Modelling growth in Suffolk and Charollais sheep populations using random regression models and validation of constrained polynomial correlation values.

Random regression modelling has been used across multiple animal species to model longitudinal data. The random regression model for growth accounts for the genetic correlation between measures of the same trait over time and the wide environmental variability in growth, but this requires adequate weight records across the age range. However, contemporary management practices in sheep in the United Kingdom generally focus on growing lambs and neglect mature weight recordings. This study examined modelling strategies for growth data in Suffolk and Charollais sheep, provided by the Agriculture and Horticulture Development Board, with polynomial random regression modelling with many early life weight recordings but limited weight recordings in mature animals. Two methods were employed to model the data. In Method A, missing mature weight records were predicted for those animals that did not have a recorded mature weight. The animals were sorted into groups based on the identity of their sires and the year in which the animal was born. Mature weight values were predicted within each group with a multiple regression model. The dataset, including predicted values, was analysed with random regression models using polynomials and simple linear regression for animal and permanent environmental (PE) effects. In Method B, the dataset with missing mature weight records was analysed using a random linear regression animal model with random animal and PE effects. Due to problems of convergence because the parameters were close to the boundary space, fixing the correlation between the intercept and slope of the Legendre polynomial at different levels was investigated. The heritability values resulting from the model with a fixed correlation between intercept and slope parameters at 0.5 for the Suffolk dataset resulted in heritability values ranging from 0.2 to 0.5 from 1 to 619 days of age. Corresponding estimates for the Charollais dataset ranged from 0.18 to 0.49 from 1 to 640 days of age. For the Suffolk data, the genetic correlations ranged from 1.00 to 0.08 between weight at day 1 to weight at day 619, while for the Charollais, the correlations ranged from 1.00 to 0.05 from 1 to 640 days of age. Validation procedures were undertaken using a multitrait approach to examine the estimated breeding values when the correlation between the intercept and slope are fixed at different levels. The results indicated that fixing the correlation at 0.5 gave the most appropriate estimates for the Suffolk and Charollais datasets.

Review: Preference elicitation methods for appropriate breeding objectives.

Breeding objectives of livestock and other agricultural species are usually profit maximising. The selection emphasis placed on specific traits to achieve a breeding objective is often informed by the financial value of a trait to a farm system. However, there are alternative, and complementary approaches to defining both the breeding objective and the selection emphasis placed on traits that are included in associated selection tools. These are based on the preferences of stakeholders, which are often heterogeneous and include broader values and motivations than profit. In this regard, stated preference methods are useful when considering traits that have either no discernible market value or whose value is not fully transferred via the market. Such approaches can guide more appropriate breeding decisions that are amenable to changing societal values, for example with reduced negative environmental externalities. However, while stated preference methods offer promising conceptualisations of value in genetic improvement programmes, there is still a substantial knowledge gap in terms of the current state of research and a catalogue of publications to date. This paper reviews publications of stated preference approaches in the field of livestock breeding (and some relevant crop breeding examples), providing a knowledge base of published applications and promoting their continued development and implementation towards the formulation of appropriate breeding objectives and selection indices. A systematic review of 84 peer-reviewed publications and an aggregate ranking of traits for the most commonly studied subject (cattle) reveals uncertainty in preference estimates which may be driven by (i) a diverse set of non-standardised methodologies, (ii) common oversights in the selection, inclusion and description of traits, and (iii) inaccurate representations of the respondent population. We discuss key considerations to help overcome these limitations, including avoiding methodological confinement to a disciplinary silo and reducing complexity so that the values of broader respondent groups may be accounted for.

Preferences of European dairy stakeholders in breeding for resilient and efficient cattle: A best-worst scaling approach.

Including resilience in the breeding objective of dairy cattle is gaining increasing attention, primarily as anticipated challenges to production systems, such as climate change, may make some perturbations more difficult to moderate at the farm level. Consequently, the underlying biological mechanisms by which resilience is achieved are likely to become an important part of the system itself, increasing value on the animal's ability to be unperturbed by variable production circumstances, or to quickly return to pre-perturbed levels of productivity and health. However, because the value of improving genetic traits to a system is usually based on known profit functions or bioeconomic models linked to current production conditions, it can be difficult to define longer-term value, especially under uncertain future production circumstances and where nonmonetary values may be progressively more important. We present the novel application of a discrete choice experiment, used to investigate potential antagonisms in the values of genetic improvements for 8 traits to dairy cattle system stakeholders in Europe when the production goal was either efficiency or resilience. A latent class model was used to identify heterogeneous preferences within each production goal, and postestimation was used to identify associations between these preferences and sociodemographic characteristics of respondents. Results suggested 3 distinct latent preference classes for each production goal. For the efficiency goal, yield and feed efficiency traits were generally highly valued, whereas for the resilience goal, health and robustness traits were generally highly valued. In both cases, these traits generally carried a low value in the other production scenario. Overall, in both scenarios, longevity was highly valued; however, the value of this trait in terms of resilience will depend on phenotyping across diverse environments to sufficiently capture performance under various anticipated system challenges. Additionally, results showed significant associations between membership of latent preference classes with education level and profession. In conclusion, as resilience becomes increasingly important, it is likely that a continued reliance on the short-term economic value of traits alone will lead decision makers to misrepresent the importance of some traits, including those with substantial contextual values in terms of resilience.

Current situations of animal data recording, dairy improvement infrastructure, human capacity and strategic issues affecting dairy production in sub-Saharan Africa.

An online survey on the state of existing dairy data, dairy improvement infrastructure and human capacity in sub-Saharan Africa (SSA) was undertaken with the aim of assessing whether the state of existing animal recording, dairy improvement methods and key issues facing dairy production together with means of addressing the issues differ among countries and regions of SSA. Respondents comprised experts and practitioners in livestock production and genetic resources from research institutes, animal breeding companies, universities, non-governmental organisations and government agricultural ministries. The main dairy farming system in which the respondents were involved was mixed crop-livestock system (30.2%), and this was mainly practised in the private land tenure system (46.3%). Data were analysed using linear model and paired Student t test in R software package. Respondents identified key issues affecting dairy production as poor genetic assessment of imported exotic breeds and crosses in Africa (62.3%), fluctuations in milk prices within both the formal and informal markets (50.9%), no comprehensive sire ranking systems (39.6%), housing and health management regimes which adversely affect milk yield (32.1%), poor market networks for dairy products (25.5%), poor feeding (13.3%), inadequate genetic technologies (9.4%) and poor animal performance recording systems (9.4%). Respondents emphasised the need for updated breeding policies, sire ranking systems, adequate farm management systems, capacity building, across-country collaborations and joint genetic assessments of dairy breeds found in sub-Saharan Africa. The current situation of dairy production though similar for the different countries, differed in order of emphasis and magnitude across the countries and regions in sub-Saharan Africa.

Heterogeneous variances and genetics by environment interactions in genetic evaluation of crossbred lambs.

Accounting for environmental heteroscedasticity and genetics by environment interaction (G×E) in genetic evaluation is important because animals may not perform predictably across environments. The objectives of this study were to evaluate the presence and consequences of heteroscedasticity and G×E on genetic evaluation. The population considered was crossbred lambs sired by terminal sires and reared under commercial conditions in the UK. Data on 6325 lambs sired by Charollais, Suffolk and Texel rams were obtained. The experiment was conducted between 1999 and 2002 on three farms located in England, Scotland and Wales. There were 2322, 2137 and 1866 lambs in England, Scotland and Wales, respectively. A total of 89 sires were mated to 1984 ewes of two types (Welsh and Scottish Mules). Most rams were used for two breeding seasons with some rotated among farms to create genetic links. Lambs were reared on pasture and had their parentage, birth, 5 week, 10 week, and slaughter weights recorded. Lambs were slaughtered at a constant fatness, at which they were ultrasonically scanned for fat and muscle depth. Heteroscedasticity was evaluated in two ways. First, data were separated into three subsets by farm. Within-farm variance component estimates were then compared with those derived from the complete data (Model 1). Second, the combined data were fitted, but with a heterogeneous (by farm) environmental variance structure (Model 2). To investigate G×E, a model with a random farm by sire (F×S) interaction was used (Model 3). The ratio of the F×S variance to total variance was a measure of the level of G×E in the population. Heterogeneity in environmental variability across farm was identified for all traits (P<0.01). Rank correlations of sire estimated breeding value between farms differed for Model 1 for all traits. However, sires ranked similarly (rank correlation of 0.99) for weight traits with Model 2, but less so for ultrasonic measures. Including the F×S interaction (Model 3) improved model fit for all traits. However, the F×S term explained a small proportion of variation in weights (<2%) although more in ultrasonic traits (at least 10%). In conclusion, heteroscedasticity and G×E were not large for these data, and can be ignored in genetic evaluation of weight but, perhaps, not ultrasonic traits. Still, before incorporating heteroscedasticity and G×E into routine evaluations of even ultrasonic traits, their consequences on selection response in the breeding goal should be evaluated.

Genetic evaluation of days to harvest in crossbred lambs.

Days to harvest (DTH) is the number of days a lamb is fed before reaching a target level of fatness. Although economically relevant, this trait has not been thoroughly evaluated in sheep. Most lambs harvested in the United Kingdom are crossbreds sired by purebred terminal sires, with Charollais, Suffolk, and Texel most commonly used. Sires from these breeds were selected on an index designed to increase lean growth while constraining fat. The purpose of this research was to 1) evaluate the effects of index selection in terminal sires on DTH and 2) evaluate the feasibility of incorporating DTH into genetic evaluation programs. Charollais, Suffolk, and Texel sheep had participated in sire referencing schemes where genetic links among flocks were established by sharing rams. Rams with high or low index scores were chosen from these schemes and mated to crossbred ewes at 3 farms in the United Kingdom. Lambs were harvested at a target 11% subcutaneous fat. Records on DTH from 6,350 lambs were analyzed in 2 ways: 1) as time to harvest fitting a survival model and 2) as a normally distributed variable in a bivariate analysis with weight at harvest. The survival analysis was stratified by rearing type (single or twin). In both approaches, sires were fitted using a multivariate normal distribution with a relationship matrix. Regardless of model fitted, sire index did not affect DTH (P>0.10). However, Texel-sired lambs reached harvest faster (P<0.01) than either Charollais- or Suffolk-sired lambs although DTH in those 2 breed types did not differ (P>0.1). Ewe lambs reached harvest faster than wethers (P<0.01). Lambs from older ewes were harvested faster (P<0.001). The heritability of DTH was 0.21 from the survival model and 0.20 from the bivariate model. Rank correlation of sire EBV between methods was 0.9, suggesting strong agreement. The use of high or low index sires did not extend DTH in lambs harvested at a target fatness. Importantly, there is no antagonism between improving carcass merit and extending the grazing season. Furthermore, DTH is moderately heritable. If economically justified within a breeding program, it could be reduced through genetic selection.

Index selection in terminal sires improves lamb performance at finishing.

Lamb meat is often perceived by consumers as fatty, and consumption has decreased in recent decades. A lean growth index was developed in the UK for terminal sire breeds to increase carcass lean content and constrain fat content at a constant age end point. The purposes of this study were 1) to evaluate the effects of index selection of terminal sires on their crossbred offspring at finishing and 2) to evaluate its effectiveness within terminal sire breeds. Approximately 70% of lambs marketed in the UK have been sired by rams of breeds typically thought of as specialized terminal sires. The most widely used are Charollais, Suffolk, and Texel. These breeds participated in sire referencing schemes from the early 1990s by sharing rams among flocks selected on the lean growth index. From 1999 to 2002 approximately 15 "high" and 15 "low" lean growth index score rams were selected from within their sire referencing schemes and mated to Welsh and Scottish Mule ewes. Their crossbred offspring were commercially reared on 3 farms in the UK. Lambs were finished to an estimated 11% subcutaneous fat by visual evaluation. At finishing, lambs were weighed, ultrasonically scanned, and assessed for condition score and conformation. Records were obtained for 6356 lambs on finishing BW (FWT), ultrasonic muscle depth (UMD), ultrasonic fat depth, overall condition score (OCS), and conformation of gigot, loin, and shoulder. Ultrasonic fat depth was log transformed (logUFD) to approach normality. High-index-sired lambs were heavier at finishing (1.2±0.2 kg) with thicker UMD (0.7±0.2 mm) and less logUFD (0.08±0.01 mm; P<0.05). There were no differences in OCS or conformation based on the sire index or breed (P>0.08). Suffolk-sired lambs were heavier than Charollais (1.0±0.3 kg), which were heavier than Texel (0.9±0.3 kg; P<0.001). Texel-sired lambs had thicker UMD than Charollais (0.7±0.2 mm; P<0.001) but were not different than Suffolk. Charollais-sired lambs had greater logUFD than both Texel (0.098±0.016 mm) and Suffolk (0.061±0.017 mm) sired lambs (P<0.001). Within a breed, high- and low-index-sired lambs differed in performance with the exceptions of FWT and UMD in Suffolks. Index selection produced heavier and leaner lambs at finishing. Producers have flexibility in choosing the terminal sire that best fits their production system.

Index selection in terminal sires improves early lamb growth.

The use of terminal sires (TS) for crossbreeding is integral to the UK sheep industry where approximately 71% of market lambs are sired by TS rams. Early growth of these crossbred lambs affects profitability. The objectives of this study were i) to evaluate the effectiveness of index selection among TS on BW and ADG of their crossbred offspring; and ii) to compare the efficacy of that selection within TS breeds. The most widely used TS breeds in the United Kingdom are Charollais, Suffolk, and Texel. These participated in sire referencing schemes in which they were evaluated on a lean growth index designed to increase carcass lean weight at a given age. From 1999 to 2002, approximately 15 high and 15 low lean growth index rams per breed (93 in total, differing in index on average by 4.6 SD) were selected from within their sire referencing schemes and mated to Welsh and Scottish Mule ewes. Their crossbred offspring were reared commercially on 3 experimental farms in England, Scotland, and Wales. A total of 6,515 lambs were born between 2000 and 2003. Lambs were weighed at birth (BWT), 5 wk (5WT), and 10 wk (10WT), and their ADG from birth to 10 wk was calculated. Lambs sired by high index rams were on average, across breeds, heavier at all ages (P < 0.01) with 0.07 ± 0.03, 0.3 ± 0.1, and 0.4 ± 0.1 kg greater BWT, 5WT, and 10WT, respectively. Their ADG was 5.1 ± 1.9 g/d greater than low-index-sired lambs (P < 0.01). Suffolk-sired lambs were on average heavier at all ages, with greater ADG, whereas Charollais-sired lambs were lightest with smallest ADG. Overall, there was no significant interaction between sire index and sire breed (P > 0.10). Within Suffolk-sired lambs, there was little difference between high and low index sires for the traits studied (P > 0.3). High and low index Charollais-sired lambs differed in BWT (0.09 ± 0.04 kg) and 5WT (0.3 ± 0.1 kg), and Texel-sired lambs differed in 5WT (0.5 ± 0.1 kg), 10WT (0.9 ± 0.2 kg), and ADG (10.2 ± 3.3 g/d; P < 0.01). Lambs from Scottish Mule dams were heavier, with greater ADG, than lambs born to Welsh Mules (P < 0.01). Lambs reared in Scotland were heavier at all ages (P < 0.01). The results suggest that using index selection in TS can improve the growth of their commercial offspring reared on grass.

The effect of improving cow productivity, fertility, and longevity on the global warming potential of dairy systems.

This study compared the environmental impact of a range of dairy production systems in terms of their global warming potential (GWP, expressed as carbon dioxide equivalents, CO(2)-eq.) and associated land use, and explored the efficacy of reducing said impact. Models were developed using the unique data generated from a long-term genetic line × feeding system experiment. Holstein-Friesian cows were selected to represent the UK average for milk fat plus protein production (control line) or were selected for increased milk fat plus protein production (select line). In addition, cows received a low forage diet (50% forage) with no grazing or were on a high forage (75% forage) diet with summer grazing. A Markov chain approach was used to describe the herd structure and help estimate the GWP per year and land required per cow for the 4 alternative systems and the herd average using a partial life cycle assessment. The CO(2)-eq. emissions were expressed per kilogram of energy-corrected milk (ECM) and per hectare of land use, as well as land required per kilogram of ECM. The effects of a phenotypic and genetic standard deviation unit improvement on herd feed utilization efficiency, ECM yield, calving interval length, and incidence of involuntary culling were assessed. The low forage (nongrazing) feeding system with select cows produced the lowest CO(2)-eq. emissions of 1.1 kg/kg of ECM and land use of 0.65 m(2)/kg of ECM but the highest CO(2)-eq. emissions of 16.1t/ha of the production systems studied. Within the herd, an improvement of 1 standard deviation in feed utilization efficiency was the only trait of those studied that would significantly reduce the reliance of the farming system on bought-in synthetic fertilizer and concentrate feed, as well as reduce the average CO(2)-eq. emissions and land use of the herd (both by about 6.5%, of which about 4% would be achievable through selective breeding). Within production systems, reductions in CO(2)-eq. emissions per kilogram of ECM and CO(2)-eq. emissions per hectare were also achievable by an improvement in feed utilization. This study allowed development of models that harness the biological trait variation in the animal to improve the environmental impact of the farming system. Genetic selection for efficient feed use for milk production according to feeding system can bring about reductions in system nutrient requirements, CO(2)-eq. emissions, and land use per unit product.

Online prediction of fatty acid profiles in crossbred Limousin and Aberdeen Angus beef cattle using near infrared reflectance spectroscopy.

The objective of this study was to examine the online use of near infrared reflectance (NIR) spectroscopy to estimate the concentration of individual and groups of fatty acids (FA) as well as intramuscular fat (IMF) in crossbred Aberdeen Angus (AA×) and Limousin (LIM×) cattle. This was achieved by direct application of a fibre-optic probe to the muscle immediately after exposing the meat surface in the abattoir at 48 h post mortem. Samples of M. longissimus thoracis from 88 AA× and 106 LIM× were scanned over the NIR spectral range from 350 to 1800 nm and samples of the M. longissimus lumborum were analysed for IMF content and FA composition. Statistically significant differences (P < 0.001) were observed in most FA between the two breeds studied, with FA concentration being higher in AA× meat mainly. NIR calibrations, tested by cross-validation, showed moderate to high predictability in LIM× meat samples for C16:0, C16:1, C18:0, trans11 C18:1, C18:1, C18:2 n-6, C20:1, cis9, trans11 C18:2, SFA (saturated FA), MUFA (monounsaturated FA), PUFA (polyunsaturated FA) and IMF content with R(2) (SE(CV), mg/100 g muscle) of 0.69 (146), 0.69 (28), 0.71 (62), 0.70 (8.1), 0.76 (192), 0.65 (13), 0.71 (0.9), 0.71 (2.9), 0.68 (235), 0.75 (240), 0.64 (17) and 0.75 (477), respectively. FA such as C14:0, C18:3 n-3, C20:4 n-6, C20:5 n-3, C22:6 n-3, n-6 and n-3 were more difficult to predict by NIR in these LIM× samples (R(2) = 0.12 to 0.62; SECV = 0.5 to 26 mg/100 g muscle). In contrast, NIR showed low predictability for FA in AA× beef samples. In particular for LIM×, the correlations of NIR measurements and several FA in the range from 0.81 to 0.87 indicated that the NIR spectroscopy is a useful online technique for the early, fast and relatively inexpensive estimation of FA composition in the abattoir.

Risk factors for culling in Holstein-Friesian dairy cows.

Risk factors associated with voluntary and involuntary culling within a Holstein-Friesian dairy cow research herd were identified. Data were studied from 3498 completed lactations from the Langhill Holstein-Friesian dairy herd between January 1990 and June 2008. During this period the cows were based on two different farms in Scotland. The culling rate of the milking herd was approximately 25 per cent per annum. Approximately 68 per cent of cows culled were classified as involuntary. The association between different risk factors and the incidence of culling was investigated using a general linear mixed model. Of the 838 cows culled, 59 per cent were culled before the fourth lactation. Culling was associated with cows that had an assisted calving (P<0.01), aborted (P<0.01) and/or suffered from mastitis (P<0.05). Cows that were culled were also more likely to be older cows (P<0.01), have a low number of milking days (P<0.001) and/or a greater number of days from calving to conception (P<0.01). Culling was also associated with conception failure (r=0.752, P<0.001). Further work might help reduce the number of animals culled involuntarily, by identifying key factors associated with the incidence of an assisted calving, abortion and mastitis, and improving milking and fertility performance using detailed data from the Langhill herd.

Comparison of repeatability and multiple trait threshold models for litter size in sheep using observed and simulated data in Bayesian analyses.

Bayesian analyses were used to estimate genetic parameters on 5580 records of litter size in the first four parities from 1758 Mule ewes. To examine the appropriateness of fitting repeatability (RM) or multiple trait threshold models (MTM) to litter size of different parities, both models were used to estimate genetic parameters on the observed data and were thereafter compared in a simulation study. Posterior means of the heritabilities of litter size in different parities using a MTM ranged from 0.12 to 0.18 and were higher than the heritability based on the RM (0.08). Posterior means of the genetic correlations between litter sizes of different parities were positive and ranged from 0.24 to 0.71. Data sets were simulated based on the same pedigree structure and genetic parameters of the Mule ewe population obtained from both models. The simulation showed that the relative loss in accuracy and increase in mean squared error (MSE) was substantially higher when using the RM, given that the parameters estimated from the observed data using the opposite model are the true parameters. In contrast, Bayesian information criterion (BIC) selected the RM as most appropriate model given the data because of substantial penalty for the higher number of parameters to be estimated in the MTM model. In conclusion, when the relative change in accuracy and MSE is of main interest for estimation of breeding values of litter size of different parities, the MTM is recommended for the given population. When reduction in risk of using the wrong model is the main aim, the BIC suggest that the RM is the most appropriate model.

Predicting beef cuts composition, fatty acids and meat quality characteristics by spiral computed tomography.

The potential of X-ray computed tomography (CT) as a predictor of cuts composition and meat quality traits using a multivariate calibration method (partial least square regression, PLSR) was investigated in beef cattle. Sirloins from 88 crossbred Aberdeen Angus (AAx) and 106 Limousin (LIMx) cattle were scanned using spiral CT. Subsequently, they were dissected and analyzed for technological and sensory parameters, as well as for intramuscular fat (IMF) content and fatty acid composition. CT-PLSR calibrations, tested by cross-validation, were able to predict with high accuracy the subcutaneous fat (R2, RMSECV=0.94, 34.60 g and 0.92, 34.46 g), intermuscular fat (R2, RMSECV=0.81, 161.54 g and 0.86, 42.16 g), total fat (R2, RMSECV=0.89, 65.96 g and 0.93, 48.35 g) and muscle content (R2, RMSECV=0.99, 58.55 g and 0.97, 57.45 g) in AAx and LIMx samples, respectively. Accurate CT predictions were found for fatty acid profile (R2=0.61-0.75) and intramuscular fat content (R2=0.71-0.76) in both sire breeds. However, low to very low accuracies were obtained for technological and sensory traits with R2 ranged from 0.01 to 0.26. The image analysis evaluated provides the basis for an alternative approach to deliver very accurate predictions of cuts composition, IMF content and fatty acid profile with lower costs than the reference methods (dissection, chemical analysis), without damaging or depreciating the beef cuts.

Assessing beef carcass tissue weights using computed tomography spirals of primal cuts.

More than 800 beef primal cuts from 44 Aberdeen Angus and Limousin-cross steers carcasses were scanned using spiral computed tomography (CT) and dissected. Thresholds for the segmentation of fat, muscle and bone in the CT spirals were estimated with the objective of assessing the weight of these tissues in the primal cuts and in the entire carcasses. Thresholds were estimated using half of the dataset (DBE) and then validated in the other half (DBV). Automatic image analysis procedures were used to assess tissue weights. The R(2) of the regression between primal tissue weight by dissection and CT were high in both datasets for fat (DBE, 0.89; DBV, 0.92), muscle (DBE, 0.99; DBV, 0.99) and bone (DBE, 0.95; DBV, 0.97). The estimation of total carcass tissue weights were also very accurate for the three tissues (R(2) values of 0.95 to 0.96), indicating that CT scanning may deliver very accurate information on beef carcass composition faster and with lower cost than physical dissection and without damaging or depreciating the primal joints.

Epistatic analysis of carcass characteristics in pigs reveals genomic interactions between quantitative trait loci attributable to additive and dominance genetic effects.

The present study focused on the identification of epistatic QTL pairs for body composition traits (carcass cut, lean tissue, and fat tissue weights) measured at slaughter weight (140 kg of BW) in a 3-generation full-sib population developed by crossing Pietrain sires with a crossbred dam line. Depending on the trait, phenotypic observations were available for 306 to 315 F(2) animals. For the QTL analysis, 386 animals were genotyped for 88 molecular markers covering chromosomes SSC1, SSC2, SSC4, SSC6, SSC7, SSC8, SSC9, SSC10, SSC13, and SSC14. In total, 23 significant epistatic QTL pairs were identified, with the additive x additive genetic interaction being the most prevalent. Epistatic QTL were identified across all chromosomes except for SSC13, and epistatic QTL pairs accounted for between 5.8 and 10.2% of the phenotypic variance. Seven epistatic QTL pairs were between QTL that resided on the same chromosome, and 16 were between QTL that resided on different chromosomes. Sus scrofa chromosome 1, SSC2, SSC4, SSC6, SSC8, and SSC9 harbored the greatest number of epistatic QTL. The epistatic QTL pair with the greatest effect was for the entire loin weight between 2 locations on SSC7, explaining 10.2% of the phenotypic variance. Epistatic associations were identified between regions of the genome that contain the IGF-2 or melanocortin-4 receptor genes, with QTL residing in other genomic locations. Quantitative trait loci in the region of the melanocortin-4 receptor gene and on SSC7 showed significant positive dominance effects for entire belly weight, which were offset by negative dominance x dominance interactions between these QTL. In contrast, the QTL in the region of the IGF-2 gene showed significant negative dominance effects for entire ham weight, which were largely overcompensated for by positive additive x dominance genetic effects with a QTL on SSC9. The study shows that epistasis is of great importance for the genomic regulation of body composition in pigs and contributes substantially to the variation in complex traits.

Developing breeding schemes to assist mitigation of greenhouse gas emissions.

Genetic improvement of livestock is a particularly effective technology, producing permanent and cumulative changes in performance. This paper highlights some of the options for including mitigation in livestock breeding schemes, focusing on ruminant species, and details three routes through which genetic improvement can help to reduce emissions per kg product via: (i) improving productivity and efficiency, (ii) reducing wastage in the farming system and (iii) directly selecting on emissions, if or when these are measurable. Selecting on traits that improve the efficiency of the system (e.g. residual feed intake, longevity) will have a favourable effect on the overall emissions from the system. Specific examples of how genetic selection will have a favourable effect on emissions for UK dairy systems are described. The development of breeding schemes that incorporate environmental concerns is both desirable and possible. An example of how economic valuation of public good outcomes can be incorporated into UK dairy selection indices is given. This paper focuses on genetic selection tools using, on the whole, currently available traits and tools. However, new direct and indirect measurement techniques for emissions will improve the potential to reduce emissions by genetic selection. The complexities of global forces on defining selection objectives are also highlighted.

Predicting beef carcass composition using tissue weights of a primal cut assessed by computed tomography.

The potential of the composition of the forerib measured by X-ray computed tomography (CT) as a predictor of carcass composition was evaluated using data recorded on 30 Aberdeen Angus and 43 Limousin crossbred heifers and steers. The left sides of the carcasses were split into 20 cuts, which were CT scanned and fully dissected into fat, muscle and bone. Carcass and forerib tissue weights were assessed by dissection and CT. Carcass composition was assessed very accurately by CT scanning of the primal cuts (adj-R2 = 0.97 for the three tissues). CT scanning predicted weights of fat, muscle and bone of the forerib with adj-R2 of 0.95, 0.91 and 0.75, respectively. Single regression models with the weights of fat, muscle or bone in the forerib measured by CT as the only predictors to estimate fat, muscle or bone of the left carcass obtained by CT showed adjusted coefficients of determination (adj-R2) of 0.79, 0.60 and 0.52, respectively. By additionally fitting breed and sex, accuracy increased to 0.85, 0.73 and 0.67. Using carcass and forerib weights in addition to the previous predictors improved significantly the prediction accuracy of carcass fat and muscle weights to adj-R2 values of 0.92 and 0.96, respectively, while the highest value for carcass bone weight was 0.77. In general, equations derived using CT data had lower adj-R2 values for bone, but better accuracies for fat and muscle compared to those obtained using dissection. CT scanning could be considered as an alternative very accurate and fast method to assess beef carcass composition that could be very useful for breeding programmes and research studies involving a large number of animals, including the calibration of other indirect methods (e.g. in vivo and carcass video image analysis).

Genetic relationship between longevity and objectively or subjectively assessed performance traits in sheep using linear censored models.

Genetic parameters of longevity in crossbred Mule ewes, and genetic relationships among longevity, growth, body composition, and subjectively assessed traits on Mule lambs and ewes have been estimated using Bayesian linear censored models. Additionally, the genetic associations between longevity and culling reasons were examined. Data comprised 1,797 observations of Mule ewes for longevity, culling reasons, growth, body composition, mouth scores, and type traits. Longevity was defined as the time (in years) from 2 yr of age (the age at first lambing of most ewes) to culling or death. Censored data (i.e., observations for which only the lower bound of the true longevity is known, such as when the animals are still alive) comprised 24% of all observations for longevity. Bivariate analyses were used to analyze the longevity of the ewe with each performance trait by fitting linear Bayesian models considering censored observations. Longevity was split into 3 different sub-traits: age at culling due to teeth/mouth conditions, age at culling due to udder conditions, and age at culling due to other culling reasons. These sub-traits and their aggregation into the overall trait of longevity were analyzed in a multiple-trait model. The heritability of longevity was moderate at 0.27, whereas heritabilities of the growth and body composition traits ranged from 0.11 for average of shoulder, loin, and gigot conformation to 0.36 for ewe BW at first premating. Mouth scores and type traits had heritabilities ranging from 0.13 for jaw position to 0.39 for fleece quality. All analyzed traits showed low genetic correlations with longevity, ranging from -0.20 for average conformation scores in live animals to 0.18 for tooth angle. Teeth/mouth conditions resulted in the greatest heritability (0.15) among the sub-traits based on the separate culling reasons. Genetic correlations between separate culling reasons were low to high (0.12 to 0.63 for teeth/mouth conditions with udder conditions and other culling reasons, respectively). Longevity may be preferred as a selection criterion because of (i) its moderate heritability compared with its component sub-traits based on specific culling reasons, and (ii) its moderate to high genetic correlation with these component sub-traits. The moderate heritability for longevity reflects the potential of this trait for genetic improvement, especially when longevity is based on clearly defined culling reasons.

Predicting tissue distribution and partitioning in terminal sire sheep using x-ray computed tomography.

The utility of x-ray computed tomography (CT) scanning in predicting carcass tissue distribution and fat partitioning in vivo in terminal sire sheep was examined using data from 160 lambs representing combinations of 3 breeds (Charollais, Suffolk, and Texel), 3 genetic lines, and both sexes. One-fifth of the lambs were slaughtered at each of 14, 18, and 22 wk of age, and the remaining two-fifths at 26 wk of age. The left side of each carcass was dissected into 8 joints with each joint dissected into fat (intermuscular and subcutaneous), lean, and bone. Chemical fat content of the LM was measured. Tissue distribution was described by proportions of total carcass tissue and lean weight contained within the leg, loin, and shoulder regions of the carcass and within the higher-priced joints. Fat partitioning variables included proportion of total carcass fat contained in the subcutaneous depot and intramuscular fat content of the LM. Before slaughter, all lambs were CT scanned at 7 anatomical positions (ischium, midshaft of femur, hip, second and fifth lumbar vertebrae, sixth and eighth thoracic vertebrae). Areas of fat, lean, and bone (mm(2)) and average fat and lean density (Hounsfield units) were measured from each cross-sectional scan. Areas of intermuscular and subcutaneous fat were measured on 2 scans (ischium and eighth thoracic vertebra). Intramuscular fat content was predicted with moderate accuracy (R(2) = 56.6) using information from only 2 CT scans. Four measures of carcass tissue distribution were predicted with moderate to high accuracy: the proportion of total carcass (R(2) = 54.7) and lean (R(2) = 46.2) weight contained in the higher-priced joints and the proportion of total carcass (R(2) = 77.7) and lean (R(2) = 55.0) weight in the leg region. Including BW in the predictions did not improve their accuracy (P > 0.05). Although breed-line-sex combination significantly affected fit of the regression for some tissue distribution variables, the values predicted were changed only trivially. Within terminal sire type animals, using a common set of prediction equations is justified. Tissue distribution and fat partitioning affect eating satisfaction and efficiency of production and processing; therefore, including such carcass quality measures in selection programs is increasingly important, and CT scanning appears to provide opportunities to do so.