It has been shown previously that lipid metabolism is regulated by fatty acids (FA) and that thyroid hormones are important regulators of energy metabolism. The effects of weight, dietary fat level and dietary FA profile on thyroid hormone levels and expression of lipogenic genes and tissue FA composition were studied. Sixty-one crossbred gilts weighing 62 ± 5.2 kg BW average were either slaughtered at the beginning of the trial (n = 5) or fed one of seven diets (n = 8 pigs per diet): a semi-synthetic diet formulated to contain a very low level of fat (NF) and six diets based on barley–soybean meal supplemented with approximately 10% fat of different origin and slaughtered at 100 kg BW. The supplemental fats were tallow, high-oleic sunflower oil, sunflower oil (SFO), linseed oil, fat blend (55% tallow, 35% sunflower oil, 10% linseed oil) and fish oil blend (40% fish oil, 60% linseed oil). In general, the dietary FA profiles altered the FA composition of liver, semimembranosus muscle and adipose tissues. Pigs fed the NF diet had the highest free and total triiodothyronine (T3) values followed by pigs fed SFO. Total T3 levels were higher in pigs at 60 kg than in pigs at 100 kg. Correlations between thyroid hormones and genes encoding enzymes of fat synthesis in adipose tissue (acetyl CoA carboxylase (ACACA), fatty acid synthase and stearoyl CoA desaturase (SCD)) and the large differences in expression of lipogenic genes at different weights (60 and 100 kg BW), suggest a role for thyroid hormones and for T3, in particular, in regulating whole animal fat metabolism, with effects brought about by altered expression of lipogenic genes. Liver sterol receptor element binding protein-1 (SREBP1) mRNA content was affected by dietary treatment (P < 0.001) and was correlated with ACACA and SCD, whereas adipose tissue SREBP1 was not correlated with the mRNA abundance of any lipogenic enzyme. Weight and tissue factors showed greater influence on mRNA abundance of genes related with lipid metabolism than diet and tissue FA composition. In the pig, FA synthesis appear to be of greater magnitude in adipose tissue than in the liver as suggested by the higher expression of lipogenic genes in adipose tissue.

This study examined the relationship of muscular and skeletal scores and ultrasound measurements in the live animal, and carcass conformation and fat scores with carcass composition and value using 336 steers, slaughtered at 2 years of age. Live animal scores and measurements were recorded at 8 to 12 months of age and pre-slaughter. Following slaughter, each carcass was classified for conformation and fatness and the right side dissected into meat, fat and bone. Carcass conformation scores and fat scores were both measured on a continuous 15-point scale and ranged from 2.0 to 12.0 and from 2.8 to 13.3, respectively. Pre-slaughter muscular scores showed positive correlations (P < 0.001) ranging from 0.31 to 0.86 with carcass meat proportion, proportion of high-value cuts in the carcass, conformation score and carcass value, significant negative correlations with carcass fat (r = −0.13) and bone (r = −0.81) proportions, and generally low non-significant relationships with the proportion of high-value cuts in meat and carcass fat score. Pre-slaughter ultrasound muscle depth and carcass conformation score showed similar correlations with carcass traits to those using the pre-slaughter muscular scoring procedure. Pre-slaughter ultrasound fat depth showed positive correlations (P < 0.001) with carcass fat proportion (r = 0.59) and fat score (r = 0.63), and significant negative correlations (−0.23 to −0.50) with carcass meat and bone proportions, high-value cuts in the carcass and in meat, and carcass value. Pre-slaughter skeletal scores generally showed poor correlations ranging from −0.38 to 0.52 with the various carcass traits. Corresponding correlations (−0.26 to 0.44) involving records collected at 8 to 12 months of age were lower than those using pre-slaughter records. A one-unit increase in carcass conformation score increased carcass meat proportion and value by 11.2 g/kg and 5.6 cents/kg, respectively. Corresponding values for fat score were −8.2 g/kg and −5.1 cents/kg. In conclusion, both pre-slaughter live animal scores/measurements and carcass classification scores, explained an appreciable amount of the total variation in carcass meat, fat and bone proportions and carcass value, and a moderate amount of the variation in proportion of high-value meat cuts in the carcass.

Increasing resistance to acute salmonellosis (defined as bacteraemia in animals showing symptoms) is not sufficient for food safety, because of the risk of carrier state (when animals excrete bacteria without showing any symptoms). Increased resistance to Salmonella carrier state is therefore needed. Two experiments of divergent selection on resistance at a younger and a later age lead to significant differences between lines and allowed estimating genetic parameters on 4262 animals. Heritability of resistance was estimated at 0·16 in chicks, while it varied from 0·14 to 0·23 with analysed organ in adult hens. Genetic correlations between contamination of the different organs ranged from 0·46 to 0·67, while correlations between resistance at both ages were estimated at −0·50, showing that increasing genetic resistance of hens will reduce resistance in chicks. Highest estimated absolute values of genetic correlations between resistance and production traits were, for chicken contamination level, with number of eggs laid between 41 and 60 (0·37) and, for adult contamination, with number of eggs laid between 18 and 24 (0·37) or 25 and 40 (−0·33) weeks of age.

We present an approach to describe and evaluate changes in genetic diversity and to calculate bounds for improvement. This pedigree-based analysis was applied to the Kromfohrländer dog (FCI Gr9 Sec10). Pedigrees trace back to the foundation of the breed and were available for 5527 individuals. Based on this dataset the population structure and historical bottlenecks were studied. Distributions of allele frequencies were estimated by Monte Carlo simulation. To monitor changes in mating systems throughout the breeding history, the homozygosity of alleles was compared with their expectations in Hardy–Weinberg equilibrium. Different breeding lines were identified by hierarchical cluster analysis and were characterized by ancestor contributions. Our calculations showed that the founder event in 1945 was followed by two bottlenecks. One was caused by strong selection in a very small population, and the other was triggered by rigorous disease management. The necessary amount of purging that arised due to the bottlenecks was also discussed.

In mapping of quantitative trait loci (QTLs), performing hypothesis tests of linkage to a phenotype of interest across an entire genome involves multiple comparisons. Furthermore, linkage among loci induces correlation among tests. Under many multiple comparison frameworks, these problems are exacerbated when mapping multiple QTLs. Traditionally, significance thresholds have been subjectively set to control the probability of detecting at least one false positive outcome, although such thresholds are known to result in excessively low power to detect true positive outcomes. Recently, false discovery rate (FDR)-controlling procedures have been developed that yield more power both by relaxing the stringency of the significance threshold and by retaining more power for a given significance threshold. However, these procedures have been shown to perform poorly for mapping QTLs, principally because they ignore recombination fractions between markers. Here, I describe a procedure that accounts for recombination fractions and extends FDR control to include simultaneous control of the false non-discovery rate, i.e. the overall error rate is controlled. This procedure is developed in the Bayesian framework using a direct posterior probability approach. Data-driven significance thresholds are determined by minimizing the expected loss. The procedure is equivalent to jointly maximizing positive and negative predictive values. In the context of mapping QTLs for experimental crosses, the procedure is applicable to mapping main effects, gene–gene interactions and gene–environment interactions.

Correlation statistics can be used to measure the amount of linkage disequilibrium (LD) between two loci in subdivided populations. Within populations, the square of the correlation of gene frequencies, r2, is a convenient measure of LD. Between populations, the statistic rirj, for populations i and j, measures the relatedness of LD. Recurrence relationships for these two parameters are derived for the island model of population subdivision, under the assumptions of the linked identity-by-descent (LIBD) model in which correlation measures are equated to probability measures. The recurrence relationships closely predict the build-up of r2 and rirj following population subdivision in computer simulations. The LIBD model predicts that a steady state will be reached with r2 equal to 1/[1+4Nec(1+(k−1)ρ)], where k is the number of island populations, Ne is the effective local population (island) size, and ρ measures the ratio of migration (m) to recombination (c) and is equal to m/[c(k−1)+m]. For low values of m/c, ρ=0, and E(r2) is equal to 1/(1+4Nec). For high values of m/c, ρ=1, and E(r2) is equal to 1/(1+4kNec). The value of rirj following separation eventually settles down to a steady state whose expectation, E(rirj), is equal to E(r2) multiplied by ρ. Equations predicting the change in rirj values are applied to the separation of African (Yoruba – YRI) and non-African (European – CEU) populations, using data from Hapmap. The primary data lead to an estimate of separation time of less than 1000 generations if there has been no migration, which is around one-third of minimum current estimates. Ancient rather than recent migration can explain the form of the data.

Fine scale analyses of signatures of selection allow assessing quantitative aspects of a species' evolutionary genetic history, such as the strength of selection on genes. When several selected loci lie in the same genomic region, their epistatic interactions may also be investigated. Here, we study how the neutral polymorphism pattern was shaped by two close recombining loci that cause ‘sex-ratio’ meiotic drive in Drosophila simulans, as an example of strong selection with potentially strong epistasis. We compare the polymorphism data observed in a natural population with the results of forward stochastic simulations under several contexts of epistasis between the candidate loci for the drive. We compute the likelihood of different possible scenarios, in order to determine which configuration is most consistent with the data. Our results highlight that fine scale analyses of well-chosen candidate genomic regions provide information-rich data that can be used to investigate the genotype–phenotype–fitness map, which can hardly be studied in genome-wide analyses. We also emphasize that initial conditions and time of observation (here, time after the interruption of a partial selective sweep) are crucial parameters in the interpretation of real data, while these are often overlooked in theoretical studies.

In self-pollinating populations, individuals are characterized by a high degree of inbreeding. Additionally, phenotypic observations are highly influenced by genotype-by-environment interaction effects. Usually, Bayesian approaches to predict breeding values (in self-pollinating crops) omit genotype-by-environment interactions in the statistical model, which may result in biased estimates. In our study, a Bayesian Gibbs sampling algorithm was developed that is adapted to the high degree of inbreeding in self-pollinated crops and accounts for interaction effects between genotype and environment. As related lines are supposed to show similar genotype-by-environment interaction effects, an extended genetic relationship matrix is included in the Bayesian model. Additionally, since the coefficient matrix C in the mixed model equations can be characterized by rank deficiencies, the pseudoinverse of C was calculated by using the nullspace, which resulted in a faster computation time. In this study, field data of spring barley lines and data of a ‘virtual’ parental population of self-pollinating crops, generated by computer simulation, were used. For comparison, additional breeding values were predicted by a frequentist approach. In general, standard Bayesian Gibbs sampling and a frequentist approach resulted in similar estimates if heritability of the regarded trait was high. For low heritable traits, the modified Bayesian model, accounting for relatedness between lines in genotype-by-environment interaction, was superior to the standard model.

The limitations of the alkane technique in estimating the diet components of herbivores call for the introduction of new diet composition markers. Recently, long-chain alcohols (alcohols) and long-chain fatty acids (acids) have received the most attention and show great potential, when combined with alkanes, to estimate composition of complex diets. In the current study, faecal recoveries of alcohols and acids were determined in sheep in four different live weight groups fed three herbage species, either Leymus chinensis, L. dasystachys or Elymus sibiricum. Analysis of variance (ANOVA) was used to examine the effects of herbage species and live weight of sheep on faecal recoveries of individual alcohols and acids. Further, an indoor experiment with six sheep fed a diet of equal proportions, on dry matter (DM) basis, of three herbages was performed, allowing to assess the accuracy of alcohols and/or acids in combination with alkanes, to estimate diet composition. A one-sample t-test was carried out to test the accuracy of these estimates. Results of the first experiment indicated that the faecal recoveries of alcohols and acids were significantly affected by herbage species (P < 0.05). While the effects were significant or near significant for the faecal recoveries of some alcohols (C24-ol, C30-ol and C26-ol) (P ⩽ 0.05), no effect of live weight on faecal recoveries of acids was observed (P > 0.05). Therefore, adjustments based on diet-specific faecal recoveries might improve diet composition estimates. This was illustrated by the results of the second experiment. The diet composition estimated from alcohols or all combinations of alcohols with other marker types, after diet-specific correction of faecal recoveries, did not significantly differ from the actual composition (P > 0.05). However, using acids as additional markers resulted in poorer diet composition estimates. This study confirmed the utility of alcohols, combined with alkanes, as markers to estimate composition of complex diets. Although corrections based on mean faecal recoveries, average over animals and diets, resulted in some accuracy loss, results were still satisfactory and better than without recovery correction.

The experiment measured lamb responses to supplementation of the pregnant ewe diet with vitamin E above requirement. Crossbred ewes were mated with either Suffolk or Texel rams. Twin-bearing ewes were randomly allocated (approximately 21 months of age at allocation) to one of four treatment groups (20 ewes per group, 10 mated with Suffolk and 10 with Texel rams). Treatments imposed were 50, 100, 150 or 250 IU supplementary vitamin E per ewe per day to give a four treatment by two sire-type factorial experimental design. Ewes were fed concentrates to meet energy requirements for stage of pregnancy and hay ad libitum. Diets were introduced approximately 6 weeks before lambing. Blood samples were obtained prior to introduction of diets, 17 days after introduction of diets and within 24 h of lambing from a subset of eight ewes per treatment (32 total). Colostrum samples were obtained from 10 ewes per treatment, 12 h after birth of the first lamb. All births were observed and a lamb vigour score was assigned to each lamb 5 min after birth. At 1 and 12 h after birth, rectal temperature, and at 12 h after birth, sex, crown-rump length and BW of each lamb were recorded. Mean ewe plasma α-tocopherol concentration prior to introduction of the diets was 1.5 μg/ml (s.e.m. 0.09) and did not differ between groups. There were positive linear (P < 0.001) effects of dietary vitamin E on plasma (17 days after introduction of diets) and colostrum (12 h after birth) α-tocopherol concentrations. Lamb vigour scores were superior (P < 0.001) for lambs sired by Texel rather than Suffolk rams but there were no differences as a result of vitamin E supplementation. Lamb mortality was low and unrelated to either sire or supplementary vitamin E. Lamb birth and weaning weights were also unaffected by vitamin E supplementation. Supplementing the ewe with vitamin E therefore had no effect on any lamb measurements.

Evaluation of lifetime productivity is sensible to target interventions for improving productivity of smallholder dairy systems in the highlands of East Africa, because cows are normally not disposed of based on productive reasons. Feeding strategies and involuntary culling may have long-term effects on productive (and therefore economic) performance of dairy systems. Because of the temporal scale needed to evaluate lifetime productivity, experimentation with feedstuffs in single lactations is not enough to assess improvements in productivity. A dynamic modelling approach was used to explore the effect of feeding strategies on the lifetime productivity of dairy cattle. We used LIVSIM (LIVestock SIMulator), an individual-based, dynamic model in which performance depends on genetic potential of the breed and feeding. We tested the model for the highlands of Central Kenya, and simulated individual animals throughout their lifetime using scenarios with different diets based on common feedstuffs used in these systems (Napier grass, maize stover and dairy concentrates), with and without imposing random mortality on different age classes. The simulations showed that it is possible to maximise lifetime productivity by supplementing concentrates to meet the nutrient requirements of cattle during lactation, and during early development to reduce age at first calving and extend productive life. Avoiding undernutrition during the dry period by supplementing the diet with 0.5 kg of concentrates per day helped to increase productivity and productive life, but in practice farmers may not perceive the immediate economic benefits because the results of this practice are manifested through a cumulative, long-term effect. Survival analyses indicated that unsupplemented diets prolong calving intervals and therefore, reduce lifetime productivity. The simulations with imposed random mortality showed a reduction of 43% to 65% in all productivity indicators. Milk production may be increased on average by 1400 kg per lactation by supplementing the diet with 5 kg of concentrates during early lactation and 1 kg during late lactation, although the optimal supplementation may change according to milk and concentrate prices. Reducing involuntary culling must be included as a key goal when designing interventions to improve productivity and sustainability of smallholder dairy systems, because increasing lifetime productivity may have a larger impact on smallholders’ income than interventions targeted to only improving daily milk yields through feeding strategies.

Contractile and metabolic properties of bovine muscles play an important role in meat sensorial quality, particularly tenderness. Earlier studies based on Myosin heavy chain isoforms analyses and measurements of glycolytic and oxidative enzyme activities have demonstrated that the third trimester of foetal life in bovine is characterized by contractile and metabolic differentiation. In order to complete this data and to obtain a precise view of this phase and its regulation, we performed a proteomic analysis of Semitendinosus muscle from Charolais foetuses analysed at three stages of the third trimester of gestation (180, 210 and 260 days). The results complete the knowledge of important changes in the profiles of proteins from metabolic and contractile pathways. They provide new insights about proteins such as Aldehyde dehydrogenase family, Enolase, Dihydrolipoyl dehydrogenase, Troponin T or Myosin light chains isoforms. These data have agronomical applications not only for the management of beef sensorial quality but also in medical context, as bovine myogenesis appears very similar to human one.

Angora goats are known to be vulnerable to cold stress, especially after shearing, but their thermoregulatory responses to shearing have not been measured. We recorded activity, and abdominal and subcutaneous temperatures, for 10 days pre-shearing and post-shearing, in 10 Angora goats inhabiting the succulent thicket of the Eastern Cape, South Africa, in both March (late summer) and September (late winter). Within each season, environmental conditions were similar pre-shearing and post-shearing, but September was an average 5°C colder than March. Shearing resulted in a decreased mean (P < 0.0001), minimum (P < 0.0001) and maximum daily abdominal temperature (P < 0.0001). Paradoxically, the decrease in daily mean (P = 0.03) and maximum (P = 0.01) abdominal temperatures, from pre-shearing to post-shearing, was greater in March than in September. Daily amplitude of body temperature rhythm (P < 0.0001) and the maximum rate of abdominal temperature rise (P < 0.0001) increased from pre-shearing to post-shearing, resulting in an earlier diurnal peak in abdominal temperature (P = 0.001) post-shearing. These changes in amplitude, rate of abdominal temperature rise and time of diurnal peak in abdominal temperature suggest that the goats’ thermoregulatory system was more labile after shearing. Mean daily subcutaneous temperatures also decreased post-shearing (P < 0.0001), despite our index goat selecting more stable microclimates after shearing in March (P = 0.03). Following shearing, there was an increased difference between abdominal and subcutaneous temperatures (P < 0.0001) at night, suggesting that the goats used peripheral vasoconstriction to limit heat loss. In addition to these temperature changes, mean daily activity increased nearly two-fold after March shearing, but not September shearing. This increased activity after March shearing was likely the result of an increased foraging time, food intake and metabolic rate, as suggested by the increased water influx (P = 0.0008). Thus, Angora goats entered a heat conservation mode after shearing in both March and September. That the transition from the fleeced to the shorn state had greater thermoregulatory consequences in March than in September may provide a mechanistic explanation for Angora goats’ vulnerability to cold in summer.

Pasture-based Holstein–Friesian cows from three genetic groups differing in the Irish ‘Economic Breeding Index’ (EBI) value and genetic background, namely North-American (NA) national average EBI genetic merit (LOW-NA, n = 42), North-American high EBI genetic merit (HIGH-NA, n = 42) and New Zealand (NZ) high EBI genetic merit (HIGH-NZ, n = 42), were studied. These genetic groups have been selected in different environments: pasture for NZ and confinement for NA. The objective was to determine the effect of genetic group on haematological and acute phase proteins profiles (white blood cell (WBC) counts, red blood cell (RBC) counts, acute phase proteins: serum amyloid A (SAA) and haptoglobin), health (rectal temperature (RT), clinical mastitis (CM) and somatic cell score), calving performance (stillbirth, calving assistance) and post-partum reproductive parameters (endometritis and ovarian cyclicity). Blood sampling and data recording took place 3 weeks pre-calving up to 7 weeks post-calving. Linear mixed models, logistic regression and generalised estimating equations were used for data analysis. HIGH-NZ animals had the highest (P < 0.05) RBC mean corpuscular volume (50.0 fl), exhibited a different WBC distribution pattern (P < 0.05) and had the lowest (P < 0.05) mean RT (38.4°C) for the first 10 days post-calving. These findings suggest enhanced reticulocyte turnover, peripartum response mechanisms and thermoregulation in the HIGH-NZ compared to the other two genetic groups. LOW-NA animals had the highest SAA peak throughout the peripartum period (55.12 mg/l, P < 0.05) and a tendency for higher somatic cell scores (P < 0.10) in early lactation. The HIGH-NA animals had the lowest incidence of udder quarter milk sample bacteria at calving, suggesting better udder health when commencing lactation. No differences were detected between genetic groups in calving performance, post-partum reproductive parameters or CM in the first 42 days post-calving. These results suggest that while inherited peripartum adaptation strategies have been developed by the different genetic groups selected in different environments (pasture = NZ v. confinement = NA), such differences have minimal impact on peripartum clinical health.

Enterotoxigenic Escherichia coli (ETEC) is a major cause of diarrhoea in neonatal and postweaning pigs. F41 is one of ETEC fimbriae that adhere to the small intestinal epithelium and lead to development of diarrhoea. The genetic architecture of susceptibility to ETEC F41 remains elusive in pigs. In this study, we determined the in vitro adhesion phenotypes of ETEC F41 in a total of 835 F2 animals from a White Duroc × Erhualian intercross, and performed a genome scan using both F2 and half-sib analyses with 183 microsatellite markers to detect quantitative trait loci (QTL) for porcine susceptibility to ETEC F41. The two analyses consistently revealed a 1% genome-wide significant QTL on pig chromosome 4. Moreover, we determined F41 adhesion phenotypes in 14 purebred Erhualian and 14 White Duroc pigs. The results showed that both the founder breeds are segregating for the F41 adhesion phenotype, while less percentage of Erhualian pigs were adhesive to ETEC F41 compared to White Duroc pigs.

Selenium (Se), an essential micronutrient, is believed to enhance neutrophil functions. This study aimed to compare the effects of supplemented organic (Sel-Plex®) and inorganic (sodium selenite) Se on neutrophil functions in high-producing dairy cows, during the periparturient period. Twenty-five Holstein cows were randomly allocated to five dietary treatments as follows: control diet (basal diet without Se supplementation), IN 0.3 (basal diet supplemented with inorganic Se at 0.3 mg/kg dry matter (DM)), IN 0.5 (inorganic Se at 0.5 mg/kg DM), OR 0.3 (organic Se at 0.3 mg/kg DM) and OR 0.5 (organic Se at 0.5 mg/kg DM). Some evaluated parameters included neutrophil functions and plasma Se concentrations in cows and plasma Se concentrations in calves. Neutrophil phagocytosis did not significantly differ among the five groups. However, organic Se supplementation significantly increased (P < 0.01) the respiratory burst of neutrophils when compared to cows fed IN 0.3 and the control diet. In comparison to inorganic Se, neutrophil apoptosis was decreased (P < 0.01) when cows were fed organic Se or the control diets. These effects of organic Se on respiratory burst activities and apoptosis of neutrophils were in a dose-dependent manner. Calf plasma Se concentrations were higher (P < 0.05) when cows were fed OR 0.5 and IN 0.5.