regulation in Iberian pigs.

Intramuscular fat (IMF) is an important trait influencing meat quality, and intramuscular stromal-vascular cell (MSVC) differentiation is a key factor affecting IMF deposition. Quantitative real-time PCR (qPCR) is often used to screen the differentially expressed genes during differentiation of MSVCs, where proper reference genes are essential. In this study, we assessed 31 of previously reported reference genes for their expression suitability in porcine MSVCs derived form longissimus dorsi with qPCR. The expression stability of these genes was evaluated using NormFinder, geNorm and BestKeeper algorithms. NormFinder and geNorm uncovered ACTB, ALDOA and RPS18 as the most three stable genes. BestKeeper identified RPL13A, SSU72 and DAK as the most three stable genes. GAPDH was found to be the least stable gene by all of the three software packages, indicating it is not an appropriate reference gene in qPCR assay. These results might be helpful for further studies in pigs that explore the molecular mechanism underlying IMF deposition.

The retail market share of organic eggs in Denmark is high, and the consumers expect high animal welfare standards in the organic production. Documentation of animal welfare is important, however, knowledge about the associations between animal-based welfare indicators is limited. The aims of the study were to investigate the associations between selected welfare indicators at two ages (peak and end of lay), and to examine the development with age of the chosen welfare indicators. The chosen welfare indicators were Ascaridia galli (roundworm) infection, Heterakis sp. (caecal worm) infection, keel bone damages, back feathering, body feathering, foot damages, comb colour and wounds on the body. An observational study with 12 organic egg farms was conducted in 2012 and 2013 with a total of 214 hens assessed individually at the peak and the end of lay. Insufficient data were obtained on helminth infection at the peak of lay. At the end of lay, all helminth infected hens were positive for A. galli, and only three of them had in addition a Heterakis sp. infection. Foot damages, pale combs and wounds on the body occurred at frequencies <5% and were therefore, together with the prevalence of Heterakis sp. infection, left out of the analysis of associations. A graphical model was used to analyse the associations between the remaining clinical welfare indicators, A. galli infection, housing systems and age of the hens at end of lay. A. galli infection was only directly associated with back feathering at end of lay (P=0.011) with an increased incidence of A. galli infection in hens with good back feathering. Between the two visits, the prevalence of hens with keel bone damages increased (P<0.001), and the plumage condition deteriorated (P<0.001), whereas the number of hens with plantar abscess (P=0.037) and pale combs (P=0.020) decreased. No significant differences were found for other foot damages or for skin damage. In conclusion, back feathering at end of lay provided information about a possible helminth infection, but this is not a useful indicator in daily on-farm management. In addition, evidence was found that the deterioration of the plumage condition with age was not only due to accumulation of damage over time.

Access to drinking water is essential for animal welfare, but it is unclear if temporary water restriction during the night represents a welfare problem. The aim of the present study was to investigate the effect of various durations of nightly restriction of water on thirst in loose housed lactating sows from day 10 to 28 of lactation. A total of 48 sows were deprived of water for either 0 h (n=12; control), 3 h (n=12; 0500 to 0800 h), 6 h (n=12; 0200 to 0800 h) or 12 h (n=12; 2000 to 0800 h). Control sows consumed 22% of their water intake during the night (2000 to 0800 h), whereas water consumption during this time was reduced to 13%, 7% and 0% in sows restricted for 3, 6 and 12 h. With increased duration of nightly water restriction a reduced latency to drink (26.8, 18.0, 5.3 and 6.7 min for 0, 3, 6 and 12 h sows; P<0.001) and an increased water intake during the 1st hour after water became accessible (2.1, 3.4, 4.7 and 5.6 l for 0, 3, 6 and 12 h sows; P<0.001) was seen. During the last 30 min before water became accessible more sows deprived of water investigated (0%, 50%, 75%,and 50% of 0, 3, 6 and 12 h sows; P<0.01) or forcefully manipulated (0%, 17%, 50% and 33% of 0, 3, 6 and 12 h sows; P<0.05) the water trough, suggesting frustration and a negative experience of thirst. When all signs of imminent water access were provided, but access was delayed by 25 min, a tendency for more of the sows deprived of water for 6 and 12 h to interact forcefully with the water trough was seen (22%, 18%, 42% and 67% of 0, 3, 6 and 12 h sows; P=0.09). Duration of water restriction did not affect water consumption on a 24-h basis, nursing behaviour or performance. In conclusion, behavioural indicators of thirst increased with increasing duration of nightly water restriction in lactating sows.

Lameness is an important issue in group-housed sows. Automatic detection systems are a beneficial diagnostic tool to support management. The aim of the present study was to evaluate data of a positioning system including acceleration measurements to detect lameness in group-housed sows. Data were acquired at the Futterkamp research farm from May 2012 until April 2013. In the gestation unit, 212 group-housed sows were equipped with an ear sensor to sample position and acceleration per sow and second. Three activity indices were calculated per sow and day: path length walked by a sow during the day (Path), number of squares (25×25 cm) visited during the day (Square) and variance of the acceleration measurement during the day (Acc). In addition, data on lameness treatments of the sows and a weekly lameness score were used as reference systems. To determine the influence of a lameness event, all indices were analysed in a linear random regression model. Test day, parity class and day before treatment had a significant influence on all activity indices (P<0.05). In healthy sows, indices Path and Square increased with increasing parity, whereas variance slightly decreased. The indices Path and Square showed a decreasing trend in a 14-day period before a lameness treatment and to a smaller extent before a lameness score of 2 (severe lameness). For the index acceleration, there was no obvious difference between the lame and non-lame periods. In conclusion, positioning and acceleration measurements with ear sensors can be used to describe the activity pattern of sows. However, improvements in sampling rate and analysis techniques should be made for a practical application as an automatic lameness detection system.

The meat fats content associated to nutritional and sensory characteristics are the most important concerns of consumers. To study the effect of caponisation on the meat quality of two different breed chickens, slaughtered at 18 weeks of age, raised under the same conditions, the physicochemical and sensory characteristics of capons (castrated males at 8 weeks of age) and roosters’ meat of native Amarela Portuguesa and native Pedrês Portuguesa breeds were evaluated. Forty Amarela (20 roosters and 20 capons), 40 Pedrês (20 roosters and 20 capons) chickens, and also, six free-range chicken and six broilers were evaluated. The pH, water-holding capacity, Warner-Bratzler shear force, moisture content, ash, myoglobin, collagen, CP, total fat and fatty acids profile were evaluated in breast and leg meat, according to standard procedures. Leg meat capon showed greater intramuscular fat content (P⩽0.05), monounsaturated fatty acids (MUFA) and CP (P⩽0.001) than leg roosters. Caponisation increased the content of myoglobin and MUFA (P⩽0.05) and reduced the moisture content in the leg (P⩽0.05). The main fatty acids found were oleic acid (C18:1), palmitic acid (C16:0) and linoleic acid (C18:2). The greatest value of C18:1 was observed in capon’s breast (P⩽0.01). Sensory analysis was made to compare the Amarela and Pedrês meat with a free-range chicken and a broiler. The sensory taste panel classified the capon’s meat (Amarela and Pedrês) as juicier, less fibrous and tougher than rooster’s meat. The broiler was in general juicier, tenderer and less fibrous than the other birds. The results of sensory analysis complement those obtained in physicochemical analysis, suggesting that caponisation promotes an overall improvement in meat quality.

Delivering beef of consistent quality to the consumer is vital for consumer satisfaction and will help to ensure demand and therefore profitability within the beef industry. In Australia, this is being tackled with Meat Standards Australia (MSA), which uses carcass traits and processing factors to deliver an individual eating quality guarantee to the consumer for 135 different ‘cut by cooking methods’ from each carcass. The carcass traits used in the MSA model, such as ossification score, carcass weight and marbling explain the majority of the differences between breeds and sexes. Therefore, it was expected that the model would predict with eating quality of bulls and dairy breeds with good accuracy. In total, 8128 muscle samples from 482 carcasses from France, Poland, Ireland and Northern Ireland were MSA graded at slaughter then evaluated for tenderness, juiciness, flavour liking and overall liking by untrained consumers, according to MSA protocols. The scores were weighted (0.3, 0.1, 0.3, 0.3) and combined to form a global eating quality (meat quality (MQ4)) score. The carcasses were grouped into one of the three breed categories: beef breeds, dairy breeds and crosses. The difference between the actual and the MSA-predicted MQ4 scores were analysed using a linear mixed effects model including fixed effects for carcass hang method, cook type, muscle type, sex, country, breed category and postmortem ageing period, and random terms for animal identification, consumer country and kill group. Bulls had lower MQ4 scores than steers and females and were predicted less accurately by the MSA model. Beef breeds had lower eating quality scores than dairy breeds and crosses for five out of the 16 muscles tested. Beef breeds were also over predicted in comparison with the cross and dairy breeds for six out of the 16 muscles tested. Therefore, even after accounting for differences in carcass traits, bulls still differ in eating quality when compared with females and steers. Breed also influenced eating quality beyond differences in carcass traits. However, in this case, it was only for certain muscles. This should be taken into account when estimating the eating quality of meat. In addition, the coefficients used by the Australian MSA model for some muscles, marbling score and ultimate pH do not exactly reflect the influence of these factors on eating quality in this data set, and if this system was to be applied to Europe then the coefficients for these muscles and covariates would need further investigation.

European conformation and fat grades are a major factor determining carcass value throughout Europe. The relationships between these scores and sensory scores were investigated. A total of 3786 French, Polish and Irish consumers evaluated steaks, grilled to a medium doneness, according to protocols of the ‘Meat Standards Australia’ system, from 18 muscles representing 455 local, commercial cattle from commercial abattoirs. A mixed linear effects model was used for the analysis. There was a negative relationship between juiciness and European conformation score. For the other sensory scores, a maximum of three muscles out of a possible 18 demonstrated negative effects of conformation score on sensory scores. There was a positive effect of European fat score on three individual muscles. However, this was accounted for by marbling score. Thus, while the European carcass classification system may indicate yield, it has no consistent relationship with sensory scores at a carcass level that is suitable for use in a commercial system. The industry should consider using an additional system related to eating quality to aid in the determination of the monetary value of carcasses, rewarding eating quality in addition to yield.

Understanding of biological impact of proteome profile on meat quality is vital for developing different approaches to improve meat quality. Present study was conducted to unravel the differences in biochemical, ultrastructural and proteome profile of longissimus dorsi muscle between buffaloes (Bubalus bubalis) of different age groups (young v. old). Higher (P<0.05) myofibrillar and total protein extractability, muscle fibre diameter, and Warner-Bratzler shear force (WBSF) values was observed in old buffalo meat relative to meat from young buffaloes. Scanning electron microscopy photographs revealed reduced fibre size with increased inter-myofibrillar space in young compared with old buffalo meat. Transmission electron microscopy results revealed longer sarcomeres in young buffalo meat relative to meat from old buffaloes. Proteomic characterization using two-dimensional gel electrophoresis (2DE) found 93 differentially expressed proteins between old and young buffalo meat. Proteome analysis using 2DE revealed 191 and 95 differentially expressed protein spots after 6 days of ageing in young and old buffalo meat, respectively. The matrix assisted laser desorption ionization time-of flight/time-of flight mass spectrometry (MALDI-TOF/TOF MS) analysis of selected gel spots helped in identifying molecular markers of tenderness mainly consisting of structural proteins. Protein biomarkers identified in the present study have the potential to differentiate meat from young and old buffaloes and pave the way for optimizing strategies for improved buffalo meat quality.

The reliability of genomic breeding values (DGV) decays over generations. To keep the DGV reliability at a constant level, the reference population (RP) has to be continuously updated with animals from new generations. Updating RP may be challenging due to economic reasons, especially for novel traits involving expensive phenotyping. Therefore, the goal of this study was to investigate a minimal RP update size to keep the reliability at a constant level across generations. We used a simulated dataset resembling a dairy cattle population. The trait of interest was not included itself in the selection index, but it was affected by selection pressure by being correlated with an index trait that represented the overall breeding goal. The heritability of the index trait was assumed to be 0.25 and for the novel trait the heritability equalled 0.2. The genetic correlation between the two traits was 0.25. The initial RP (n=2000) was composed of cows only with a single observation per animal. Reliability of DGV using the initial RP was computed by evaluating contemporary animals. Thereafter, the RP was used to evaluate animals which were one generation younger from the reference individuals. The drop in the reliability when evaluating younger animals was then assessed and the RP was updated to re-gain the initial reliability. The update animals were contemporaries of evaluated animals (EVA). The RP was updated in batches of 100 animals/update. First, the animals most closely related to the EVA were chosen to update RP. The results showed that, approximately, 600 animals were needed every generation to maintain the DGV reliability at a constant level across generations. The sum of squared relationships between RP and EVA and the sum of off-diagonal coefficients of the inverse of the genomic relationship matrix for RP, separately explained 31% and 34%, respectively, of the variation in the reliability across generations. Combined, these parameters explained 53% of the variation in the reliability across generations. Thus, for an optimal RP update an algorithm considering both relationships between reference and evaluated animals, as well as relationships among reference animals, is required.

The aim of this study was to test how genetic gain for a trait not measured on the nucleus animals could be obtained within a genomic selection pig breeding scheme. Stochastic simulation of a pig breeding program including a breeding nucleus, a multiplier to produce and disseminate semen and a production tier where phenotypes were recorded was performed to test (1) the effect of obtaining phenotypic records from offspring of nucleus animals, (2) the effect of genotyping production animals with records for the purpose of including them in a genomic selection reference population or (3) to combine the two approaches. None of the tested strategies affected genetic gain if the trait under investigation had a low economic value of only 10% of the total breeding goal. When the relative economic weight was increased to 30%, a combination of the methods was most effective. Obtaining records from offspring of already genotyped nucleus animals had more impact on genetic gain than to genotype more distant relatives with phenotypes to update the reference population. When records cannot be obtained from offspring of nucleus animals, genotyping of production animals could be considered for traits with high economic importance.

Recent genomic evaluation studies using real data and predicting genetic gain by modeling breeding programs have reported moderate expected benefits from the replacement of classic selection schemes by genomic selection (GS) in small ruminants. The objectives of this study were to compare the cost, monetary genetic gain and economic efficiency of classic selection and GS schemes in the meat sheep industry. Deterministic methods were used to model selection based on multi-trait indices from a sheep meat breeding program. Decisional variables related to male selection candidates and progeny testing were optimized to maximize the annual monetary genetic gain (AMGG), that is, a weighted sum of meat and maternal traits annual genetic gains. For GS, a reference population of 2000 individuals was assumed and genomic information was available for evaluation of male candidates only. In the classic selection scheme, males breeding values were estimated from own and offspring phenotypes. In GS, different scenarios were considered, differing by the information used to select males (genomic only, genomic+own performance, genomic+offspring phenotypes). The results showed that all GS scenarios were associated with higher total variable costs than classic selection (if the cost of genotyping was 123 euros/animal). In terms of AMGG and economic returns, GS scenarios were found to be superior to classic selection only if genomic information was combined with their own meat phenotypes (GS-Pheno) or with their progeny test information. The predicted economic efficiency, defined as returns (proportional to number of expressions of AMGG in the nucleus and commercial flocks) minus total variable costs, showed that the best GS scenario (GS-Pheno) was up to 15% more efficient than classic selection. For all selection scenarios, optimization increased the overall AMGG, returns and economic efficiency. As a conclusion, our study shows that some forms of GS strategies are more advantageous than classic selection, provided that GS is already initiated (i.e. the initial reference population is available). Optimizing decisional variables of the classic selection scheme could be of greater benefit than including genomic information in optimized designs.

This paper reviews strategies and methods to improve accuracies of genomic predictions from the perspective of a numerically small population. Improvements are realized by influencing one or both of the main factors: (1) improve or increase genomic connections to phenotypic records in training data. (2) Models and strategies to focus genomic predictions on markers closer to the causative variants. Combining populations into a joint reference population results in high improvements when combining populations of the same breed and diminishes as the genetic distance between populations increases. For distantly related breeds sophisticated Bayesian variable selection models in combination with denser markers sets or functional subsets of markers is needed. This is expected to be further improved by the efficient use of sequence information. In addition predictions can be improved by the use of phenotypes of genotyped and non-genotyped cows directly. For a small population the optimal approach will combine the above components.

In modern dairy cattle breeding, genomic breeding programs have the potential to increase efficiency and genetic gain. At the same time, the requirements and the availability of genotypes and phenotypes present a challenge. The set-up of a large enough reference population for genomic prediction is problematic for numerically small breeds but also for hard to measure traits. The first part of this study is a review of the current literature on strategies to overcome the lack of reference data. One solution is the use of combined reference populations from different breeds, different countries, or different research populations. Results reveal that the level of relationship between the merged populations is the most important factor. Compiling closely related populations facilitates the accurate estimation of marker effects and thus results in high accuracies of genomic prediction. Consequently, mixed reference populations of the same breed, but from different countries are more promising than combining different breeds, especially if those are more distantly related. The use of female reference information has the potential to enlarge the reference population size. Including females is advisable for small populations and difficult traits, and maybe combined with genotyping females and imputing those that are un-genotyped.

The efficient use of imputation for un-genotyped individuals requires a set of genotyped related animals and well-considered selection strategies which animals to choose for genotyping and phenotyping. Small populations have to find ways to derive additional advantages from the cost-intensive establishment of genomic breeding schemes. Possible solutions may be the use of genomic information for inbreeding control, parentage verification, within-herd selection, adjusted mating plans or conservation strategies.

The second part of the paper deals with the issue of high-quality phenotypes against the background of new, difficult and hard to measure traits. The use of contracted herds for phenotyping is recommended, as additional traits, when compared to standard traits used in dairy cattle breeding can be measured at set moments in time. This can be undertaken even for the recording of health traits, thus resulting in complete contemporary groups for health traits. Future traits to be recorded and used in genomic breeding programs, at least partly will be traits for which traditional selection based on widespread phenotyping is not possible. Enabling phenotyping of sufficient numbers to enable genomic selection will rely on cooperation between scientists from different disciplines and may require multidisciplinary approaches.