The 3D shape of live animals plays an important role in achieving good husbandry and in selecting breeding stock. Many shape features are subtle and cannot be extracted from 2D images. With 3D data, it would be possible to extract cross-sectional areas and volumes, and to measure features such as the squareness of the back muscles, which are known indicators of lean muscle mass (Whittemore 1998). However, there is currently no simple method to measure 3D shape in live animals. In this work a system has been developed for freezing the motion of a pig using flash photography and processing the images to extract the 3D surface shape. The imaging system is based on stereo photogrammetry. Three stereo pods, each consisting of two digital cameras, were set up at perpendicular directions in order to cover the whole of a cuboidal imaging volume. The imaging volume dimensions were 1300 mm long × 900 mm high × 700 mm deep. The imaging system was calibrated prior to capturing the pig images. Multiresolution correlation-based stereo matching (Siebert and Urquhart, 1994) was used to establish correspondences between the left and right images in each stereo pair. The output of the stereo matching of each pod was a 2.5D range image. These range images were integrated into a 3D model.

Integrated management systems (IMS) for pigs offer the prospects of optimising meat production and minimising nitrogenous pollution through closed-loop control of pig growth by nutritional control (Whittemore, et al., 2001). Such an IMS requires a real-time sensor system, a nutritional model which is optimised in response to data collected in by the sensor system, and a control system which uses forward predictions of the model to predict the nutritional regime required to satisfy growth and pollution targets. An experiment was carried out to determine the accuracy to which a novel IMS system can direct pig weight gain and fatness towards preset targets through nutritional control.

Hill sheep breeds are required to survive and rear lambs in harsh conditions, and good maternal characteristics contribute to their success. However, improved carcass characteristics are also required to meet market requirements. This paper evaluates lamb performance characteristics after 4 years of selection using indexes tailored to improve overall productivity in different hill sheep production systems.

Generally, selection indices used for the selection of livestock are linear combinations of estimated breeding values (EBVs), with each EBV weighted according to its marginal or relative economic value. This approach can be extended to non linear combinations. In both cases knowledge of economic weights is required. When economic values are not known, one can determine the relative weights that lead to the desired genetic progress. This approach was taken by Simm and Dingwall (1989) when designing the lean index for British terminal sire breeds. A weighting of +3 for lean in the carcase and -1 for fat in the carcase leads to near-maximum increase in lean, while maintaining amount of fat. This index has been highly effective over the last decade (MLC, 2002) to the extent that in recent years breeders have expressed concerns that offspring from high index ram have insufficient fat cover at slaughter. The current study aims to design an index that is broadly similar to the lean index, but puts a penalty on animals with a genetic merit for low fat cover.

We have recently developed a Fertility Index for UK dairy cattle (Wall et al., 2003). After examining national data it was decided that the Fertility Index should be based on sire PTAs for calving interval (CI) and nonreturn rate (NR) after 56 days weighted by their relative economic weights. However, just under half of the available bulls have no milking daughters in the UK. It would take about 4 years from the time of first use in the UK, for a bull to have sufficient daughters for a reliable fertility proof. Waiting this long for fertility information on which to base selection decisions will slow genetic progress and is undesirable as many of these bulls could have fertility proofs in their country of first test. This study examines the feasibility of converting foreign fertility proofs to UK equivalents.

The test day model (TDM) has become the method of choice for genetic evaluation of production traits in dairy cattle. However, in the UK, complete test day (TD) records are only available from 1995 compared with 305d yields utilised in the current animal model (IAM) dating back to 1975. The analysis of TD records only would significantly reduce accuracy of evaluations through limited data including loss of dam information on cows with records prior to 1995. An optimum solution would be the joint analysis of TD and 305d records. This paper presents a TDM used for the joint analysis of TD and lactation records in the UK and results from its application to the Holstein Friesian (HOL), Jersey (JER) and Guernsey (GUE) breeds.

The UK beef industry has over recent years seen a decline in the quantity and quality of heifers available as replacements to the suckler herd. Historically the dairy industry supplied the beef suckler herd with surplus dairy cross beef heifers. However, with the Holstenisation of the UK dairy herd and a reduction in size of the national dairy herd beef farmers are looking towards alternative replacement strategies. Many breeds of cattle are available for use in UK beef production and many different combinations of breeds can be used in crossbreeding scenarios. Tools have been developed recently to identify the best individuals from the most appropriate breeds to be used in the optimum breeding strategy. To identify appropriate breeds for specific production functions required quantification of performance traits for the breeds of cattle used commercially. At an enterprise level a deterministic bioeconomic model BREEDS (Beef Replacement Enterprise Evaluation Decisions Support) was developed (Roughsedge et al., 2003) to evaluate changes in breeds and breeding systems. The model simulates all aspects of beef production including the transition of the breed composition, over generations, as well as biological and economic performance of animals within the herd, over time. Breed performance parameters used in BREEDS were derived by combining results of a meta-analysis of published breed comparison experiments (Roughsedge et al., 2001) with performance data collected on cattle in Britain by MLC Signet, including aspects of maternal performance. Once appropriate breeds are identified breeding values will help to identify the best individuals to use. This study outlines the traits considered for maternal estimated breeding values (EBVs) to allow breeders to improve maternal aspects of breed performance and commercial producers to select bulls appropriate to their replacement breeding needs.

The profit index currently used in the UK was designed in 1992 to combine production and longevity in an optimal manner. There have been no enhancements to this index for some years but during this period the industry has suffered wide-scale disruptions as a consequence of BSE and foot and mouth disease. The quality of data on reasons for culling has reduced, putting greater emphasis on prediction of longevity from type traits, and other issues relating to animal management have risen in priority. Increasing the emphasis on welfare associated traits such as lifespan and health in a widely used selection index will lead to both increased health and welfare of dairy cows and increased public confidence in dairy farming. The objectives of this project were to (1) enhance the prediction of lifespan by incorporating farmer-friendly composite type traits (2) re-evaluate economic weights of traits in £PLI to account for changes in costs/returns and (3) enhance £PLI by the addition of health traits (somatic cell count and lameness).

A calf’s weight at weaning is influenced not only by its own genes for growth (direct genetic effects) but also its mother’s genes for maternal (milking) ability. Selection for genetic improvement in both maternal ability and growth are an important part of current breeding programmes for many beef breeds. Estimated breeding values for both components are obtained by separating the direct and maternal effects on live weights around weaning by fitting appropriate statistical models. Many previous studies have estimated large negative genetic correlations between the direct and maternal components (rAM) of a round -0.5 (Meyer, 1997). Whether these estimates are a true reflection of the actual biological relationships have frequently been questioned. Meyer (1997) showed that by fitting additional random terms in the model [i.e. sire or sire*year environmental terms, dam-offspring environmental covariance/correlation (rAeDe)] the magnitude of the negative rAM estimates could be reduced. The aims of this study were: (i) to estimate the magnitude of the rAM in a UK population, (ii) to investigate the relative importance of various additional terms, and (iii) to test the importance of including a non-zero rAM in these alternative models.

There is considerable research efforts aimed towards detecting disease resistance genes or QTL. If found and used in breeding programmes, such genes should reduce the likelihood and severity of epidemics. A critical question is which genes should be used and what will their impact be? Genetic epidemiological modeling techniques (MacKenzie and Bishop, 2001) can give insights into how we should prioritise the prospective resistance traits, hence candidate genes or QTL corresponding to these traits, for specific diseases. Here, a stochastic genetic epidemiological model is used to investigate the relative importance of different genetic control options and the effect of host genetic heterogeneity in controlling the transmission of a microparasitic, e.g. viral or bacterial, infection.

In standard models of the genetic basis of quantitative traits such as growth rate and milk yield, it is assumed that genotypes differ in their effect on the mean but not on the variance. There is much evidence of differences in variability among environments, and more limited but quite conclusive evidence of differences in residual variability among genotypes (e.g. CanCristobal-Gaudy et al, 1998; Sorensen and Waagepetersen, 2003). Differences among genotypes at an individual locus in their residual phenotypic variation or in the environmental variation among whole genotypes may influence rates of genetic progress and rates of change in variability. We propose models and quantify such changes for directional selection (see also Hill, 2002; Hill and Zhang, 2004).

Widespread international use of AI and best linear unbiased prediction (BLUP) breeding values for milk yield has increased genetic gain in many dairy populations, including the UK. The proliferation of few sires through AI and the coselection of relatives favoured by BLUP has however increased the relatedness and inbreeding of the UK population. Inbreeding is undesirable for a number of reasons and it is important to monitor the rate at which it accumulates. Currently, the level and rates of inbreeding (∆F) are not routinely reported for UK dairy cattle. Optimised selection procedures that maximise genetic gain while constraining ∆F to a pre-defined level have been shown to control ∆F and increase genetic gain over truncation selection at the same ∆F (e.g. Avendaño et al. 2003). The objective of this study was to determine the current rates of inbreeding and to assess the potential of using optimised selection procedures in the UK dairy population.

Inbreeding depression leads to the reduction of the mean phenotypic value. There has been a steady increase in inbreeding (F) in the UK since the introduction of reproductive techniques (AI, MOET). There has been an increase in the percent Holstein (%H) in the UK population due to the influx of North American Holstein genes. Crossing these Holsteins to British Friesians can result in the favourable effect of heterosis (het), whereby crossbred progeny out-perform the mid-parent mean for that trait. Of the heterosis in the F1 population, a proportion is lost due to recombination (rec) between parental line genes and is a measure of the epistatic interaction of genes. The purpose of this study was to examine the impact of nonadditive genetic effects (F, het, rec, %H) on the estimation of dairy cow fertility breeding values in the UK.

Precise description of growth and development is important for efficient lamb production. In order to meet tight market specifications, lamb producers require accurate genetic information to make informed selection and management decisions on their animals. There is also interest in selection of animals with more efficient growth and development patterns, and information is needed on how carcase traits are correlated to each other and how they can develop over time. Hence, the aim of this study was to evaluate repeated weight, fat and muscle measures on Poll Dorset sheep using random regression (RR) models to investigate how these traits change through time.

Traditionally, the dairy herd has been the primary source of cross-bred females for use as beef suckler cows in Northern Ireland. However, in view of concerns relating to potential detrimental effects of increasing Holsteinisation of the dairy herd on progeny carcass quality and herd fertility, there has been increasing interest in retaining beef-bred heifers for use as replacements in the beef herd. The objective of this study was to evaluate the effect of dam genotype, originating from either dairy or suckler herds, on maternal and progeny characteristics.

Computed tomography (CT) gives accurate in vivo estimates of sheep carcass composition based on information provided by cross-sectional CT reference scans (Young et al., 2001). Spiral CT is a novel imaging technology in which contiguous cross-sectional scans of a known thickness are collected. This data allows the reconstruction of images in three dimensions, giving the possibility of a comprehensive assessment of characteristics that are defined in terms of shape, such as conformation and muscularity. The development of automatic procedures for image analysis is of high priority due to the large amount of information contained in the spiral scans. The first step in image analysis is isolating the carcass components of each cross-sectional image, called segmentation. An algorithm to automatically segment the cross-sectional images in the spiral scan was developed, with the objective of investigating in vivo assessments of conformation and muscularity in sheep. The aim of this study was to compare the muscle areas obtained by manual and automatic segmentations.

Fifty-three per cent of prime beef production in Northern Ireland is currently sourced from the beef herd and this proportion is likely to decrease post implementation of the Mid-Term Review (MTR) of the Common Agricultural Policy (CAP). The Northern Ireland suckler industry currently incorporates a very diverse range of genotypes which produces a very varied product in terms of carcass weight, fatness and conformation. However, there is an increasing need for the industry to produce a more consistent product, as beef production will be market driven in a subsidy free environment post implementation of the MTR of the CAP. The objective of the present study was to evaluate the potential of 10 of the most common dam genotypes used for beef production in Northern Ireland.

Computed Tomography (CT) is a non-invasive method used to provide accurate information on body composition of breeding animals. It is being applied in sheep breeding programmes in the UK to predict whole carcass composition in terms of muscle, fat, and bone. Previous studies established the equations to predict the total weights of muscle, fat and bone in different breeds from conventional CT scans. The average prediction accuracies were 92, 96 and 81% for muscle, fat and bone, respectively, in meat sheep and hill breed lambs (Young et al., 2001). Spiral CT scans provide a means of assessing directly the composition of the whole body and its different regions, in addition to muscularity and conformation. Although an automatic procedure to quantify the carcass components in cross-sectional images was developed previously, new software to segment images from spiral CT scans is now being evaluated. The aim of this study was to determine the accuracy of the automated image analysis in the estimation of total muscle volume of the hind leg, which is the most valuable joint.

Breed of terminal sire used in suckler beef systems is one of the most important decisions taken by beef producers, as the terminal sire contributes 50% of the total genetic make-up of the progeny. In view of the inherent variability of carcass weight and grading characteristics of progeny, the objective of the present study was to evaluate the potential of a range of terminal sire breeds for beef production under Northern Ireland conditions.

In the past, concerns about farm animal welfare have mainly related to husbandry systems, with much less attention given to the effects of breeding. Over the years selective breeding programmes have led to great increases in productive output and efficiency in farm livestock, particularly poultry, pigs and dairy cattle. These species have also become increasingly specialised for a specific function such as producing eggs, meat or milk. But there is strong evidence that in many cases where there is a narrow focus on improving production, these selective breeding programmes are associated with serious welfare costs (Rauw et al., 1998), despite the existence of legislation that, in theory, prohibits such a situation. The European Directive on farm animal welfare (Directive 98/58/EC) states that: ‘No animals shall be kept for farming purposes unless it can reasonably be expected, on the basis of their genotype or phenotype, that they can be kept without detrimental effect on their health or welfare.’ Negative effects of selective breeding on welfare are due to over-emphasis on production traits in relation to other aspects of the animal’s biology. The animal is ‘genetically pre-programmed’ to allocate a disproportionately large amount of resources to the particular production trait (such as producing a large breast muscle or huge quantities of milk), often at the expense of the rest of the body’s functions. The biological balance of the animal is disturbed, with much of the body’s emphasis on particular traits. In their report on the welfare of chickens (2000), the European Commission’s Scientific Committee on animal health and animal welfare concluded that: ‘…the major welfare problems in broilers are those which can be regarded as side effects of the intense selection mainly for growth and feed conversion. ’ Animals selected on the basis of production often maintain high output whatever the cost to them. For example, high yielding dairy cows may continue to produce milk even when in negative energy balance. Body reserves will be mobilised to allow milk production to continue which, if prolonged, can lead to health and fertility problems (Pryce et al., 2002).