The aim of the study was to analyse the influence on tail-biting in undocked pigs during the rearing period of crude fibre in piglets' rations. All pigs were fed the same pre-starter until weaning. The study comprised two trials with four experimental groups each. The first trial contained: a control group (CG1) with conventional feed (up to 40 g/kg crude fibre), two groups with an increased crude fibre content of up to 50 g/kg (G5) and 60 g/kg (G6), respectively, and one group with conventional feed and crude fibre provision ad libitum (AL). The second trial consisted of a control group (CG2) which received the same conventional feed as CG1 and three treatment groups with either soya hulls (SS), dried sugar beet pulp (DP) or oat fibre (OF) admixed to their ration, to achieve a crude fibre content of 60 g/kg in all three groups. The rearing week, the batch, the treatment group (only in trial one) and the interaction between batch and treatment group had a significant influence on tail-lesions (P < 0.05). The tail-biting process started in rearing week 3 (trial one) and 5 (trial two), respectively. Due to the low frequency of tail-biting during the present study, crude fibre seems to have no major influence on tail-biting during the rearing period. This unexpected result may be caused by the optimized conditions in which the piglets were kept and the intensive animal observation carried out by the employees. However, the batch effect was most influential.

Antimicrobial use in pig farming is influenced by a range of risk factors, including herd characteristics, biosecurity level, farm performance, occurrence of clinical signs and vaccination scheme, as well as farmers’ attitudes and habits towards antimicrobial use. So far, the effect of these risk factors has been explored separately. Using an innovative method called multiblock partial least-squares regression, this study aimed to investigate, in a sample of 207 farrow-to-finish farms from Belgium, France, Germany and Sweden, the relative importance of the six above mentioned categories or ‘blocks’ of risk factors for antimicrobial use in pig production. Four country separate models were developed; they showed that all six blocks provided useful contribution to explaining antimicrobial use in at least one country. The occurrence of clinical signs, especially of respiratory and nervous diseases in fatteners, was one of the largest contributing blocks in all four countries, whereas the effect of the other blocks differed between countries. In terms of risk management, it suggests that a holistic and country-specific mitigation strategy is likely to be more effective. However, further research is needed to validate our findings in larger and more representative samples, as well as in other countries.

The housing and management of laying hens and their productivity has gone through enormous developments in the last century. Housing has changed from free-range systems, via battery cages to a variety of loose housing and different types of battery cages, and back to outdoor access systems. Although battery cages are still the main system used worldwide, the number of hens housed in aviaries and free-range systems has increased in Europe, Australasia and some parts of the USA, but aviaries and free-range systems are still considered a niche sector compared to caged housing. The following paper reviews how breeding and selection have responded to changes in housing and management and whether different types of housing require different breeding programmes and, more specifically, whether a dedicated breeding programme should be developed for aviary and free-range systems.

From the available literature it was concluded that broadening the selection goal in existing lines is the best option for breeding programmes to provide genotypes that are suitable for a range of housing systems.

Newcastle disease (ND) is one of the most important poultry diseases worldwide and can lead to annual losses of up to 80% of backyard chickens in Africa. All bird species are considered susceptible to ND virus (NDV) infection but little is known about the role that wild birds play in the epidemiology of the virus. We present a long-term monitoring of 9000 wild birds in four African countries. Overall, 3·06% of the birds were PCR-positive for NDV infection, with prevalence ranging from 0% to 10% depending on the season, the site and the species considered. Our study shows that ND is circulating continuously and homogeneously in a large range of wild bird species. Several genotypes of NDV circulate concurrently in different species and are phylogenetically closely related to strains circulating in local domestic poultry, suggesting that wild birds may play several roles in the epidemiology of different NDV strains in Africa. We recommend that any strategic plan aiming at controlling ND in Africa should take into account the potential role of the local wild bird community in the transmission of the disease.

Genome-wide association analysis on monozygotic twin-pairs offers a route to discovery of gene–environment interactions through testing for variability loci associated with sensitivity to individual environment/lifestyle. We present a genome-wide scan of loci associated with intra-pair differences in serum lipid and apolipoprotein levels. We report data for 1,720 monozygotic female twin-pairs from GenomEUtwin project with 2.5 million SNPs, imputed or genotyped, and measured serum lipid fractions for both twins. We found one locus associated with intra-pair differences in high-density lipoprotein cholesterol, rs2483058 in an intron of SRGAP2, where twins carrying the C allele are more sensitive to environmental factors (P = 3.98 × 10−8). We followed up the association in further genotyped monozygotic twins (N = 1,261), which showed a moderate association for the variant (P = 0.200, same direction of an effect). In addition, we report a new association on the level of apolipoprotein A-II (P = 4.03 × 10−8).

High density single nucleotide polymorphism (SNP) genotyping panels provide an alternative to microsatellite markers for genome scans. However, genotype errors have a major impact on power to detect linkage or association and are difficult to detect for SNPs. We estimated error rates with the Affymetrix GeneChip® SNP platform in samples from a family with a mixed set of monozygotic (MZ) and dizygotic (DZ) triplets using lymphocyte, buccal DNA and samples from whole genome amplification using the multiple displacement amplification (MDA) technique. The average call rate from 58,960 SNPs for five genomic samples was 99.48%. Comparison of results for the MZ twins showed only three discordant genotypes (concordance rate 99.995%). The mean concordance rate for comparisons of samples from lymphocyte and buccal DNA was 99.97%. Mendelian inconsistencies were identified in 46 SNPs with errors in one or more family members, a rate of 0.022%. Observed genotype concordance rates between parents, between parents and children, and among siblings were consistent with previously reported allele frequencies and Hardy–Weinberg equilibrium. Using the MDA technique, results for two samples had equivalent high accuracy to results with genomic samples. However, the SNP call rate for the remaining seven samples varied from 72.5% to 99.5%, with an average of 86.11%. Quality of the DNA sample following the MDA reaction appears to be the critical factor in SNP call rate for MDA samples. Our results demonstrate highly accurate and reproducible genotyping for the Affymetrix GeneChip® Human Mapping Set in lymphocyte and buccal DNA samples.

People meeting diagnostic criteria for anxiety or depressive disorders tend to score high on the personality scale of neuroticism. Studying this dimension of personality can therefore give insights into the etiology of important psychiatric disorders. Neuroticism can be assessed easily via self-report questionnaires in large population samples. We have examined the genetic and phenotypic stability of neuroticism, measured up to 4 times over 22 years, on different scales, on a data set of 4999 families with over 20,000 individuals completing at least 1 neuroticism questionnaire. The neuroticism scales used were the Eysenck Personality Questionnaire revised (EPQ-R), the EPQ-R shortened form, and the NEO 5 factor inventory personality questionnaire. The estimates of heritability of the individual measures ranged from .26 ± .04 to .36 ± .03. Genetic, environmental, and phenotypic correlations averaged .91, .42, and .57 respectively. Despite the range in heritabilities, a more parsimonious ‘repeatability model’ of equal additive genetic variances and genetic correlations of unity could not be rejected. Use of multiple measures increases the effective heritability from .33 for a single measure to .43 for mean score because of the reduction in the estimate of the environmental variance, and this will increase power in genetic linkage or association studies of neuroticism.

Dense marker genotypes allow the construction of the realized relationship matrix between individuals, with elements the realized proportion of the genome that is identical by descent (IBD) between pairs of individuals. In this paper, we demonstrate that by replacing the average relationship matrix derived from pedigree with the realized relationship matrix in best linear unbiased prediction (BLUP) of breeding values, the accuracy of the breeding values can be substantially increased, especially for individuals with no phenotype of their own. We further demonstrate that this method of predicting breeding values is exactly equivalent to the genomic selection methodology where the effects of quantitative trait loci (QTLs) contributing to variation in the trait are assumed to be normally distributed. The accuracy of breeding values predicted using the realized relationship matrix in the BLUP equations can be deterministically predicted for known family relationships, for example half sibs. The deterministic method uses the effective number of independently segregating loci controlling the phenotype that depends on the type of family relationship and the length of the genome. The accuracy of predicted breeding values depends on this number of effective loci, the family relationship and the number of phenotypic records. The deterministic prediction demonstrates that the accuracy of breeding values can approach unity if enough relatives are genotyped and phenotyped. For example, when 1000 full sibs per family were genotyped and phenotyped, and the heritability of the trait was 0·5, the reliability of predicted genomic breeding values (GEBVs) for individuals in the same full sib family without phenotypes was 0·82. These results were verified by simulation. A deterministic prediction was also derived for random mating populations, where the effective population size is the key parameter determining the effective number of independently segregating loci. If the effective population size is large, a very large number of individuals must be genotyped and phenotyped in order to accurately predict breeding values for unphenotyped individuals from the same population. If the heritability of the trait is 0·3, and Ne=1000, approximately 5750 individuals with genotypes and phenotypes are required in order to predict GEBVs of un-phenotyped individuals in the same population with an accuracy of 0·7.

We report on the status of the R&D for a digital Time Projection Chamber based on Micromegas detectors using the CMOS chip TimePix as a direct readout anode protected by highly resistive a-Si:H layer. A small chamber was built as a demonstrator of the 2-D and 3-D imaging capabilities of this technique. We illustrate the new capabilities of this detector for x-ray observation with data taken from radioactive sources. This small TPC is a very useful tool both for studying gas properties thanks to its good efficiency for single electrons, and for reconstructing photoelectron direction for use as a soft x-ray polarimeter.

Cost-effective prevention strategies to prevent weight gain and the development of obesity should be based on appropriate knowledge of the determinants of weight gain. The body of evidence on the dietary determinants of weight gain is, however, fragmentary at best, partly because inappropriate research methods are used to study the determinants of obesity under normal circumstances. Evidence from studies using experimental diets have shortcomings because of their short duration and selection of highly-motivated subjects and because the outcomes can be easily influenced by the choice of foods to be used in the intervention. Of the observational studies, many have severe methodological shortcomings, e.g. ecological studies, cross-sectional surveys and classical cohort studies in which the baseline diet is linked to subsequent weight development over long periods of time. Longitudinal studies with repeated measurements in which changes in diet and physical activity are linked to changes in weight are probably the most informative, but these studies are relatively rare. There is a great interest in interventions that are effective and efficient for the prevention of obesity. Many countries and research funding agencies seem to show a strong tendency to develop interventions for children and adolescents exclusively. It can be easily shown, however, that intervention programmes are much more likely to be cost-effective in older adults than in children, which indicates that adults should not be neglected as target populations for obesity prevention. Obesity prevention should follow a life-course approach, as currently recommended for non-communicable diseases in general by the WHO.

Many species exhibit skewed sex ratios at birth. Here we investigate the relationships between environmental and maternal variables (as surrogates for maternal condition) and foetal sex in African buffalo Syncerus caffer and elephant Loxodonta africana of the Kruger National Park, South Africa. Using logistic regression no significant effect was found of year, maternal lactational status, maternal age, rainfall or density on foetal sex ratio. Using a subset of our data, it was also concluded that maternal body condition did not affect foetal sex ratio in buffalo. Our analyses failed to support hypotheses predicting that mothers will skew the sex ratios of their offspring in relation to their body condition. In this study, buffalo and elephant produced offspring with a sex ratio close to parity. Our results are discussed in light of the implications for testing such hypotheses in analyses of population level.

A common study design to map quantitative trait loci (QTL) is to compare the phenotypes and marker genotypes of two or more siblings in a sample of unrelated sib groups, and to test for linkage between chromosome location and quantitative trait values. The simplest case is sib pairs only, in particular dizygotic twin pairs, and a simple and elegant regression method was proposed by Haseman & Elston in 1972 to test for linkage. Since then, several other methods have been proposed to test for linkage. In this study, we derived the statistical power of linear regression and maximum likelihood methods to map QTL from sib pair data analytically, and determined which methods are superior under which set of population parameters. In particular, we considered four regression-based and three maximum likelihood-based approaches, and derived asymptotic approximations of the mean test statistic and statistical power for each method. It was found, both analytically and by computer simulation, that the revisited or new Haseman–Elston method (based upon the mean-corrected crossproduct of the observations on sib-pairs) is less powerful than a full maximum likelihood approach and is also inferior to the Haseman–Elston method under a realistic range of values for the population parameters. We found that a simple regression method, based upon both the squared difference and the mean-corrected squared sum of the observations on sib-pairs, is as powerful as a full maximum likelihood approach. Our derivations of statistical power for regression and maximum likelihood methods provide a simple way to compare alternative methods and obviate the need to perform elaborate computer simulations. DZ twin pairs are likely to be more powerful for linkage analysis than ordinary siblings because they may share more common environmental effects, thereby increasing the proportion of within-family variance that is explained by a QTL.

Possible correlated or pleiotropic effects on food intake, growth rate and carcass traits (meat quality and carcass composition traits) were investigated for the prolificacy related Booroola gene (FecB). This gene was introgressed in a Texel sheep population by systematic backcrossing with sires carrying the Booroola gene. In a 3-year experiment 273 spring-born male lambs were offered concentrates ad libitum, after weaning. Lamb carrier effects and dam carrier effects for the FecB gene were estimated, accounting for year, backcross generation, slaughter weight, weaning age, concentrate type, rearing code, age of the dam and litter size as fixed effects. Carriers of the FecB had a higher dressing percentage (+1·15%), longissimus muscle depth (+0·26 mm to +0·7 5mm) and cross-sectional area (+0·98 cm2). However the gene also had a positive effect on subcutaneous fatness (+0·12 points), KKCF (+30 g) and a substantial positive lamb carrier effect on carcass fat tissue content (+3·09%), which reflects a relative increase in fatness of 11·9%. The FecB gene had also very small, significant effects on some meat colour traits. The dam carrier effects of the Booroola gene were negatively associated with food efficiency and with longissimus muscle depth (–1·38 to –2·25 mm). The increased fatness of lambs could imply that for optimal use of FecB, non-carrier terminal sires should be used on heterozygous dams.

A study was conducted to find early predictors of the Booroola gene in several generations of a crossbred sheep population. Merino carriers of the Booroola gene were mated with Texel sheep to improve prolificacy of the latter. Ovulation rate at 8 months of age, litter size at 1 and 2 years of age and FSH and inhibin levels at 3, 4, 5 and 6 weeks of age were determined in about 700 females.

Gibbs sampling was applied for inference in a mixed inheritance model. Estimates for the gene effect in heterozygous females were +1·5 corpora lutea and +1·3 lambs at 2 years of age. The gene effect on litter size at 1 year was small. The only significant major gene effect for hormone levels found was for lnINH4 (–0·66).

A number of hormone levels and combinations of hormone levels appeared to be useful predictors of carrier status of individual animals. In comparison with a situation where only parents' genotype is known, posterior probabilities for non-carriers were on average increased from 50 to over 95% when FSH levels were used. However, the combined posterior probabilities of carriers and non-carriers increased only up to 67%. So in general, classification with Gibbs sampling resulted in too few animals being identified as carrier. The sum of FSH levels at 3, 4, 5 and 6 weeks of age is proposed as a predictor of presence of the Booroola gene in an animal. Multivariate analysis of mixed inheritance models could help to find more effective combinations.

A statistical analysis strategy for the detection of quantitative trait loci (QTLs) in half-sib populations is outlined. The initial exploratory analysis is a multiple regression of the trait score on a subset of markers to allow a rapid identification of possible chromosomal regions of interest. This is followed by multiple marker interval mapping with regression methods within and across families fitting one or two QTLs. Empirical thresholds are determined by experiment-wise permutation tests for different significance levels and empirical confidence intervals for the QTLs' positions are obtained by bootstrapping methods. For traits with evidence for a significant single-QTL effect, an approximate maximum likelihood analysis is performed to obtain estimates of QTL effect and the probability of the QTL genotype for each parent of a group of half-sibs. The strategy is demonstrated in an analysis of previously published data on chromosome 6 and five production traits from a granddaughter design in dairy cattle. The results confirm and extend evidence for QTLs affecting protein percentage. Informativeness of markers limited the possibility of mapping more than one QTL on the same linkage group.

Customized sire selection indices were developed for Australian dairy bulls in order to promote more objective use of estimated breeding values in commercial breeding programmes. It was assumed that the breeding goal for commercial dairy farmers is the profitability of a bull's progeny. Seven characteristics of the progeny were identified as having a major impact on profitability and were included in the breeding objective: milk, fat and protein yield, survival, body weight, milking speed and temperament. Traits in the selection indices used to predict profit were milk, fat and protein yield, survival, milking speed, temperament, size, overall type and fore teat placement. Size was included because of its correlation with body weight, and overall type and front teat placement because of their correlation with survival. To avoid double counting the benefits of milk production traits, temperament and milking speed, the survival trait in the objective was defined as survival independent of voluntary culling for these traits. Customization of the breeding objective was achieved by adjusting the economic weights for traits in the objective to take account of important characteristics of farmers' herds, the milk payment system under which they operate and make allowance for their own value judgements. An assessment of the impact of customization suggested that, even though there is a wide range in the economic weights that are applicable in different areas of Australia, there would be little loss of efficiency in using a single national index. However, customization is still believed to be desirable given that it is likely that a substantial proportion offarmers will be reluctant to use a national index, especially in those states which have quotas and focus on the liquid milk market. The algorithms described in the paper have been incorporated into a user-friendly microcomputer program called $electabull which is now commercially available to farmers.