This study was conducted to investigate the effects of incorporation into pig diets of 20% of different co-products from the biofuel industries, which are rich in fibre, on animal growth performance, on nitrogen (N) and carbon (C) excretions, and on the subsequent ammonia volatilisation and methane production during the storage of slurry. Five experimental diets mainly based on wheat and soyabean meal were formulated: two control diets, a control high-protein (CHP) diet with 17.5% of crude protein (CP) and a control low-protein (CLP) diet with 14.0% of CP and three experimental diets with 20% of (i) dried distiller’s grain with solubles (DDGS), (ii) sugar beet pulp (SBP) or (iii) fatty rapeseed meal (FRM). The animals used (20 castrated males) were housed individually in metabolism cages and fed one of the five diets (i.e. four pigs per diet). Urine and faeces were collected separately from each pig in order to measure nutrient digestibility and the excretory patterns of N and C. For each diet, ammonia volatilisation was measured from samples of slurry subsequently produced, over a 16-day storage period in a laboratory pilot scale system. The ultimate methane potential (B0, expressed in litres CH4/kg organic matter (OM)) was measured from the same slurry, for each diet, in anaerobic storage conditions over 100 days. The addition of sources of fibres to the diet decreased (P < 0.05) the animal growth performance by 13% and increased (P < 0.05) the amount of faeces excreted by 100%, whereas the amount of urine was not affected. For the high-fibre diets, there was a shift of N partitioning from urine to faeces, resulting in a much higher faecal N excretion (10 v. 5 g N/pig per day). Concurrently, the fibre enrichment in diets significantly increased (P < 0.05) the C content of the faeces by 68%. Ammonia emission from slurry was significantly reduced (P < 0.05) by 19% to 33% for the high-fibre diets, compared to the CHP diet. Ammonia emission was also reduced (P < 0.05) by 33% for the CLP compared to the CHP diet. B0 values ranged from 428 to 484 l CH4/kg OM. When these are expressed per pig and per day, the B0 from slurry was, on average, 70 l for the two control diets, and 121, 91 and 130 l for the slurry originating from the DDGS, SBP and FRM diets, respectively.

Wheat grain (WG) is unique in possessing extensive starch and nitrogen fermentation (i.e. >85% in ground and steam-processed WG), low cation–anion difference and high-intake properties, making it a potentially useful prepartal dietary choice. The objective was to determine the effects of WG provision to pre-partum first-calf heifers on metabolic, health and productive criteria during the transition period. WG replaced barley grain that was commonly used earlier. Fifteen Holstein heifers at 31 ± 6 days pre partum were blocked based on expected calving date and assigned to three treatments or feeding totally mixed rations containing either (i) barley grain (13.8%) and wheat bran (6.1%), (ii) 10% WG (WG10) or (iii) 18% WG (WG18; dry matter (DM) basis) from 31 days pre partum until calving. In replacing WG for barley grains, some changes in WG use and slight changes in soybean and cottonseed meals use were made to properly formulate balanced rations for net energy for lactation, CP, calcium and P. Prepartal diets contained no supplemental anionic salts. Cows were monitored until 21-day post partum and received the same early lactation diet. The prepartal provision of WG and related dietary changes reduced urine pH at 7-day pre partum, and elevated blood calcium and glucose at 7-day pre partum and at 3-day post partum. Milk fat and protein yields were increased during the 21 days post partum by prepartal WG provision and related diet changes. Blood albumin, globulins, total proteins and urea concentrations were similar among treatments. Feeding diets with WG did not affect body condition score, calving difficulty, calf weight, placenta weight and the time interval from calving to placenta expulsion. It is suggested that prepartal provision of WG with necessary dietary changes led to simultaneous improvements in energy and calcium status of the heifers experiencing their first periparturient phase without compromising parturition status.

Intensive livestock grazing can largely deplete the natural fodder resources in semi-arid, subtropical highlands and together with the low nutritional quality of the pasture vegetation limit the growth and production of grazing animals. To evaluate the contribution of homestead feeding of grazing goats to rangeland conservation and animal nutrition, two researcher-managed on-farm trials were conducted in a mountain oasis of Northern Oman. Goats’ feed intake on pasture in response to four rations containing different levels of locally available green fodder and concentrate feeds was determined in six male goats each (35 ± 10.2 kg body weight (BW)). Total feed intake was estimated using titanium dioxide as external fecal marker as well as the diet organic matter (OM) digestibility derived from fecal crude protein concentration. The nutritional quality of selected fodder plants on pasture was analyzed to determine the animals’ nutrient and energy intake during grazing. The pasture vegetation accounted for 0.46 to 0.65 of the goats’ total OM intake (87 to 107 g/kg0.75 BW), underlining the importance of this fodder resource for the husbandry system. However, metabolizable energy (7.2 MJ/kg OM) and phosphorus concentrations (1.4 g/kg OM) in the consumed pasture plants were low. Homestead feeding of nutrient and energy-rich by-products of the national fishery and date palm cultivation to grazing goats increased their daily OM intake (R2 = 0.36; P = 0.005) and covered their requirements for growth and production. While the OM intake on pasture was highest in animals fed a concentrate-based diet (P = 0.003), the daily intake of 21 g OM/kg0.75 BW of cultivated green fodder reduced the animals’ feed intake on pasture (R2 = 0.44; P = 0.001). Adjusting homestead supplementation with locally available feedstuffs to the requirements of individual goats and to the nutritional quality of the pasture vegetation improves animal performance and eases the grazing pressure exerted on the natural vegetation. This management strategy therefore appears to be a valuable alternative to intensive livestock feeding in zero-grazing systems and may contribute to sustainable livestock production in ecologically fragile, semi-arid mountain regions.

Despite their major contribution to the energy supply of ruminants, the production of volatile fatty acids (VFA) in the rumen is still poorly predicted by rumen models. We have developed an empirical approach, based on the interpretation of large bibliographic databases gathering published in vivo measurements of ruminal VFA production rate (PR), rates of duodenal and faecal digestion and molar percentages of VFA in the rumen. These databases, covering a wide range of intake levels and dietary composition, were studied by meta-analysis using within-experiment models. We established models to quantify response laws of total VFA-PR and individual VFA molar percentages in the rumen to variations in intake level and dietary composition. The rumen fermentable organic matter (RfOM) intake, estimated from detailed knowledge of the chemical composition of diets according to INRA Feed Tables, appears as an accurate explanatory variable of measured total VFA-PR, with an average increment of 8.03 ± 0.64 mol total VFA/kg RfOM intake. Similar results were obtained when total VFA-PR was estimated from measured apparent RfOM (total VFA-PR/RfOM averaging 8.3 ± 1.2 mol/kg). The VFA molar percentages were related to dry matter intake and measured digestible organic matter (OM), digestible NDF and rumen starch digestibility, with root mean square error of 1.23, 1.45, 0.88 and 0.41 mol/100 mol total VFA for acetate, propionate, butyrate and minor VFA, respectively, with no effect of pH on the residuals. Stoichiometry coefficients were calculated from the slopes of the relationships between individual VFA production (estimated from measured apparent RfOM and individual VFA molar percentages) and measured fermented fractions. Coefficients averaged, respectively, 66, 17, 14 and 3 mol/100 mol for NDF; 41, 44, 12 and 4 mol/100 mol for starch; and 46, 35, 13 and 6 mol/100 mol for crude protein. Their use to predict VFA molar percentages appear relevant for most dietary conditions, that is, when the digested NDF/digested OM ratio exceeded 0.12. This study provides a quantitative review on VFA yield in the rumen. It contributes to the development of feed evaluation systems based on nutrient fluxes.

The effects of continuing spatial restraint were examined in domestic pigs. For this purpose, the animals (German Landrace barrows) were housed individually in metabolic cages (12 animals) and, as controls, in single pens (six animals). In six replications with two experimental animals and one control animal, we collected saliva each morning (0730 h) for the cortisol analysis, recorded the behaviour and the heart beat for 3 h/day (0800 to 0900 h, 1100 to 1200 h, 1400 to 1500 h). Each replication consisted of 5 days of habituation to single housing and 8 experimental days during which the experimental animals lived continuously in the metabolic cages. Weight gain, cortisol, heart rate and heart rate variability were not significantly affected by experimental narrow confinement that only had a significant influence on the behaviours, locomotion and sitting. In conclusion, the experimental animals adapted very fast and did not show physiological indications of chronic stress. However, the absence of apparent stress does not exclude other, subtler, welfare impairments.

The delivery of certain living microorganisms in food has long been suggested as having positive health effects in humans. This practice has extended into food animal production, with a variety of microorganisms being used; lactic acid bacteria, various Bacillus species and the yeast Saccharomyces cerevisiae have been particularly used in the pig industry. The increased interest in probiotics is essentially due to the problem of microbial resistance to antibiotics and following the ban of the use of antibiotics in animal production, probiotics being considered an alternative means to reduce pathogen infection and improve animal health especially around the time of weaning. However, there is still a need to clarify the probiotic effectiveness in pigs, and the underlying mechanisms. When assessing the efficacy of probiotics one must consider the particular strain of organism being used and the production stage of the pigs being treated. The reproducible delivery of probiotics in industrial pig production is problematic as maintenance of viability is key to their beneficial activity, but difficult to achieve with commonly used feed processing technologies. One specific context where probiotics organisms may be reliably delivered is in systems utilising fermented liquid feeds. Liquid feed may be fermented by the activity of wild lactic acid bacteria or may be stimulated using specific isolates as ‘starters’; the latter system has advantages in terms of reproducibility and speed of fermentation. The farm context in which the organism is used is likely to be critical; the use of probiotics is more likely to result in measurable economic gains in animals living in sub-optimal conditions rather than in those reared in the highest welfare and husbandry conditions. The establishment of a beneficial lactic acid bacteria population at birth may lead to healthier animals, this may be most effectively achieved by treating sows, which provide an amplification step and flood the neonatal pigs’ environment with desirable bacterial strains. In contrast, it may be sufficient to provide a supportive, protective microbiota around the time of weaning as this is a time of major crisis with instability and loss of certain bacterial populations.

Historical information can be used, in addition to pedigree, traits and genotypes, to map quantitative trait locus (QTL) in general populations via maximum likelihood estimation of variance components. This analysis is known as linkage disequilibrium (LD) and linkage mapping, because it exploits both linkage in families and LD at the population level. The search for QTL in the wild population of Soay sheep on St. Kilda is a proof of principle. We analysed the data from a previous study and confirmed some of the QTLs reported. The most striking result was the confirmation of a QTL affecting birth weight that had been reported using association tests but not when using linkage-based analyses.

Food shortage is a stress factor that commonly affects organisms in nature. Resistance to food shortage or starvation resistance (SR) is a complex quantitative trait with direct implications on fitness. However, surveys of natural genetic variation in SR at different geographic scales are scarce. Here, we have measured variation in SR in sets of lines derived from nine natural populations of Drosophila melanogaster collected in western Argentina. Our study shows that within population variation explained a larger proportion of overall phenotypic variance (80%) than among populations (7·2%). We also noticed that an important fraction of variation was sex-specific. Overall females were more resistant to starvation than males; however, the magnitude of the sexual dimorphism (SD) in SR varied among lines and explained a significant fraction of phenotypic variance in all populations. Estimates of cross-sex genetic correlations suggest that the genetic architecture of SR is only partially shared between sexes in the populations examined, thus, facilitating further evolution of the SD.

Analysis of the temporal variation in allele frequencies is useful for studying microevolutionary processes. However, many statistical methods routinely used to test temporal changes in allele frequencies fail to establish a proper hypothesis or have theoretical or practical limitations. Here, a Bayesian statistical test is proposed in which the distribution of the distances among sampling frequencies is approached with computer simulations, and hypergeometric sampling is considered instead of binomial sampling. To validate the test and compare its performance with other tests, agent-based model simulations were run for a variety of scenarios, and two real molecular databases were analysed. The results showed that the simulation test (ST) maintained the significance value used (α=0·05) for a vast combination of parameter values, whereas other tests were sensitive to the effect of genetic drift or binomial sampling. The differences between binomial and hypergeometric sampling were more complex than expected, and a novel effect was described. This study suggests that the ST is especially useful for studies with small populations and many alleles, as in microsatellite or sequencing molecular data.

TP5, a P element inserted in the telomere-associated sequences of the X chromosome, represses the excision of other P elements in the germ line through a combination of maternal and zygotic effects. The maternal component of this repression is impaired by heterozygous mutations in the aubergine and Suppressor of variegation 205 genes; one mutation in the piwi gene also appears to impair repression. In the female germ line, the level of TP5 mRNA is increased by these impairing mutations. The impairing aubergine and piwi mutations also increase the level of germ-line mRNA from CP, a transgene that encodes the P-element transposase; however, the Suppressor of variegation 205 mutation does not. These findings are discussed in terms of a model of P-element regulation that involves post-transcriptional and chromatin re-organizing events mediated by maternally transmitted small RNAs derived from the telomeric P element.

Prediction of genetic values is a central problem in quantitative genetics. Over many decades, such predictions have been successfully accomplished using information on phenotypic records and family structure usually represented with a pedigree. Dense molecular markers are now available in the genome of humans, plants and animals, and this information can be used to enhance the prediction of genetic values. However, the incorporation of dense molecular marker data into models poses many statistical and computational challenges, such as how models can cope with the genetic complexity of multi-factorial traits and with the curse of dimensionality that arises when the number of markers exceeds the number of data points. Reproducing kernel Hilbert spaces regressions can be used to address some of these challenges. The methodology allows regressions on almost any type of prediction sets (covariates, graphs, strings, images, etc.) and has important computational advantages relative to many parametric approaches. Moreover, some parametric models appear as special cases. This article provides an overview of the methodology, a discussion of the problem of kernel choice with a focus on genetic applications, algorithms for kernel selection and an assessment of the proposed methods using a collection of 599 wheat lines evaluated for grain yield in four mega environments.

Hu & Xu (2008) developed a statistical method for computing the statistical power for detecting a quantitative trait locus (QTL) located in a marker interval. Their method is based on the regression interval mapping method and allows experimenters to effectively investigate the power for detecting a QTL in a population. This paper continues to work on the power analysis of separating multiple-linked QTLs. We propose simple formulae to calculate the power of separating closely linked QTLs located in marker intervals. The proposed formulae are simple functions of information numbers, variance inflation factors and genetic parameters of a statistical model in a population. Both regression and maximum likelihood interval mappings suitable for detecting QTL in the marker intervals are considered. In addition, the issue of separating linked QTLs in the progeny populations from an F2 subject to further self and/or random mating is also touched upon. One of the primary keys to our approach is to derive the genotypic distributions of three and four loci for evaluating the correlation structures between pairwise unobservable QTLs in the model across populations. The proposed formulae allow us to predict the power of separation when several factors, such as sample sizes, sizes and directions of QTL effects, distances between QTLs, interval sizes and relative QTL positions in the intervals, are considered together at a time in different experimental populations. Numerical justifications and Monte Carlo simulations were provided for confirmation and illustration.