The influence of dietary protein supply on the nutritional penalty associated with the acquisition phase of the immune response to gastrointestinal nematodes in lambs was investigated. Groups of lambs were offered either a low-protein diet (L; 62 g metabolizable protein (MP)/kg dry matter (DM)) or high-protein diet (H; 95 g MP/kg DM) while being either infected with the equivalent of 2.000 L3 Trichostrongylus colubriformis/day (IF), similarly infected and concurrently immuno-suppressed with methylprednisolone acetate (ISIF), immuno-suppressed only (IS) or kept as uninfected controls (C). Body composition of all animals was measured on days −8 and 76 of infection using X-ray computed tomography. Temporal changes in serum phosphate and serum albumin concentrations, which provided an indicator of pathological damage, in addition to patterns of total daily nematode egg excretion and comparative worm burdens at slaughter indicated that a protective immune response was developed in H-IF, but not L-IF, H-ISIF or L-ISIF groups. Compared to their respective non-infected controls, the gross efficiency of use of metabolizable energy (ME) for net energy (NE) deposition in the carcass was reduced by 0.23 in H-IF (P < 0.05), 0.13 in H-ISIF (P > 0.05), 0.49 in L-IF (P < 0.01) and 0.23 in L-ISIF (P > 0.05). It is concluded that the reduction in ME utilization and reduced performance, which can be attributed to the immunological response, are lessened in animals offered a high-protein diet. Furthermore, evidence is presented to indicate a possible association between T. colubriformis L3 IgA antibody production and loss of performance in lambs infected with this nematode.

Test-day records for average flow rate (AFR) from the routine dairy recording from Bavarian Fleckvieh cows were analysed. Two data sets with observations on approximately 20 000 cows each were sampled from the total data set. For the estimation of variance parameters, a two-step approach was applied. In a first step multiple-trait restricted maximum likelihood (REML) analyses were carried out. For each of the first three lactations, six time periods with up to 33 days were defined. An algorithm for iterative summing of expanded part matrices was applied in order to combine the estimates. In a second step covariance functions (CF) for additive-genetic variances and non-genetic animal variances were derived using second-order Legendre polynomials plus an exponential term. Estimates of test-day heritability for AFR ranged from 0.21 to 0.40, and were largest in lactation 1. For lactations 1 and 3, heritabilities decreased considerably towards the end of lactation. Genetic correlation estimates within lactation decreased as the distance between days in milk (DIM) increased. Genetic correlations between corresponding DIM in the three lactations were generally large, ranging from 0.80 to 0.99. The largest estimates were found between DIM from lactations 2 and 3. Results from this study suggest that including AFR data from second and third lactations in genetic evaluation systems could the improve accuracy of genetic selection.

The present study was aimed to compare the developmental changes of carcass composition, meat quality characteristics and organ weight in pigs of different breeds. Six pigs (sex balance) of each breed were slaughtered at 35, 80 and 125 days of age, respectively. The carcass was chilled and the left carcass side was dissected into bone, lean meat, fat and skin; additionally, organ weight and meat quality parameters were observed. Carcasses of the Jinhua pig were lighter (P < 0.001), contained less lean meat percentage (P < 0.01) and more carcass fat percentage (P < 0.05) than did carcasses of the Landrace. L*-values were lower in Jinhua pigs than in Landrace at 125 days of age (P < 0.05), but the Jinhua pig had higher a*-values compared with Landrace at the age of 80 days (P < 0.01) and 125 days (P < 0.01), respectively. In addition, Jinhua pigs showed lower colour scores (P < 0.05), higher intramuscular fat (IMF) percentage (P < 0.05), less marbling scores (P < 0.05) and lower drip loss (P < 0.05) than Landrace. For organ weight, Jinhua pigs had higher relative heart weight at the age of 80 days (P < 0.05) and 125 days (P < 0.001), and higher relative liver weight at 125 days of age (P < 0.01) than that of Landrace. In addition, the relative kidney weight was heavier (P < 0.001) in the Jinhua pig than in the Landrace during the whole experiment. These results indicated that developmental changes of carcass composition, meat quality parameters and organ weight displayed breed differences. Jinhua pigs were fatter than Landrace but the former had better quality characteristics in the meat.

This paper reviews the evidence for host genetic variation in resistance to infectious diseases for a wide variety of diseases of economic importance in poultry, cattle, pig, sheep and Atlantic salmon. Further, it develops a method of ranking each disease in terms of its overall impact, and combines this ranking with published evidence for host genetic variation and information on the current state of genomic tools in each host species. The outcome is an overall ranking of the amenability of each disease to genomic studies that dissect host genetic variation in resistance. Six disease-based assessment criteria were defined: industry concern, economic impact, public concern, threat to food safety or zoonotic potential, impact on animal welfare and threat to international trade barriers. For each category, a subjective score was assigned to each disease according to the relative strength of evidence, impact, concern or threat posed by that particular disease, and the scores were summed across categories. Evidence for host genetic variation in resistance was determined from available published data, including breed comparison, heritability studies, quantitative trait loci (QTL) studies, evidence of candidate genes with significant effects, data on pathogen sequence and on host gene expression analyses. In total, 16 poultry diseases, 13 cattle diseases, nine pig diseases, 11 sheep diseases and three Atlantic salmon diseases were assessed. The top-ranking diseases or pathogens, i.e. those most amenable to studies dissecting host genetic variation, were Salmonella in poultry, bovine mastitis, Marek’s disease and coccidiosis, both in poultry. The top-ranking diseases or pathogens in pigs, sheep and Atlantic salmon were Escherichia coli, mastitis and infectious pancreatic necrosis, respectively. These rankings summarise the current state of knowledge for each disease and broadly, although not entirely, reflect current international research efforts. They will alter as more information becomes available and as genome tools become more sophisticated for each species. It is suggested that this approach could be used to rank diseases from other perspectives as well, e.g. in terms of disease control strategies.

A feeding trial involving four Thoroughbred race horses was undertaken to establish whether inclusion of grape seed extract (GSE) in the diet of horses undergoing mild exercise had any effects on their general health, intake and digestion. Supplementation with GSE had no effect on either feed or water intake of the horses and the supplement was readily palatable to the horses at all levels of inclusion. Feeding GSE caused no adverse effects in terms of animal health (temperature, pulse and respirations rates), and there were some positive effects related to a presumed alteration in fermentation in the hindgut. Feeding GSE increased faecal pH, changing from acid faeces (pH 6.6) when no GSE was fed to neutral faeces (pH 7.0) when 150 mg GSE/kg body weight (BW) was fed. In addition, blood glucose concentrations were significantly (P < 0.05) decreased when GSE was fed at 100 and 150 mg/kg BW (5.50 ± 0.26 and 5.32 ± 0.72 mmol/l, respectively) compared with the control diet (5.77 ± 0.31 mmol/l). The actual mechanisms causing these alterations are yet to be elucidated, but could have important implications for the prevention of acidosis.

A trial was conducted to study the effect of sire line (Duroc (DU) and Pietrain (PI)) on carcass, meat and fat quality of pigs reared outdoor and destined to dry-cured meat production. No differences between sire genotypes were detected in carcass fat thickness (P > 0.10) but carcasses from DU-sired pigs were longer (P < 0.05) and tended to have a higher yield of trimmed shoulders (P = 0.07) and hams (P = 0.06) than carcasses from PI-sired pigs. Loins from DU-sired genotype showed higher (P < 0.05) L* value and lower (P < 0.01) a* value than loins from PI-sired genotype. Pork from DU-sired offspring tended to have higher (P = 0.09) intramuscular fat (IMF) percentage and lower (P < 0.05) moisture proportion than meat from PI-sired offspring. Also, loins from DU-sired pigs had lower (P < 0.001) thawing losses than loins from PI-sired pigs. The subcutaneous fat from the DU-sired line tended to show lower (P = 0.08) percentage of total polyunsaturated fatty acids (PUFAs) than that from the PI-sire line, mostly due to the higher proportion of C18:2 (P = 0.09) and C20:3 (P < 0.01). However, no effect of crossbreed was detected on the total proportion of saturated, monounsaturated fatty acid (MUFAs) or PUFAs of IMF (P > 0.10). We conclude that both sire lines can be used successfully under outdoor conditions but DU boars are more adequate than PI boars for the production of heavy pigs intended for the dry-cured meat industry.

The nutrient transportation ability of placenta depends on placental size, vascular density and permeability. Regulation of angiogenesis in the placenta is critical for successful gestation. Placenta vascularity exhibits disparity in different gestation stages and different pig breeds. To investigate the expression of genes related to permeability in the porcine placenta of different gestation stages and breeds, molecular cloning and gene expression analysis of six porcine genes, vascular endothelial growth factor (VEGF), VEGF-R1, VEGF-R2, endothelial nitric oxide synthase (eNOS), vascular endothelial cadherin (CDH5) and β-arrestin2 (Arrb2), were performed in this study. The results demonstrated that from gestation day 33 to day 90, Landrace exhibited significant increase (P < 0.05) in placental VEGF and Arrb2 mRNA expression. Moreover, expression levels of VEGF, VEGF-R1, VEGF-R2 and eNOS mRNA were higher (P < 0.01) in the placenta of Erhualian than those in Landrace on day 90 of gestation. In contrast, CDH5 placental mRNA expression level exhibited significant decrease (P < 0.05) from day 33 to day 90 gestation in Landrace. Erhualian placental CDH5 and Arrb2 expression levels were significantly lower (P < 0.01) than those in Landrace conceptuses on day 90 of gestation. Our study offered new data on the expression of genes in VEGF signal transduction pathway in porcine placenta.

Lysine is usually taken up in excess by the mammary gland (MG) relative to milk protein output, allowing for mammary synthesis of non-essential (NE) amino acids (AA) from Lys-N. It is unclear whether this NEAA synthesis from Lys is obligate or whether more efficient use of Lys can be made under limiting conditions. Six multi-catheterized dairy cows received a basal diet low in protein plus an abomasal infusion of AA (560 g/day) with or without Lys (50.3 g/day), in a crossover design with 7-day periods. On day 7, all cows received a 7.5-h jugular infusion of [2-15N]lysine. Six blood samples were collected from arterial, portal, hepatic and mammary vessels at 45 min intervals. In addition, cows were milked at 6 and 7 h with the milk casein plus arterial and mammary plasma collected at 7 h analyzed for AA enrichment. Milk protein concentration and casein yield tended (P < 0.10) to decrease with Lys deletion, while Lys secretion in milk protein was lowered (P < 0.05). The addition of Lys in the AA mixture increased the net portal absorption of Lys by the amount infused, suggesting limited oxidation of this extra supply by the gut. Net liver flux of Lys was unaltered by treatment and, therefore, net splanchnic release of Lys reflected closely the amounts absorbed. For both treatments, however, post-liver supply was greater than mammary uptake, which exceeded milk output. Nonetheless, while Lys deletion decreased mammary uptake by 10.1 mmol/h, Lys in milk protein secretion was reduced by only 3.9 mmol/h. On a net basis, there was no evidence of the additional uptake of any other measured AA during the Lys deletion. The mammary uptake to output ratio of Lys decreased from 1.37 to 1.12, but still showed an excess with Lys deletion. The total amount of 15N in milk protein did not change with treatment but the distribution into AA was altered. In conditions that simulated normal feeding (Lys infused), 83% of the 15N was present as Lys, with Glx, Asx, Ser and Ala harvesting, respectively, 6.8%, 2.4%, 2.1% and 1.0%. With Lys depletion, N-transfers from Lys to other AA within the MG were still present, but rates were considerably lower. This would suggest that part, at least, of Lys catabolism in the MG is either needed or cannot be prevented completely, even at low supply of Lys. Such catabolism will provide N to support the synthesis of NEAA.

Two experiments were carried out to investigate the effect of pelleting on the apparent total tract digestibility (ATTD) of energy and nutrients according to the dietary fibre (DF) level in growing pigs (experiment 1) and in adult sows (experiment 2). Four diets based on wheat, barley, maize and soybean meal and supplemented with increased contents of a mixture of wheat bran, maize bran, soybean hulls and sugar beet pulp (116, 192, 268 and 344 g NDF/kg dry matter (DM) in diets 1 to 4) were tested. In experiment 1, 32 growing pigs (62 kg average BW), in two replicates and according to a factorial design, were fed one of the four diets, either as mash or as pellets. The digestibility of energy, organic matter (OM) and all nutrients decreased with DF increasing for both feed forms; the reduction was about 1% for each 1% NDF increase in the diet (P < 0.001). Pelleting improved moderately the digestibility of energy and OM (+1.5% and +1.0%, respectively; P < 0.05) in connection with greater DF (+5%; P < 0.05) and fat digestibility (+25%). Thus, pelleting improved the digestible energy content of diets on average by 0.3 MJ/kg of feed DM (P < 0.01). In experiment 2, four adult dry sows (235 kg average BW) were used in a 4 × 4 Latin square design and fed the four diets used in experiment 1 as pellets. The digestibility of energy, OM and macronutrients also decreased with DF increase (P < 0.001; −0.4% per 1% increase of dietary NDF for energy) while the digestibility of DF (i.e. crude fibre (CF) or ADF) increased (P < 0.001) or remained at a high level. In conclusion, increasing DF in diets decreases the digestibility of nutrients and energy in pigs and in sows. Although positive, the pelleting impact is minor on the energy and nutrients digestibility of fibre-rich diets in growing pigs, even in high-DF diets.

The National Scrapie Plan (NSP) was launched in Great Britain in 2001, with the aim of eventually eradicating scrapie, a small ruminant transmissible spongiform encephalopathy, from the national sheep flock. Specifically, a selective breeding programme, the Ram Genotyping Scheme, was devised enabling pedigree ram breeders to reduce the number of scrapie-susceptible genotypes from their flocks. The effect of large-scale manipulation of PrP genotypes on commercially important traits within the sheep industry is, however, unknown. We have therefore examined production traits in a total of 43 968 lambs from 32 pedigree breeders across three British hill breeds, comprising 8163 North Country Cheviot (Hill), 21 366 Scottish Blackface and 14 439 Welsh Mountain lambs. Traits examined included: weights at birth, 8 and 20 weeks; ultrasonic fat and muscle depth, and average daily weight gain from 8 to 20 weeks. Linear mixed models were fitted for each trait, including animal (direct) genetic effects and up to three maternal effects. Potential associations with the PrP gene were assessed by fitting either PrP genotype or number of copies of individual alleles as fixed effects. A number of breed-specific significant associations between production traits and the PrP gene were found, but no consistent significant effects were detected across the three breeds. Breed-specific effects were as follows: (i) 0.37 kg higher birth weights (BWTs) in AHQ homozygous North Country Cheviot (Hill) lambs (P < 0.01); (ii) 0.16 kg higher BWTs in ARR homozygous Scottish Blackface lambs (P < 0.05); (iii) 0.5 kg higher 8-week weights in VRQ heterozygous Scottish Blackface lambs (P < 0.01); (iv) a 0.72 kg decrease in scan weight associated with homozygous ARR Welsh Mountain lambs (P < 0.01); (v) 0.51 mm higher ultrasonic muscle depths in AHQ homozygous Welsh Mountain lambs (P < 0.01); (vi) 0.48 mm lower ultrasonic muscle depths in Welsh Mountain lambs carrying one or more copies of the ARR allele (P < 0.05) and (vii) 0.2 mm higher ultrasonic fat depths in heterozygous VRQ Welsh Mountain lambs (P < 0.05). The use of a Bonferroni correction to define appropriate significance thresholds across the three datasets, which account for the large number of independent comparisons made, resulted in breed-specific comparisons, with P < 0.01 becoming significant at P∼0.05, and the remaining breed-specific comparisons no longer being significant. The absence of a common effect across the three breeds suggests that any true association found may be due to breed-specific alleles of neighbouring genes in linkage disequilibrium with the PrP locus.

Molecular cloning, tissue distribution and ontogenetic regulation of sodium/proton exchanger isoform 2 (NHE-2) mRNA expression were evaluated in the pig small intestine during postnatal development. The 2872-bp porcine full cDNA sequence of the NHE-2 (EF672046) cloned in this study showed 80% and 70% homology with known human and mouse gene sequence, respectively. Hydrophobic prediction suggests 13 putative membrane-spanning domains within porcine NHE-2. The porcine NHE-2 mRNA was detected in the brain, liver, kidney, heart, lung, small intestine and muscle. The small intestine had the highest NHE-2 mRNA abundance and the brain, lung and liver had the lowest NHE-2 mRNA abundance (P < 0.05). Along the longitudinal axis, the duodenum had the highest NHE-2 mRNA abundance and the ileum and colon had the lowest NHE-2 mRNA abundance (P < 0.05). The NHE-2 mRNA level was increased from day 1 to day 26 in the duodenum (P < 0.05) and dropped dramatically on day 30 (P < 0.05). There is no difference between day 1 and day 7 (P > 0.05). After day 30, the NHE-2 mRNA level remained the same except on day 90 (P > 0.05). The mRNA expression of NHE-2 was not only differentially regulated by age but also differentially distributed along the small intestine of piglets at early stages and growing stages of life, which may contribute to changes in NHE activity.

A competing risk approach was used to evaluate the influence of several factors on culling risk for 587 Duroc sows. Three different analyses were performed according to whether sow failure was due to death during productive life (DE) or to one of two causes for voluntary culling: low productivity (LP) and low fertility (LF). Sow survival was analyzed by the Cox model. Year at first farrowing (batch effect) significantly affected sow survival in all three analyses (P < 0.05 for DE and P < 0.001 for LP and LF) whereas farm of origin accounted for relevant variation in the LP and LF analyses. LP culling increased with backfat thickness of more than 19 mm at the end of the growth period (P < 0.05), bad teat condition (P < 0.05) and reduced piglets born alive (P < 0.001). For the LF competing risk analysis, culling increased with age at first farrowing (P < 0.1). Special emphasis was placed on the influence of leg and teat conformation on sow survivability, although they did not affect sow failure due to DE (P > 0.1). The overall leg-conformation score significantly influenced sow longevity in LP (P < 0.001) and LF competing risk analyses (P < 0.001), showing a higher hazard ratio (HR) for poorly conformed sows (1.013 and 4.366, respectively) than for well-conformed sows (0.342 and 0.246, respectively). Survival decreased with the presence of abnormal hoof growth in LP and LF analyses (HR = 3.372 and 6.002, respectively; P < 0.001) and bumps or injuries to legs (HR = 4.172 and 5.839, respectively; P < 0.01). Plantigradism reduced sow survival in the LP analysis (P < 0.05), while sickle-hooked leg (P < 0.05) impaired sow survival in the fertility-specific analysis. Estimates of heritability for longevity related to LP culling ranged from 0.008 to 0.024 depending on the estimation procedure, whereas heritability values increased to between 0.017 and 0.083 in LF analysis. These analyses highlighted substantial discrepancies in the sources of variation and genetic background of sow longevity depending on the cause of failure. The estimated heritabilities suggested that direct genetic improvement for sow longevity seemed feasible, although only a small genetic progress was expected.

Three different stages of pig antral follicles have been studied in a granulosa-cell transcriptome analysis on nylon microarrays (1152 clones). The data have been generated from seven RNA follicle pools and several technical replicates were made. The objective of this paper was to state the feasibility of a transcriptomic protocol for the study of folliculogenesis in the pig. A statistical analysis was chosen, relying on the linear mixed model (LMM) paradigm. Low variability within technical replicates was hence checked with a LMM. Relevant genes that might be involved in the studied process were then selected. For the most significant genes, statistical methods such as principal component analysis and unsupervised hierarchical clustering were applied to assess their relevance, and a random forest analysis proved their predictive value. The selection of genes was consistent with previous studies and also allowed the identification of new genes whose role in pig folliculogenesis will be further investigated.

Susceptibility to scrapie is known to be associated with polymorphisms at the prion protein (PrP) gene, and this association is the basis of current selective programmes implemented to control scrapie in many countries. However, these programmes might have unintended consequences for other traits that might be associated with PrP genotype. The objective of this study was to investigate the relationship between PrP genotype and coat colour characteristics in two UK native sheep breeds valued for their distinctive coat colour patterns. Coat colour pattern, darkness and spotting and PrP genotype records were available for 11 674 Badgerfaced Welsh Mountain and 2338 Shetland sheep. The data were analysed with a log–linear model using maximum likelihood. Results showed a strong significant association of PrP genotype with coat colour pattern in Badgerfaced Welsh Mountain and Shetland sheep and with the presence of white spotting in Shetland sheep. Animals with the ARR/ARR genotype (the most scrapie resistant) had higher odds of having a light dorsum and a dark abdomen than the reverse pattern. The implication of these associations is that selection to increase resistance to scrapie based only on PrP genotype could result in change in morphological diversity and affect other associated traits such as fitness.

A linkage–linkage disequilibrium map that describes the pattern and extent of linkage dis-equilibrium (LD) decay with genomic distance has now emerged as a viable tool to unravel the genetic structure of population differentiation and fine-map genes for complex traits. The prerequisite for constructing such a map is the simultaneous estimation of the linkage and LD between different loci. Here, we develop a computational algorithm for simultaneously estimating the recombination fraction and LD in a natural outcrossing population with multilocus marker data, which are often estimated separately in most molecular genetic studies. The algorithm is founded on a commonly used progeny test with open-pollinated offspring sampled from a natural population. The information about LD is reflected in the co-segregation of alleles at different loci among parents in the population. Open mating of parents will reveal the genetic linkage of alleles during meiosis. The algorithm was constructed within the polynomial-based mixture framework and implemented with the Expectation–Maximization (EM) algorithm. The by-product of the derivation of this algorithm is the estimation of outcrossing rate, a parameter useful to explore the genetic diversity of the population. We performed computer simulation to investigate the influences of different sampling strategies and different values of parameters on parameter estimation. By providing a number of testable hypotheses about population genetic parameters, this algorithmic model will open a broad gateway to understand the genetic structure and dynamics of an outcrossing population under natural selection.

We compute an accurate approximation to the probability of fixation for a beneficial mutation in a population fluctuating with a stationary distribution of population size. The population dynamics are described by the theta-logistic model with environmental variance, assuming that the population size is large enough to ignore demographic variance. We show that stochastic fluctuations of population size reduce the probability of fixation. However, it is not the magnitude of the population fluctuations per se that creates this reduction. Only the environmental variance has a substantial effect on the probability of fixation. The strength of density dependence (or expected return time to equilibrium) and the functional form of density-regulation, given by the parameter θ in the theta-logistic model, have little effect on the fixation probability. Effective population size based on harmonic mean population size will therefore underestimate the expected fixation rate of beneficial mutations in fluctuating populations.