The objective of this study was to define different terminal sire flock environments, based on a range of environmental factors, and then investigate the presence of genotype by environment interactions (G×E) between the environments identified. Data from 79 different terminal sire flocks (40 Texel, 21 Charollais and 18 Suffolk), were analysed using principal coordinate and non-hierarchical cluster analyses, the results of which identified three distinct environmental cluster groups. The type of grazing, climatic conditions and the use of vitamins and mineral supplements were found to be the most important factors in the clustering of flocks. The presence of G×E was then investigated using data from the Charollais flocks only. Performance data were collected for 12 181 lambs, between 1990 and 2010, sired by 515 different sires. Fifty six of the sires had offspring in at least two of the three different cluster groups and pedigree information was available for a total of 161 431 animals. Traits studied were the 21-week old weight (21WT), ultrasound muscle depth (UMD) and log transformed backfat depth (LogUFD). Heritabilities estimated for each cluster, for each trait, ranged from 0.32 to 0.45. Genetic correlations estimated between Cluster 1 and Cluster 2 were all found to be significantly lower than unity, indicating the presence of G×E. They were 0.31 (±0.17), 0.68 (±0.14) and 0.18 (±0.21) for 21WT, UMD and LogUFD, respectively. Evidence of sires re-ranking across clusters was also observed. Providing a suitable strategy can be identified, there is potential for the optimisation of future breeding programmes, by taking into account the G×E observed. This would enable farmers to identify and select animals with an increased knowledge as to how they will perform in their specific farm environment thus reducing any unexpected differences in performance.

This study aimed to identify genetic evaluation models (GEM) to accurately select cattle for milk production when only limited data are available. It is based on a data set from the Pakistani Sahiwal progeny testing programme which includes records from five government herds, each consisting of 100 to 350 animals, with lactation records dating back to 1968. Different types of GEM were compared, namely: (1) multivariate v. repeatability model when using the first three lactations, (2) an animal v. a sire model, (3) different fixed effects models to account for effects such as herd, year and season; and (4) fitting a model with genetic parameters fixed v. estimating the genetic parameters as part of the model fitting process. Two methods were used for the comparison of models. The first method used simulated data based on the Pakistani progeny testing system and compared estimated breeding values with true breeding values. The second method used cross-validation to determine the best model in subsets of actual Australian herd-recorded data. Subsets were chosen to reflect the Pakistani data in terms of herd size and number of herds. Based on the simulation and the cross-validation method, the multivariate animal model using fixed genetic parameters was generally the superior GEM, but problems arise in determining suitable values for fixing the parameters. Using mean square error of prediction, the best fixed effects structure could not be conclusively determined. The simulation method indicated the simplest fixed effects structure to be superior whereas in contrast, the cross-validation method on actual data concluded that the most complex one was the best. In conclusion it is difficult to propose a universally best GEM that can be used in any data set of this size. However, some general recommendations are that it is more appropriate to estimate the genetic parameters when evaluating for selection purposes, the animal model was superior to the sire model and that in the Pakistani situation the repeatability model is more suitable than a multivariate.

Genomic prediction utilizes single nucleotide polymorphism (SNP) chip data to predict animal genetic merit. It has the advantage of potentially capturing the effects of the majority of loci that contribute to genetic variation in a trait, even when the effects of the individual loci are very small. To implement genomic prediction, marker effects are estimated with a training set, including individuals with marker genotypes and trait phenotypes; subsequently, genomic estimated breeding values (GEBV) for any genotyped individual in the population can be calculated using the estimated marker effects. In this study, we aimed to: (i) evaluate the potential of genomic prediction to predict GEBV for nematode resistance traits and BW in sheep, within and across populations; (ii) evaluate the accuracy of these predictions through within-population cross-validation; and (iii) explore the impact of population structure on the accuracy of prediction. Four data sets comprising 752 lambs from a Scottish Blackface population, 2371 from a Sarda×Lacaune backcross population, 1000 from a Martinik Black-Belly×Romane backcross population and 64 from a British Texel population were used in this study. Traits available for the analysis were faecal egg count for Nematodirus and Strongyles and BW at different ages or as average effect, depending on the population. Moreover, immunoglobulin A was also available for the Scottish Blackface population. Results show that GEBV had moderate to good within-population predictive accuracy, whereas across-population predictions had accuracies close to zero. This can be explained by our finding that in most cases the accuracy estimates were mostly because of additive genetic relatedness between animals, rather than linkage disequilibrium between SNP and quantitative trait loci. Therefore, our results suggest that genomic prediction for nematode resistance and BW may be of value in closely related animals, but that with the current SNP chip genomic predictions are unlikely to work across breeds.

The 6 to 8-week period centered on parturition, known as the transition or periparturient period, is critical to welfare and profitability of individual cows. Fertility of high-producing cows is compromised by difficult transitions. Deficiencies in either nutritional or non-nutritional management increase risk for periparturient metabolic disorders and infectious diseases, which decrease subsequent fertility. A primary factor impeding fertility is the extent of negative energy balance (NEB) early postpartum, which may inhibit timing of first ovulation, return to cyclicity, and oocyte quality. In particular, pronounced NEB during the first 10 days to 2 weeks (the time of greatest occurrence of health problems) is critical for later reproductive efficiency. Avoiding over-conditioning and preventing cows from over-consuming energy relative to their requirements in late gestation result in higher dry matter intake (DMI) and less NEB after calving. A pooled statistical analysis of previous studies in our group showed that days to pregnancy are decreased (by 10 days) by controlling energy intake to near requirements of cows before calving compared with allowing cows to over-consume energy. To control energy intake, total mixed rations (TMR) must be well balanced for metabolizable protein, minerals and vitamins yet limit total DM consumed, and cows must uniformly consume the TMR without sorting. Dietary management to maintain blood calcium and rumen health around and after calving also are important. Opportunities may exist to further improve energy status in fresh cows. Recent research to manipulate the glucogenic to lipogenic balance and the essential fatty acid content of tissues are intriguing. High-producing cows that adapt successfully to lactation can have high reproductive efficiency, and nutritional management of the transition period both pre- and post-calving must facilitate that adaptation.

The objective of this study was to identify detailed fertility traits in dairy and beef cattle from transrectal ultrasonography records and quantify the associated risk factors. Data were available on 148 947 ultrasound observations of the reproductive tract from 75 949 cows in 843 Irish dairy and beef herds between March 2008 and October 2012. Traits generated included (1) cycling at time of examination, (2) cystic structures, (3) early ovulation, (4) embryo death and (5) uterine score; the latter was measured on a scale of 1 (good) to 4 (poor) characterising the tone of the uterine wall and fluid present in the uterus. After editing, 72 773 records from 44 415 dairy and beef cows in 643 herds remained. Factors associated with the logit of the probability of a positive outcome for each of the binary fertility traits were determined using generalised estimating equations; linear mixed model analysis was used for the analysis of uterine score. The prevalence of cycling, cystic structures, early ovulation and embryo death was 84.75%, 3.87%, 7.47% and 3.84%, respectively. The occurrence of the uterine heath score of 1, 2, 3 and 4 was 70.63%, 19.75%, 8.36% and 1.26%, respectively. Cows in beef herds had a 0.51 odds (95% CI=0.41 to 0.63, P<0.001) of cycling at the time of examination compared with cows in dairy herds; stage of lactation at the time of examination was the same in both herd types. Furthermore, cows in dairy herds had an inferior uterine score (indicating poorer tone and a greater quantity of uterine fluid present) compared with cows in beef herds. The likelihood of cycling at the time of examination increased with parity and stage of lactation, but was reduced in cows that had experienced dystocia in the previous calving. The presence of cystic structures on the ovaries increased with parity and stage of lactation. The likelihood of embryo/foetal death increased with parity and stage of lactation. Dystocia was not associated with the presence of cystic structures or embryo death. Uterine score improved with parity and stage of lactation, while cows that experienced dystocia in the previous calving had an inferior uterine score. Heterosis was the only factor associated with increased likelihood of early ovulation. The fertility traits identified, and the associated risk factors, provide useful information on the reproductive status of dairy and beef cows.

Most donkey and local horse breeds are vulnerable to extinction as mechanization of agriculture progress throughout the world. The present study analyzed the pedigree and herd records of the donkey Asinina de Miranda breed (RAM), identifying genealogical and human factors that may affect the breed genetic diversity in the future and suggesting suitable strategies to breed preservation, early on the conservation program. The breeding rate was very low, with a ratio of foaling/live animals of 0.23 (178/760). The estimated number of founders and ancestors contributing to the reference population was 128 and 121. The number of founder herds in the reference population was 64, with an effective number of founder herds for the reference population of 7.6. The mean age of herd owners was 65.50±0.884 years, with a negative association among the herd size and owner’s age (P<0.001). In contrast, the size of the herd and the ownership of a male were both positively associated (P<0.001) with the herd number of in-born foals. Both the owners’ age and the herd location (RAM home region v. dispersal region) were negatively associated with the foaling number (P<0.001). The main identified risk factors were: low breeding rates; low number of males and their unequal contribution to the genetic pool; unequal contribution of the herds to genetic pool; and advanced age of herd owners.

Daily methane production and feed intake were measured on 160 adult ewes, which were the progeny of 20 sires and 3 sire types (Merino, dual-purpose and terminal) from a genetically diverse flock. All animals were housed in individual pens and fed a 50/50 mix of chaffed lucerne and oaten hays at 20 g/kg liveweight (LW), with feed refusals measured for at least 10 days before the first of three 22-h measurements in respiration chambers (RC). Feed was withdrawn at 1600 h on the day before each RC test to encourage the ewes to eat the entire ration provided for them in the RC. After the first 1-day RC test, the sheep were returned to their pens for a day, then given a second 1-day RC test, followed by another day in their pens, then a third RC test. After all animals had been tested, they were ranked according to methane emissions adjusted for feed intake in the RC and on the previous day, enabling 10 low and 10 high methane animals to be chosen for repeat measurement. No variation between sires nor consistent effects of LW on feed eaten (%FE, expressed as per cent of feed offered) was evident in the 10 days before the first RC measurement. However, significant differences between sires (equivalent to an estimated heritability of 41%) were identified for %FE during the 2nd and 3rd days of RC testing (2 and 4 days after the initial RC test). The analysis of all data showed that methane emissions in the RC were related to feed intake on the day of testing and the two previous days (all P<0.0005). Before correcting for feed intake on previous days, there was some variation between sires in methane yield, equivalent to an estimated heritability of 9%. Correction for feed intake on the 2 previous days halved the residual variation, allowing other effects to be detected, including effects of LW, twins reared as singles, test batch, RC and test-day effects, but estimated sire variation fell to zero. In order to avoid potential biases, statistical models of methane emissions in the RC need to consider potential confounding factors, such as those identified as significant in this study.

The possibility of using quantitative kinematic traits as indirect selection criteria for sport performance could be beneficial to perform an early genetic evaluation of the animals. The genetic parameters for objectively measured kinematic traits under field conditions have been estimated for the first time, in order to potentially use these traits as indicators of gait quality in future selection of the Lusitano breed. The repeatability within three different types of training (dressage, bullfighting and untrained) was also discussed. A total of 176 males (4 to 14 years old) were recorded at trot in hand using a 3D videographic system. The speed and 10 kinematic traits were studied (one temporal, two linear and seven angular variables). The genetic parameters of the kinematic variables were estimated using VCE software. The heritability estimates were moderate to high (0.18 to 0.53). The stride length and the forelimb angular variables presented the highest heritabilities (0.49 to 0.53), whereas the hindlimb angular variables revealed the lowest values (0.18 to 0.40). More than half of the genetic correlations were moderately to highly positive (mostly 0.20 to 0.70; up to 0.88 between hindlimb traits). The dressage and bullfighting groups presented the highest repeatabilities (over 0.6) in the majority of the traits, maybe because of the acquired gait regularity expected in animals subjected to specific training, and suggesting a greater influence of the individuals over the kinematic traits studied in these two subpopulations than in the untrained subpopulation. The longer swing phase duration and the larger range of motion of the elbow, hock and pelvis joints observed in the dressage group may indicate a better gait quality of this group, according to FEI (International Equestrian Federation) standards. The bullfighting and untrained groups were more similar to each other in terms of kinematic traits. Selection of young horses for characteristics such as stride length and the hindlimbs traits can apparently contribute to further genetic improvement of the performance of Lusitano breed.

The objective of our study was to investigate the heritabilities and genetic correlations between traits from a linear exterior assessment system and osteochondrosis (OC) measured by computed tomography (CT), and in addition, to study the genetic trend in a population where the conformation traits have been included in the breeding goal. The data material consisted of phenotypes from a total of 4571 Norsvin Landrace test boars. At the end of the test period, all boars were subjected to a detailed exterior assessment system. Within 10 days of the assessment, the boars were CT scanned for measuring OC. The total score of osteochondrosis (OCT), used in this study, is the sum of phenotypes from the assessment on the medial and lateral condyles at the distal end of both the humerus and the femur of the right and the left leg of the boar based on images from CT. The exterior assessment traits included in the study were; ‘front leg knee’ (FKNE), ‘front leg pasterns’ (FPAS), ‘front leg stance’ (FSTA), ‘front leg twisted pasterns’ (FFLK), ‘hind leg stance’, ‘hind leg pasterns’ (HPAS), ‘hind leg standing under’ (HSTU), ‘hind leg small inner toe’, ‘dipped back’, ‘arched back’ (ARCH) and ‘waddling hindquarters’ (WADL). The estimation of (co)variance components and breeding values were performed using bivariate animal genetic models. Breeding values for HSTU, HPAS, FPAS, WADL and OCT traits were additional outputs from the same bivariate analyses. The lowest heritability was found for FFLK (h2FFLK=0.05), whereas FPAS was estimated to have the highest heritability (h2FPAS=0.36), and OCT demonstrating a heritability of 0.29. Significant genetic correlations were found between several traits; the strongest correlation was between FSTA and FFLK (0.94), which was followed by the correlation between FPAS and FKNE (0.69). The traits ARCH and FSTA had significant genetic correlations to OCT, whereas all other genetic correlations between OCT and the conformation traits were low and not significantly different from 0. Our study shows positive genetic trends for the conformation traits included in the breeding goal. In general, low genetic correlations between conformation traits and OC were observed in our study.

Nowadays, the fibre diameter (FD) is considered the main selection objective in alpaca populations all over the world. International Committee for Animal Recording recommendations define the FD and its CV as the first two traits to be considered in breeding programmes for this specie. In addition to these main criteria, other selection criteria of economic value used are comfort factor (CF) or standard deviation (s.d.); also other less important traits being used as selection objectives are these morphological traits: density (DE), crimp (CR) or lock structure (LS) for, respectively, Huacaya (HU) and Suri (SU) ecotypes, head (HE), coverage (CO) and balance (BA). The goal of this study was to establish how to implement a combined selection index starting from genetic parameters and to study the expected correlation between genetic trends by considering different alternative procedures of weighting all the involved traits, and the consequences of a wrongly proceeding way. Heritabilities and genetic and phenotypic correlations were estimated from the data set belonging to the PACOMARCA experimental farm for SU and HU. Two approaches were used to check the consequences of a set of subjective weights essayed. The coefficients of selection indexes were obtained for two sets of reference weights. In addition, equivalent weights were drawn if applied those reference values as coefficients of hypothetical selection indexes directly on phenotypes; relative expected genetic responses were computed in different cases. Results showed that almost in all cases for both ecotypes, the weight applied to CF should be surprisingly negative. Concerning genetic responses, only CO was compromised in some cases for the HU ecotype. The essayed methodology allowed explaining the differences between ecotypes in the genetic trends. The proposed methodology was shown to be effective to study the relative importance of the traits granted by the manager of a breeding scheme.

The use of inert markers in broiler diets eliminates the need to quantitatively evaluate feed intake and excreta output to determine diet digestibility, and enables nutrient uptake at specific points along the gastrointestinal tract to be examined. Titanium dioxide (TiO2) is commonly used for this purpose and measured using a UV-spectrophotometric assay. Two experiments were conducted to observe whether an inductively coupled plasma optical emission spectrophotometer (ICP-OES) assay is able to replace the UV-spectroscopy assay for rapid analysis of TiO2 in broiler feed and ileal digesta samples. In the first experiment, TiO2 was added at 5 g/kg to 19 broiler diets. Ross 308 male broilers (n=452) fed these diets were involved in a series of digestion studies to determine ileal digesta recovery of TiO2. In the second experiment, defined amounts of TiO2 were added to ileal digesta samples from Ross 308 male broilers (n=176) and TiO2 recoveries were determined. The feed and ileal samples from both experiments were analysed by both UV-spectroscopy and ICP-OES, and relatedness of the findings from the two assays was determined. Overall relatedness of the two assays was strong for determination of TiO2 concentration in both the broiler diets and ileal digesta samples (r=0.908 and r=0.884, respectively). Overall recovery of supplemented TiO2 was 97.62% by the UV-spectroscopy assay and 98.77% by the ICP-OES assay. The ICP-OES assay in this study was as accurate as spectrophotometric determination for the quantification of TiO2 content. The ICP-OES method can also be used to analyse several elements within one assay, with a single preparation step, and thus the measurement of TiO2 may be incorporated into the analysis of other minerals. Time and resources dedicated to determining diet digestibility in broilers could be minimised by using the ICP-OES assay to replace the UV-spectroscopy assay when measuring TiO2 concentration.

The objective of the present study was to compare genetic gain and inbreeding coefficients of dairy cattle in organic breeding program designs by applying stochastic simulations. Evaluated breeding strategies were: (i) selecting bulls from conventional breeding programs, and taking into account genotype by environment (G×E) interactions, (ii) selecting genotyped bulls within the organic environment for artificial insemination (AI) programs and (iii) selecting genotyped natural service bulls within organic herds. The simulated conventional population comprised 148 800 cows from 2976 herds with an average herd size of 50 cows per herd, and 1200 cows were assigned to 60 organic herds. In a young bull program, selection criteria of young bulls in both production systems (conventional and organic) were either ‘conventional’ estimated breeding values (EBV) or genomic estimated breeding values (GEBV) for two traits with low (h 2=0.05) and moderate heritability (h 2=0.30). GEBV were calculated for different accuracies (r mg), and G×E interactions were considered by modifying originally simulated true breeding values in the range from r g=0.5 to 1.0. For both traits (h 2=0.05 and 0.30) and r mg⩾0.8, genomic selection of bulls directly in the organic population and using selected bulls via AI revealed higher genetic gain than selecting young bulls in the larger conventional population based on EBV; also without the existence of G×E interactions. Only for pronounced G×E interactions (r g=0.5), and for highly accurate GEBV for natural service bulls (r mg>0.9), results suggests the use of genotyped organic natural service bulls instead of implementing an AI program. Inbreeding coefficients of selected bulls and their offspring were generally lower when basing selection decisions for young bulls on GEBV compared with selection strategies based on pedigree indices.

This study investigated the profile of locomotion score and lameness before the first calving and throughout the first (n=237) and second (n=66) lactation of 303 Holstein cows raised on a commercial farm. Weekly heritability estimates of locomotion score and lameness, and their genetic and phenotypic correlations with milk yield, body condition score, BW and reproduction traits were derived. Daughter future locomotion score and lameness predictions from their sires’ breeding values for conformation traits were also calculated. First-lactation cows were monitored weekly from 6 weeks before calving to the end of lactation. Second-lactation cows were monitored weekly throughout lactation. Cows were locomotion scored on a scale from one (sound) to five (severely lame); a score greater than or equal to two defined presence of lameness. Cows’ weekly body condition score and BW was also recorded. These records were matched to corresponding milk yield records, where the latter were 7-day averages on the week of inspection. The total number of repeated records amounted to 12 221. Data were also matched to the farm’s reproduction database, from which five traits were derived. Statistical analyses were based on uni- and bivariate random regression models. The profile analysis showed that locomotion and lameness problems in first lactation were fewer before and immediately after calving, and increased as lactation progressed. The profile of the two traits remained relatively constant across the second lactation. Highest heritability estimates were observed in the weeks before first calving (0.66 for locomotion score and 0.54 for lameness). Statistically significant genetic correlations were found for first lactation weekly locomotion score and lameness with body condition score, ranging from −0.31 to −0.65 and from −0.44 to −0.76, respectively, suggesting that cows genetically pre-disposed for high body condition score have fewer locomotion and lameness issues. Negative (favourable) phenotypic correlations between first lactation weekly locomotion score/lameness and milk yield averaged −0.27 and −0.17, respectively, and were attributed to management factors. Also a phenotypic correlation between lameness and conception rate of −0.19 indicated that lame cows were associated with lower success at conceiving. First-lactation daughter locomotion score and/or lameness predictions from sires’ estimated breeding values for conformation traits revealed a significant linear effect of rear leg side view, rear leg rear view, overall conformation, body condition score and locomotion, and a quadratic effect of foot angle.

The effect of feeding pigs in a three-phase feeding (3PF) system or a daily-phase feeding (DPF) system on growth performance, body composition, and N and P excretions was studied on 8 pens of 10 pigs each. Feeds for the 3PF and DPF treatments were obtained by mixing two feeds, one with a high nutrient concentration and the other with a low nutrient concentration. The DPF pigs tended (P=0.08) to consume more feed (+3.7%) than the 3PF pigs, but only during the first feeding phase. The DPF pigs consumed 7.3% less protein (P<0.01) but a similar amount of total P. For the whole growing period, the DPF pigs tended (P=0.08) to gain more weight (+2.4%) than the 3PF pigs, mainly because of faster growth (P=0.02) during the first feeding period. At the end of the experiment, total body protein mass was similar in the two treatment groups, but the DPF pigs had 8% more body lipids (P=0.04) than the 3PF pigs. Daily multiphase feeding reduced N excretion by 12% (P<0.01) but did not significantly reduce P excretion. In addition, feed costs, nutrient intake and nutrient excretion under the two feeding strategies were simulated and compared after different approaches were used to formulate complete feeds for each phase of the 3PF system, as well as the two feeds used in the DPF program. Simulated feed intake and growth was similar to those observed in the animal experiment. In comparison with the simulated 3PF system, the feed cost for the DPF pigs was reduced by 1.0%, the simulated N and P intakes were reduced by 7.3% and 4.4%, respectively, and the expected N and P excretions were reduced by 12.6% and 6.6%, respectively. The concomitant adjustment of the dietary concentration of nutrients to match the evaluated requirements of pig populations can be an efficient approach to significantly reduce feeding costs and N and P excretions in pig production systems.

The organogenesis of the digestive system was described in the Amazonian pimelodid catfish species Pseudoplatystoma punctifer from hatching (3.5 mm total length, TL) to 41 days post-fertilization (dpf) (58.1 mm TL) reared at 28°C. Newly hatched larvae showed a simple digestive tract, which appeared as a straight undifferentiated and unfolded tube lined by a single layer of columnar epithelial cells (future enterocytes). During the endogenous feeding period, comprised between 20 and 96 h post-fertilization (3.5 to 6.1 mm TL), the larval digestive system experienced a fast transformation with the almost complete development and differentiation of most of digestive organs (buccopahrynx, oesophagus, intestine, liver and exocrine pancreas). Yolk reserves were not completely depleted at the onset of exogenous feeding (4 dpf, 6.1 mm TL), and a period of mixed nutrition was observed up to 6 to 7 dpf (6.8 to 7.3 mm TL) when yolk was definitively exhausted. The stomach was the organ that latest achieved its complete differentiation, characterized by the development of abundant gastric glands in the fundic stomach between 10 and 15 dpf (10.9 to 15.8 mm TL) and the formation of the pyloric sphincter at the junction of the pyloric stomach and the anterior intestine at 15 dpf (15.8 mm TL). The above-mentioned morphological and histological features observed suggested the achievement of a digestive system characteristic of P. punctifer juveniles and adults. The ontogeny of the digestive system in P. punctifer followed the same general pattern as in most Siluriform species so far, although some species-specific differences in the timing of differentiation of several digestive structures were noted, which might be related to different reproductive guilds, egg and larval size or even different larval rearing practices. According to present findings on the histological development of the digestive system in P. punctifer, some recommendations regarding the rearing practices of this species are also provided in order to improve the actual larval rearing techniques of this fast-growing Neotropical catfish species.

Mixed crop–livestock (MC–L) farming has gained broad consensus as an economically and environmentally sustainable farming system. Working on a Charolais-area suckler cattle farms network, we subdivided the 66 farms of a constant sample, for 2 years (2010 and 2011), into four groups: (i) ‘specialized conventional livestock farms’ (100% grassland-based farms (GF), n=7); (ii) ‘integrated conventional crop–livestock farms’ (specialized farms that only market animal products but that grow cereal crops on-farm for animal feed, n=31); (iii) ‘mixed conventional crop–livestock farms’ (farms that sell beef and cereal crops to market, n=21); and (iv) organic farms (n=7). We analyse the differences in structure and in drivers of technical, economic and environmental performances. The figures for all the farms over 2 years (2010 and 2011) were pooled into a single sample for each group. The farms that sell crops alongside beef miss out on potential economies of scale. These farms are bigger than specialized beef farms (with or without on-farm feed crops) and all types of farms show comparable economic performances. The big MC–L farms make heavier and consequently less efficient use of inputs. This use of less efficient inputs also weakens their environmental performances. This subpopulation of suckler cattle farms appears unable to translate a MC–L strategy into economies of scope. Organic farms most efficiently exploit the diversity of herd feed resources, thus positioning organic agriculture as a prototype MC–L system meeting the core principles of agroecology.

The efficiency of milk production in pasture-based systems is heavily influenced by calving pattern, necessitating excellent reproductive performance in a short-breeding season. Where grazed pasture is the major component of the diet, cows are underfed relative to their intake potential. The cow responds by reducing milk output, but fertility is generally better than high intake confinement systems that achieve greater milk production per cow. A number of studies have identified body condition score (BCS) measurements that are related to likelihood of both submission and conception. Blood metabolites and metabolic hormones linked to fertility outcomes are now well characterized. In general, fertility variables have favourable associations with circulating concentrations of glucose, insulin and IGF-1 and unfavourable associations with non-esterified fatty acids, β-hydroxybutyrate and endogenous growth hormone. Nutritional strategies to impact these metabolic indicators have been utilized, but effects on herd fertility are inconsistent. Simply supplementing cows with additional energy in the form of standard concentrates does not appear to have a pronounced effect on fertility. Energy from additional concentrates fed during lactation is preferentially partitioned towards extra milk production rather than BCS repletion. The higher the genetic merit for milk production, the greater the partitioning of additional nutrients to the mammary gland. This review outlines the unique nutritional challenges of pasture-based systems, the role of specific metabolic hormones and metabolites in regulating reproductive function, and nutritional strategies to improve herd fertility.

Reducing the CP level of the diet allows for a reduction in N excretion without limiting performance as long as the amino acid (AA) requirements are covered. The availability of crystalline AA has permitted for a considerable reduction in the CP level of diets, practically used in pig nutrition. The adoption of low CP diets and the extent to which the CP content can be reduced further depends on the knowledge of the minimum levels of indispensable AA that maximize growth. The standardized ileal digestible (SID) Phe : Lys and Tyr : Lys requirements and the possibility to substitute Tyr by Phe have never been studied in piglets. The objectives of this study were to estimate these requirements in 10 to 20 kg pig as well as to determine the extent to which Phe can be used to cover the Tyr requirement. In three dose–response studies, six pigs within each of 14 blocks were assigned to six low CP diets (14.5% CP) sub-limiting in Lys at 1.00% SID. In experiment 1, the SID Phe : Lys requirement estimate was assessed by supplementing a Phe-deficient diet with different levels of l-Phe to attain 33%, 39%, 46%, 52%, 58%, and 65% SID Phe : Lys. Because Phe can be used for Tyr synthesis, the diets provided a sufficient Tyr supply. A similar approach was used in experiment 2 with six levels of l-Tyr supplementation to attain 21%, 27%, 33%, 39%, 45% and 52% SID Tyr : Lys. Phenylalanine was supplied at a level sufficient to sustain maximum growth (estimated in experiment 1). The SID Phe : Lys and SID Tyr : Lys requirements for maximizing daily gain were 54% and 40% using a curvilinear-plateau model, respectively. A 10% deficiency in Phe and Tyr reduced daily gain by 3.0% and 0.7%, respectively. In experiment 3, the effect of the equimolar substitution of dietary SID Tyr by Phe to obtain 50%, 57%, and 64% SID Phe : (Phe+Tyr) was studied at two limiting levels of Phe+Tyr. From 57% to 64% SID Phe : (Phe+Tyr), performance was slightly reduced. In conclusion, it is recommended not to use a Phe+Tyr requirement in the ideal AA profile but rather use a SID Phe : Lys of 54% and a SID Tyr : Lys of 40% to support maximal growth.

Paratuberculosis caused by Mycobacterium avium ssp. paratuberculosis (MAP) causes economic losses and is present in dairy herds worldwide. Different studies used different diagnostic tests to detect infection status and are the basis of genome-wide association (GWA) studies with inconsistent results. Therefore, the aim of this study was to identify and compare genomic regions associated with MAP susceptibility in the same cohort of cattle using different diagnostic tests. The GWA study was performed in German Holsteins within a case-control assay using 305 cows tested for MAP by fecal culture and additional with four different commercial ELISA-tests. Genotyping was performed with the Illumina Bovine SNP50 BeadChip. The results using fecal culture or ELISA test led to the identification of different genetic loci. Two single-nucleotide polymorphisms showed significant association with the ELISA-status. However, no significant association for MAP infection could be confirmed. Our results show that the definition of the MAP-phenotype has an important impact on the outcome of GWA studies for paratuberculosis.

TM-QTL is a quantitative trait locus (QTL) on ovine chromosome 18 (OAR18) known to affect loin muscling in Texel sheep. Previous work suggested that its mode of inheritance is consistent with paternal polar overdominance, but this has yet to be formally demonstrated. This study used purebred Texel sheep segregating for TM-QTL to confirm its presence in the chromosomal region in which it was first reported and to determine its pattern of inheritance. To do so, this study used the first available data from a Texel flock, which included homozygote TM-QTL carriers (TM/TM; n=34) in addition to homozygote non-carriers (+/+; n=40 and, heterozygote TM-QTL-carriers inheriting TM-QTL from their sire (TM/+; n=53) or their dam (+/TM; n=17). Phenotypes included a wide range of loin muscling, carcass composition and tissue distribution traits. The presence of a QTL affecting ultrasound muscle depth on OAR18 was confirmed with a paternal QTL effect ranging from +0.54 to +2.82 mm UMD (s.e. 0.37 to 0.57 mm) across the sires segregating for TM-QTL. Loin muscle width, depth and area, loin muscle volume and dissected M. longissimus lumborum weight were significantly greater for TM/+ than +/+ lambs (+2.9% to +7.9%; P<0.05). There was significant evidence that the effect of TM-QTL on the various loin muscling traits measured was paternally polar overdominant (P<0.05). In contrast, there was an additive effect of TM-QTL on both live weight at 20 weeks and carcass weight; TM/TM animals were significantly (P<0.05) heavier than +/+ (+11.1% and +7.3%, respectively) and +/TM animals (+11.9% and +11.7%, respectively), with TM/+ intermediate. Weights of the leg, saddle and shoulder region (corrected for carcass weight) were similar in the genotypic groups. There was a tendency for lambs inheriting TM-QTL from their sire to be less fat with slightly more muscle than non-carriers. For example, carcass muscle weight measured by live animal CT-scanning was 2.8% higher in TM/TM than +/+ lambs (P<0.05), carcass muscle weight measured by carcass CT-scanning was 1.36% higher in TM/+ than +/+ lambs (P<0.05), and weight of fat trimmed from the carcass cuts was significantly lower for TM/+ than +/+ lambs (−11.2%; P<0.05). No negative effects of TM-QTL on carcass traits were found. Optimal commercial use of TM-QTL within the sheep industry would require some consideration, due to the apparently different mode of action of the two main effects of TM-QTL (on growth and muscling).