Taxonomic annotation of 16S rRNA sequences of pig intestinal samples using MG-RAST and QIIME2 generated different microbiota compositions.

Environmental microbiome studies rely on fast and accurate bioinformatics tools to characterize the taxonomic composition of samples based on the 16S rRNA gene. MetaGenome Rapid Annotation using Subsystem Technology (MG-RAST) and Quantitative Insights Into Microbial Ecology 2 (QIIME2) are two of the most popular tools available to perform this task. Their underlying algorithms differ in many aspects, and therefore the comparison of the pipelines provides insights into their best use and interpretation of the outcomes. Both of these bioinformatics tools are based on several specialized algorithms pipelined together, but whereas MG-RAST is a user-friendly webserver that clusters rRNA sequences based on their similarity to create Operational Taxonomic Units (OTU), QIIME2 employs DADA2 in the construction of Amplicon Sequence Variants (ASV) by applying an error model that considers the abundance of each sequence and its similarity to other sequences. Taxonomic compositions obtained from the analyses of amplicon sequences of DNA from swine intestinal gut and faecal microbiota samples using MG-RAST and QIIME2 were compared at domain-, phylum-, family- and genus-levels in terms of richness, relative abundance and diversity. We found significant differences between the microbiota profiles obtained from each pipeline. At domain level, bacteria were relatively more abundant using QIIME2 than MG-RAST; at phylum level, seven taxa were identified exclusively by QIIME2; at family level, samples processed in QIIME2 showed higher evenness and richness (assessed by Shannon and Simpson indices). The genus-level compositions obtained from each pipeline were used in partial least squares-discriminant analyses (PLS-DA) to discriminate between sample collection sites (caecum, colon and faeces). The results showed that different genera were found to be significant for the models, based on the Variable Importance in Projection, e.g. when using sequencing data processed by MG-RAST, the three most important genera were Acetitomaculum, Ruminococcus and Methanosphaera, whereas when data was processed using QIIME2, these were Candidatus Methanomethylophilus, Sphaerochaeta and Anaerorhabdus. Furthermore, the application of differential filtering procedures before the PLS-DA revealed higher accuracy when using non-restricted datasets obtained from MG-RAST, whereas datasets obtained from QIIME2 resulted in more accurate discrimination of sample collection sites after removing genera with low relative abundances (<1%) from the datasets. Our results highlight the differences in taxonomic compositions of samples obtained from the two separate pipelines, while underlining the impact on downstream analyses, such as biomarkers identification.

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.

Application of near infrared reflectance spectroscopy to predict meat and meat products quality: A review.

Over the past three decades, near infrared reflectance (NIR) spectroscopy has been proved to be one of the most efficient and advanced tools for the estimation of quality attributes in meat and meat products. This review focuses on the use of NIR spectroscopy to predict different meat properties, considering the literature published mainly in the last decade. Firstly, the potential of NIR to predict chemical composition (crude protein, intramuscular fat, moisture/dry matter, ash, gross energy, myoglobin and collagen), technological parameters (pH value; L*, a*, b* colour values; water holding capacity; Warner-Bratzler and slice shear force) and sensory attributes (colour, shape, marbling, odour, flavour, juiciness, tenderness or firmness) are reviewed. Secondly, the usefulness of NIR for classification into meat quality grades is presented and thirdly its potential application in the industry is shown. The review indicates that NIR showed high potential to predict chemical meat properties and to categorize meat into quality classes. In contrast, NIR showed limited ability for estimating technological and sensory attributes, which may be mainly due to the heterogeneity of the meat samples and their preparation, the low precision of the reference methods and the subjectivity of assessors in taste panels. Hence, future work to standardize sample preparation and increase the accuracy of reference methods is recommended to improve NIR ability to predict those technological and sensory characteristics. In conclusion, the review shows that NIR has a considerable potential to predict simultaneously numerous meat quality criteria.

Evaluation of Video Image Analysis (VIA) technology to predict meat yield of sheep carcasses on-line under UK abattoir conditions.

The Meat and Livestock Commission's (MLC) EUROP classification based scheme and Video Image Analysis (VIA) system were compared in their ability to predict weights of primal carcass joints. A total of 443 commercial lamb carcasses under 12 months of age and mixed gender were selected by their cold carcass weight (CCW), conformation and fat scores. Lamb carcasses were classified for conformation and fatness, scanned by the VIA system and dissected into primal joints of leg, chump, loin, breast and shoulder. After adjustment for CCW, the estimation of primal joints using MLC EUROP scores showed high coefficients of determination (R(2)) in the range of 0.82-0.99. The use of VIA always resulted in equal or higher R(2). The precision measured as root mean square error (RMSE) was 27% (leg), 13% (chump), 1% (loin), 11% (breast), 5% (shoulders) and 13% (total primals) higher using VIA than MLC carcass information. Adjustment for slaughter day and gender effects indicated that estimations of primal joints using MLC EUROP scores were more sensitive to these factors than using VIA. This was consistent with an increase in stability of the prediction model of 28%, 11%, 2%, 12%, 6% and 14% for leg, chump, loin, breast and shoulder and total primals, respectively, using VIA compared to MLC EUROP scores. Consequently, VIA was capable of improving the prediction of primal meat yields compared to the current MLC EUROP carcass classification scheme used in the UK abattoirs.

Prediction of lamb meat eating quality in two divergent breeds using various live animal and carcass measurements.

This study investigated how accurately taste panel sensory assessments of meat eating quality (MEQ) could be predicted in two divergent lamb breeds, using predictors measured in live animals (weights, subjective conformation assessments, ultrasound, computed tomography (CT) and video image analysis measurements) and carcasses (weights, MLC fat and conformation classes, pH, temperature, carcass dimensions and cross-sectional tissue dimensions), individually and in optimal combinations. Grilled muscle samples from the pelvic limb (semimembranosus) and loin (Longissimus lumborum) of 120 Texel (TEX) and 112 Scottish Blackface (SBF) lambs were assessed by a trained taste panel for texture, juiciness, flavour, abnormal flavour and overall liking. Residual correlations (adjusted for fixed effects, age and sire) between MEQ and predictor traits were low to moderate in size (<±0.42). MEQ traits predicted best by single measurements were loin flavour and overall liking for TEX (using fat area in a CT scan or subcutaneous fat depth measured post-mortem), and for SBF were leg texture (using carcass weight or temperature) and juiciness (using CT fat area or shoulder conformation score). Combining live animal and carcass measurements increased MEQ prediction accuracies, compared with using either set alone, to explain >40% of residual variation in several MEQ traits, with the highest adjusted R(2) values for leg juiciness in TEX (0.53) and leg texture in SBF (0.59). The most useful predictors of MEQ depended on breed, with measurements of fatness generally more important in the lean breed and carcass size and muscling more important in the fatter breed.

On-line application of visible and near infrared reflectance spectroscopy to predict chemical-physical and sensory characteristics of beef quality.

The aim of this study was to assess the on-line implementation of visible and near infrared reflectance (Vis-NIR) spectroscopy as an early predictor of beef quality traits, by direct application of a fibre-optic probe to the muscle immediately after exposing the meat surface in the abattoir. Samples from M.longissimus thoracis from 194 heifers and steers were scanned at quartering 48h postmortem over the Vis-NIR spectral range from 350 to 1800nm. Thereafter, samples from M.longissimus thoraciset lumborum were analysed for colour (L(∗), a(∗), b(∗); 48h postmortem), cooking loss (14 days postmortem), instrumental texture (Volodkevitch, 10 days aged meat; slice shear force, 3 and 14 days aged meat) and sensory characteristics. Vis-NIR calibrations, tested by cross-validation, showed high predictability for L(∗), a(∗) and b(∗) (R(2)=0.86, 0.86 and 0.91; SE(CV)=0.96, 0.95 and 0.69, respectively). The accuracy of Vis-NIR to estimate cooking loss and instrumental texture ranged from R(2)=0.31 to 0.54, suggesting relatively low prediction ability. Sensory characteristics assessed on 14 days aged meat samples showed R(2) in the range from 0.21 (juiciness) to 0.59 (flavour). Considering the subjective assessment of sensory characteristics the correlations of Vis-NIR measurements and several meat quality traits in the range from 0.46 to 0.95 support the use of on-line Vis-NIR in the abattoir. Improvement of predictability was achieved if only extreme classes of meat characteristics have to be predicted by Vis-NIR spectroscopy.

Quantitative trait loci for chemical body composition traits in pigs and their positional associations with body tissues, growth and feed intake.

In this study, quantitative trait loci (QTL) for chemical and physical body composition, growth and feed intake in pigs were identified in a three-generation full-sib population, developed by crossing Pietrain sires with a commercial dam line. Phenotypic data from 315 F(2) animals were available for protein and lipid deposition measured in live animals by the deuterium dilution technique at 30-, 60-, 90-, 120- and 140-kg body weight. At 140-kg body weight, carcass characteristics were measured by the AutoFOM grading system and after dissection. Three hundred and eighty-six animals from 49 families were genotyped for 51 molecular markers covering chromosomes SSC2, SSC4, SSC8, SSC9, SSC10 and SSC14. Novel QTL for protein (lipid) content at 60-kg body weight and protein (lipid) accretion from 120 to 140 kg were detected on SSC9 near several previously detected QTL for lean and fat tissue in neck, shoulder and ham cuts. Another QTL for lipid accretion was found on SSC8, closely associated with a QTL for intramuscular fat content. QTL for daily feed intake were detected on SSC2 and SSC10. The favourable allele of a QTL for food conversion ratio (FCR) on SSC2 was associated with alleles for increased lean tissue and decreased fat tissue. Because no QTL for growth rate were found in the region, the QTL for FCR is most likely due to a change in body composition. These QTL provide insights into the genomic regulation of chemical or physical body composition and its association with feed intake, feed efficiency and growth.

The use of various live animal measurements to predict carcass and meat quality in two divergent lamb breeds.

Live weight, subjective scores of condition and conformation, live animal video image analysis (LVIA), ultrasound and X-ray computed tomography (CT) scanning were used to investigate the best method or combination of methods for predicting carcass and meat quality traits in live Texel and Scottish Blackface lambs. Predictors derived from CT alone accounted for a high proportion of the variance in dissected fat and muscle weight in Texel lambs (adjusted R(2)=∼0.8), as well as intra-muscular fat content in the loin (∼0.6), but lower proportions in Blackface lambs (∼0.7 for fat, 0.4-0.5 for muscle and intra-muscular fat), after adjusting for sire and fixed effects. Adding traits measured by other in vivo methods increased prediction accuracies (adjusted R(2)) by up to 0.26, depending on trait and data set. Shear force and ultimate pH could not be accurately predicted using the traits considered here (adjusted R(2)<0.4). Although the same methods tended to be best for predicting product quality traits between breeds, prediction accuracies differed.

The effect of dietary addition of nitrate or increase in lipid concentrations, alone or in combination, on performance and methane emissions of beef cattle.

Adding nitrate to or increasing the concentration of lipid in the diet are established strategies for reducing enteric methane (CH4) emissions, but their effectiveness when used in combination has been largely unexplored. This study investigated the effect of dietary nitrate and increased lipid included alone or together on CH4 emissions and performance traits of finishing beef cattle. The experiment was a 2×4 factorial design comprising two breeds (cross-bred Aberdeen Angus (AAx) and cross-bred Limousin (LIMx) steers) and four dietary treatments (each based on 550 g forage : 450 g concentrate/kg dry matter (DM)). The four dietary treatments were assigned according to a 2×2 factorial design where the control treatment contained rapeseed meal as the main protein source, which was replaced either with nitrate (21.5 g nitrate/kg DM); maize distillers dark grains (MDDG, which increased diet ether extract from 24 to 37 g/kg DM) or both nitrate and MDDG. Steers (n=20/dietary treatment) were allocated to each of the four treatments in equal numbers of each breed with feed offered ad libitum. After 28 days adaptation to dietary treatments, individual animal intake, performance and feed efficiency were recorded for 56 days. Thereafter, CH4 emissions were measured over 13 weeks (six steers/week). Increasing dietary lipid did not adversely affect animal performance and showed no interactions with dietary nitrate. In contrast, addition of nitrate to diets resulted in poorer live-weight gain (P<0.01) and increased feed conversion ratio (P<0.05) compared with diets not containing nitrate. Daily CH4 output was lower (P<0.001) on nitrate-containing diets but increasing dietary lipid resulted in only a non-significant reduction in CH4. There were no interactions associated with CH4 emissions between dietary nitrate and lipid. Cross-bred Aberdeen Angus steers achieved greater live-weight gains (P<0.01), but had greater DM intakes (P<0.001), greater fat depth (P<0.01) and poorer residual feed intakes (P<0.01) than LIMx steers. Cross-bred Aberdeen Angus steers had higher daily CH4 outputs (P<0.001) but emitted less CH4 per kilogram DM intake than LIMx steers (P<0.05). In conclusion, inclusion of nitrate reduced CH4 emissions in growing beef cattle although the efficacy of nitrate was less than in previous work. When increased dietary lipid and nitrate inclusion were combined there was no evidence of an interaction between treatments and therefore combining different nutritional treatments to mitigate CH4 emissions could be a useful means of achieving reductions in CH4 while minimising any adverse effects.

Temperament and dominance relate to feeding behaviour and activity in beef cattle: implications for performance and methane emissions.

In beef cattle, feeding behaviour and activity are associated with feed efficiency and methane (CH4) emissions. This study aimed to understand the underlying traits responsible for the contribution of cattle behaviour to individual differences in feed efficiency, performance and CH4 emissions. A total of 84 steers (530±114 kg BW) of two different breeds (crossbreed Charolais and Luing) were used. The experiment was a 2×2×3 factorial design with breed, basal diets (concentrate v. mixed) and dietary treatments (no additive, calcium nitrate or rapeseed cake) as the main factors. The individual dry matter intake (DMI; kg) was recorded daily and the BW was measured weekly over a 56-day period. Ultrasound fat depth was measured on day 56. Based on the previous data, the indexes average daily gain, food conversion and residual feed intake (RFI) were calculated. The frequency of meals, the duration per visit and the time spent feeding per day were taken as feeding behaviour measures. Daily activity was measured using the number of steps, the number of standing bouts and the time standing per day. Agonistic interactions (including the number of contacts, aggressive interactions, and displacements per day) between steers at the feeders were assessed as indicators of dominance. Temperament was assessed using the crush score test (which measures restlessness when restrained) and the flight speed on release from restraint. Statistical analysis was performed using multivariate regression models. Steers that spent more time eating showed better feed efficiency (P=0.039), which can be due to greater secretion of saliva. Feeding time was longer with the mixed diet (P<0.001), Luings (P=0.009) and dominant steers (P=0.032). Higher activity (more steps) in the pen was associated with poorer RFI, possibly because of higher energy expenditure for muscle activity. Frequent meals contributed to a reduction in CH4 emissions per kg DMI. The meal frequency was higher with a mixed diet (P<0.001) and increased in more temperamental (P=0.003) and dominant (P=0.017) steers. In addition, feed intake was lower (P=0.032) in more temperamental steers. This study reveals that efficiency increases with a longer feeding time and CH4 emissions decrease with more frequent meals. As dominant steers eat more frequently and for longer, a reduction in competition at the feeder would improve both feed efficiency and CH4 emissions. Feed efficiency can also be improved through a reduction in activity. Selection for calmer cattle would reduce activity and increase feed intake, which may improve feed efficiency and promote growth, respectively.

Associations of DNA markers with meat quality traits in pigs with emphasis on drip loss.

Phenotypic information on 1155 market pigs for several pig meat quality traits, was collected. Genotypes on 12 DNA markers, including RYR1 and PRKAG3 I199V, were also obtained on all pigs to investigate the relationship between genetic markers and meat quality. The RYR1 gene had the highest impact on meat quality, however, several other markers showed significant effects on one or more traits. Animals heterozygous at the RYR1 locus were significantly inferior in almost all meat quality traits, except ultimate pH value, initial conductivity and redness of the meat. Drip loss from case-ready meat (measured from 1 to 7 days post-mortem) was 43% higher for heterozygotes than animals of the stress resistant genotype. The homozygous genotype II at position I199V of the PRKAG3 locus also resulted in less drip loss than genotypes IV and VV, regardless of the method and time of measurement. Furthermore, the favourable genotype related to higher ultimate pH and darker meat. Both loci significantly affected the intercept, linear and quadratic terms of fitted drip loss development curves. The favourable genotypes showed a lower drip loss after one day of measurement and a slower increase and a more linear development over time. Whilst the RYR1 and PRKAG3 markers influenced numerous meat quality traits, some of the other markers were also found to have significant effects on one or two meat quality traits. Markers at MC4R and HMGA1 loci significantly affected drip loss, whereas LDHA, CAST (Hpy188I) and ATP2A1 influenced pH value. In addition, the marker ATP2A1 was associated with variation in intramuscular fat content in M. longissimus dorsi. GLUT4 affected temperature 45min post-mortem and several markers (MC4R, LDHA, GLUT4, HMGA1, CAST (Hpy188I and PvuII)) influenced one or two of the different colour measurements. The markers at MC4R, CKM, AGRP, PRKAG3, and HMGA1 loci were tested for their interactions with RYR1 regarding drip loss. Only AGRP showed a significant interaction, but this was based on only a few animals with the homozygous genotype for one allele. Our results suggest that genetic markers provide a useful tool to improve meat quality in pigs independently from RYR1, especially the mutation I199V in the PRKAG3 gene.

The impact of divergent breed types and diets on methane emissions, rumen characteristics and performance of finishing beef cattle.

This study was undertaken to further develop our understanding of the links between breed, diet and the rumen microbial community and determine their effect on production characteristics and methane (CH4) emissions from beef cattle. The experiment was of a 2×2 factorial design, comprising two breeds (crossbred Charolais (CHX); purebred Luing (LU)) and two diets (concentrate-straw or silage-based). In total, 80 steers were used and balanced for sire within each breed, farm of origin and BW across diets. The diets (fed as total mixed rations) consisted of (g/kg dry matter (DM)) forage to concentrate ratios of either 500 : 500 (Mixed) or 79 : 921 (Concentrate). Steers were adapted to the diets over a 4-week period and performance and feed efficiency were then measured over a 56-day test period. Directly after the 56-day test, CH4 and carbon dioxide (CO2) emissions were measured (six steers/week) over a 13-week period. Compared with LU steers, CHX steers had greater average daily gain (ADG; P<0.05) and significantly (P<0.001) lower residual feed intake. Crossbred Charolais steers had superior conformation and fatness scores (P<0.001) than LU steers. Although steers consumed, on a DM basis, more Concentrate than Mixed diet (P<0.01), there were no differences between diets in either ADG or feed efficiency during the 56-day test. At slaughter, however, Concentrate-fed steers were heavier (P<0.05) and had greater carcass weights than Mixed-fed steers (P<0.001). Breed of steer did not influence CH4 production, but it was substantially lower when the Concentrate rather than Mixed diet was fed (P<0.001). Rumen fluid from Concentrate-fed steers contained greater proportions of propionic acid (P<0.001) and lower proportions of acetic acid (P<0.001), fewer archaea (P<0.01) and protozoa (P=0.09), but more Clostridium Cluster XIVa (P<0.01) and Bacteroides plus Prevotella (P<0.001) than Mixed-fed steers. When the CH4 to CO2 molar ratio was considered as a proxy method for CH4 production (g/kg DM intake), only weak relationships were found within diets. In conclusion, although feeding Concentrate and Mixed diets produced substantial differences in CH4 emissions and rumen characteristics, differences in performance were influenced more markedly by breed.

Drip loss of case-ready meat and of premium cuts and their associations with earlier measured sample drip loss, meat quality and carcass traits in pigs.

Drip loss of 374 samples taken from porcine M. longissimus dorsi and M. semimembranosus was measured by using the "bag method" (BM), EZ-DripLoss (EZ-DL) from premium cuts (PC) and in retail tray (case-ready meat; CRM). This provided a comparison between these methods and their relationships to other meat quality and carcass traits. Samples were prepared at 24h post-mortem (pm) and were measured 24 and 48h after preparation (at 48 and 72h pm) using the BM and after 48h (at 72h pm) with the EZ-DL and PC. Drip loss of meat kept in retail trays was measured after 7 days (CRM(7)) and daily within a week (CRM(1-7)). Average drip loss was 1.80% and 3.10% using the BM after 24 and 48h, respectively. EZ-DL and CRM(7) showed higher drip losses of 4.71% and 4.00%. Daily loss of CRM(1-7) showed a concavely shaped curve and increased from 1.57% to 5.64% after 7 days. High correlations were obtained between drip loss of CRM(7) and BM (r=0.88) or the EZ-DL (r=0.91). The development of drip loss in case-ready meat fitted by linear-quadratic regression (y=0.439+1.245x-0.072x(2)) showed that high drip loss measured earlier by bag and EZ-DripLoss methods was highly associated with a high intercept (r=0.63-0.72), a high linear increase (r=0.77-0.81), but larger decrease in increments (r=-0.82 to -0.86) during weekly stored meat in retail trays as supplied at consumer level. Because the positive linear regression coefficient was substantially higher than the negative quadratic regression coefficient, the development of drip loss is mainly dependent on the initial drip loss. Therefore, animals with high drip loss within 72h post-mortem also showed undesirable high drip loss curves over the entire retail period. Relationships between drip loss and other meat quality traits were similar for BM, EZ-DL and CRM(7). Of these the correlation between pH(24) and drip loss was highest with r=-0.54, -0.49 and -0.47 for BM, EZ-DL and CRMH(7), respectively. Interestingly, a correlation of r=-0.35 between blood pH value and CRML(7) was obtained. Carcass traits such as loin, ham, shoulder, belly weight or loin eye area showed only marginal correlations to drip loss. In conclusion, EZ-DL was the most appropriate method to predict drip loss of case-ready meat in retail trays and its development during a 7 day storage period.

Association between body composition of growing pigs determined by magnetic resonance imaging, deuterium dilution technique, and chemical analysis.

Development of body composition of 440 growing pigs from a three generation full-sib design to identify quantitative trait loci (QTL) was determined by three different methods. Firstly, the non-invasive method deuterium dilution technique (DT), was applied to all pigs in the experiment at six weights 20, 30, 60, 90, 120 and 140kg. Secondly, at each weight class, eight pigs were slaughtered and their entire body chemically analysed (CA). Thirdly, magnetic resonance imaging (MRI) was applied on 16 live pigs at different weights. For the entire empty body (without content of the gastrointestinal tract and bladder), allometric prediction equations to predict body composition from empty body water content measured by DT were derived from chemically analysed serial slaughtered pigs. These equations showed high correlations of 0.92, 0.90 and 0.85 for the contents of body water, fat-free substance as well as protein in fat-free substance, respectively. For the soft tissue (empty body without bones and viscera), allometric prediction equation of body composition based on DT and CA showed correlations of 0.91, 0.88 and 0.82 for water content, fat-free substance, and protein content of fat free substance, respectively. Fat tissue content, fat tissue mass, and lean tissue mass measured by MRI showed allometric relationships to lipid content, lipid mass, and protein mass determined by DT with correlations of 0.98, 0.87, and 0.98, respectively. Lean (measured by MRI) and protein (determined by DT) content of soft tissue was best fitted by a linear-quadratic polynomial and resulted in a correlation of 0.86. Allometric coefficients for change of percentages of chemical components, water (b=-0.036) and protein (b=0.106) in fat-free substance of empty body during growth were similar to those in the literature indicating the consistency of accretion rates of chemical components of the fat-free substance in different studies. Means for protein- and lipid-deposition rates (determined by DT) as well as lean tissue- and fat tissue-deposition rates (measured by MRI) ranged from 95 to 154, 147 to 328, 373 to 420 and 129 to 254g in the different weight ranges. Variation between animals in protein (lean tissue) and lipid (fat tissue) deposition rate was large which can be exploited in order to identify QTL of these traits.

Impact of adding nitrate or increasing the lipid content of two contrasting diets on blood methaemoglobin and performance of two breeds of finishing beef steers.

Adding nitrate to the diet or increasing the concentration of dietary lipid are effective strategies for reducing enteric methane emissions. This study investigated their effect on health and performance of finishing beef cattle. The experiment was a two×two×three factorial design comprising two breeds (CHX, crossbred Charolais; LU, Luing); two basal diets consisting of (g/kg dry matter (DM), forage to concentrate ratios) 520 : 480 (Mixed) or 84 : 916 (Concentrate); and three treatments: (i) control with rapeseed meal as the main protein source replaced with either (ii) calcium nitrate (18 g nitrate/kg diet DM) or (iii) rapeseed cake (RSC, increasing acid hydrolysed ether extract from 25 to 48 g/kg diet DM). Steers (n=84) were allocated to each of the six basal diet×treatments in equal numbers of each breed with feed offered ad libitum. Blood methaemoglobin (MetHb) concentrations (marker for nitrate poisoning) were monitored throughout the study in steers receiving nitrate. After dietary adaptation over 28 days, individual animal intake, performance and feed efficiency were recorded for a test period of 56 days. Blood MetHb concentrations were low and similar up to 14 g nitrate/kg diet DM but increased when nitrate increased to 18 g nitrate/kg diet DM (P0.05). Neither basal diet nor treatment affected carcass quality (P>0.05), but CHX steers achieved a greater killing out proportion (P<0.001) than LU steers. Thus, adding nitrate to the diet or increasing the level of dietary lipid through the use of cold-pressed RSC, did not adversely affect health or performance of finishing beef steers when used within the diets studied.

Prediction of reduction in aggressive behaviour of growing pigs using skin lesion traits as selection criteria.

Aggression at regrouping is a common issue in pig farming. Skin lesions are genetically and phenotypically correlated with aggression and have been shown to have a significant heritable component. This study predicts the magnitude of reduction in complex aggressive behavioural traits when using lesion numbers on different body regions at two different time points as selection criteria, to identify the optimum skin lesion trait for selection purposes. In total, 1146 pigs were mixed into new social groups, and skin lesions were counted 24 h (SL24h) and 3 weeks (SL3wk) post-mixing, on the anterior, centre and posterior regions of the body. An animal model was used to estimate genetic parameters for skin lesion traits and 14 aggressive behavioural traits. Estimated breeding values (EBVs) and phenotypic values were scaled and standardised to allow direct comparison across multiple traits. Individuals with SL24h and SL3wk EBVs in the least aggressive 10% of the population were compared with the population mean to predict the expected genetic and phenotypic response in aggressive behaviour to selection. At mixing, selection for low anterior lesions was predicted to affect substantially more behavioural traits of aggressiveness than lesions obtained on other body parts, with EBVs between -0.21 and -1.17 SD below the population mean. Individuals with low central SL24h EBVs also had low EBVs for aggressive traits (-0.33 to -0.55). Individuals with high SL3wk EBVs had low EBVs for aggression at mixing (between -0.24 and -0.53 SD below the population mean), although this was predicted to affect fewer traits than selection against SL24h. These results suggest that selection against anterior SL24h would result in the greatest genetic and phenotypic reduction in aggressive behaviour recorded at mixing. Selection for increased SL3wk was predicted to reduce aggression at mixing; however, current understanding about aggressive behaviour under stable social conditions is insufficient to recommend using this trait for selection purposes.

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 associations of short- and long-term aggressiveness identified by skin lesion with growth, feed efficiency, and carcass characteristics in growing pigs.

The objective of this study was to investigate the genetic relationships between skin lesion traits in group housed growing pigs as a measure of short- (in a newly mixed group) and long- (in a socially stable group) term aggression and commonly used commercial performance measures: growth, feed intake, feed efficiency, and carcass traits. Data on 2,413 growing pigs (138 groups) were available. Pigs were mixed into new social groups of 18 animals, and skin lesions were counted 24 h (SL24h) and 5 wk (SL5wk) postmixing. The animal model was used to estimate genetic parameters for skin lesion traits, test daily gain, lifetime daily gain, daily feed intake, feed efficiency (calculated as test daily gain divided by daily feed intake), loin depth, back fat, and HCW. Skin lesions had a heritable component, ranging from 0.08 for anterior SL24h to 0.22 for central SL5wk and would, therefore, be suitable as a method of phenotyping aggression for selection purposes. Significant positive genetic correlations were found between SL24h and SL5wk (0.46 to 0.81). Positive genetic correlations were also found between SL24h (central and posterior body regions) or SL5wk (all body regions) and the production traits lifetime daily gain, test daily gain, and HCW (0.29 to 0.54). Central SL24h, anterior SL5wk, and posterior SL5wk were found to correlate positively with feed efficiency (0.39 to 0.50), suggesting that pigs with more lesions convert feed more efficiently. Where significant, the magnitude of phenotypic correlations was low but positive (0.07 to 0.10). These results suggest that, genetically, animals that receive many lesions show improved performance compared to those with few lesions, except for anterior SL24h, which had previously been shown to be genetically positively correlated with the initiation of nonreciprocal attacks. It may, therefore, be possible, via selection against anterior skin lesions at mixing, to reduce this form of 1-sided aggression without adversely affecting production traits.

Effectiveness of nitrate addition and increased oil content as methane mitigation strategies for beef cattle fed two contrasting basal diets.

The objectives of this study were to investigate the effects of (1) the addition of nitrate and (2) an increase in dietary oil on methane (CH4) and hydrogen (H2) emissions from 2 breeds (cross-bred Charolais and purebred Luing) of finishing beef cattle receiving 2 contrasting basal diets consisting (grams per kilogram DM) of 500:500 (Mixed) and 80:920 (Concentrate) forage to concentrate ratios. Within each basal diet there were 3 treatments: (i) control treatments (mixed-CTL and concentrate-CTL) contained rapeseed meal as the protein source, which was replaced with either (ii) calcium nitrate (mixed-NIT and concentrate-NIT) supplying 21.5 g nitrate/kg DM, or (iii) rapeseed cake (mixed-RSC and concentrate-RSC) to increase dietary oil from 27 (CTL) to 53 g/kg DM (RSC). Following adaption to diets, CH4 and H2 emissions were measured on 1 occasion from each of the 76 steers over a 13-wk period. Dry matter intakes tended (P = 0.051) to be greater for the concentrate diet than the mixed diet; however, when expressed as grams DMI per kilogram BW, there was no difference between diets (P = 0.41). Dry matter intakes for NIT or RSC did not differ from CTL. Steers fed a concentrate diet produced less CH4 and H2 than those fed a mixed diet (P < 0.001). Molar proportions of acetate (P < 0.001) and butyrate (P < 0.01) were lower and propionate (P < 0.001) and valerate (P < 0.05) higher in the rumen fluid from steers fed the concentrate diet. For the mixed diet, CH4 yield (grams per kilogram DMI) was decreased by 17% when nitrate was added (P < 0.01), while H2 yield increased by 160% (P < 0.001). The addition of RSC to the mixed diet decreased CH4 yield by 7.5% (P = 0.18). However, for the concentrate diet neither addition of nitrate (P = 0.65) nor increasing dietary oil content (P = 0.46) decreased CH4 yield compared to concentrate-CTL. Molar proportions of acetate were higher (P < 0.001) and those of propionate lower (P < 0.01) in rumen fluid from NIT treatments compared to respective CTL treatments. Overall, reductions in CH4 emissions from adding nitrate or increasing the oil content of the mixed diet were similar to those expected from previous reports. However, the lack of an effect of these mitigation strategies when used with high concentrate diets has not been previously reported. This study shows that the effect of CH4 mitigation strategies is basal diet-dependent.

Genetic determination of individual birth weight and its association with sow productivity traits using Bayesian analyses.

Genetic association between individual birth weight (IBW) and litter birth weight (LBW) was analyzed on records of 14,950 individual pigs born alive between 1988 and 1994 at the pig breeding farm of the University of Kiel. Dams were from three purebred lines (German Landrace, German Edelschwein, and Large White) and their crosses. Phenotypically, preweaning mortality of pigs decreased substantially from 40% for pigs with < or = 1 kg weight to less than 7% for pigs with > 1.6 kg. For these low to high birth weight categories, preweaning growth (d 21 of age) and early postweaning growth (weaning to 25 kg) increased by more than 28 and 8% per day, respectively. Bayesian analysis was performed based on direct-maternal effects models for IBW and multiple-trait direct effects models for number of pigs born in total (NOBT) and alive (NOBA) and LBW. Bayesian posterior means for direct and maternal heritability and litter proportion of variance in IBW were .09, .26, and .18, respectively. After adjustment for NOBT, these changed to .08, .22, and .09, respectively. Adjustment for NOBT reduced the direct and maternal genetic correlation from -.41 to -.22. For these direct-maternal correlations, the 95% highest posterior density intervals were -.75 to -.07, and -.58 to .17 before and after adjustment for NOBT. Adjustment for NOBT was found to be necessary to obtain unbiased estimates of genetic effects for IBW. The relationship between IBW and NOBT, and thus the adjustment, was linear with a decrease in IBW of 44 g per additionally born pig. For litter traits, direct heritabilities were .10, .08, and .08 for NOBT, NOBA, and LBW, respectively. After adjustment of LBW for NOBA the heritability changed to .43. Expected variance components for LBW derived from estimates of IBW revealed that genetic and environmental covariances between full-sibs and variation in litter size resulted in the large deviation of maternal heritability for IBW and its equivalent estimate for LBW. These covariances among full-sibs could not be estimated if only LBW were recorded. Therefore, selection for increased IBW is recommended, with the opportunity to improve both direct and maternal genetic effects of birth weight of pigs and, thus, their vitality and pre- and postnatal growth.