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.

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.

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.

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.

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.

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.

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.

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.

Evaluation of the laser methane detector to estimate methane emissions from ewes and steers.

The laser methane detector (LMD) has been proposed as a method to characterize enteric methane (CH4) emissions from animals in a natural environment. To validate LMD use, its CH4 outputs (LMD-CH4), were compared against CH4 measured with respiration chambers (chamber-CH4). The LMD was used to measure CH4 concentration (µL/L) in the exhaled air of 24 lactating ewes and 72 finishing steers. In ewes, LMD was used on 1 d for each ewe, for 2-min periods at 5 hourly observation periods (P1 to P5, respectively) after feeding. In steers fed either low- or high-concentrate diets, LMD was used once daily for a 4-min period for 3 d. The week after LMD-CH4 measurement, ewes or steers entered respiration chambers to quantify daily CH4 output (g/d). The LMD outputs consisted of periodic events of high CH4 concentrations superimposed on a background of oscillating lower CH4 concentrations. The high CH4 events were attributed to eructation and the lower background CH4 to respiration. After fitting a double normal distribution to the data set, a threshold of 99% of probability of the lower distribution was used to separate respiration from eructation events. The correlation between mean LMD-CH4 and chamber-CH4 was not high, and only improved correlations were observed after data were separated in 2 levels. In ewes, a model with LMD and DMI (adjusted R(2) = 0.92) improved the relationship between DMI and chamber-CH4 alone (adjusted R(2) = 0.79) and between LMD and chamber-CH4 alone (adjusted R(2) = 0.86). In both experiments, chamber-CH4 was best explained by models with length of eructation events (time) and maximum values of CH4 concentration during respiration events (µL/L; P < 0.01). Correlation between methods differed between observation periods, indicating the best results of the LMD were observed from 3 to 5 h after feeding. Given the short time and ease of use of LMD, there is potential for its commercial application and field-based studies. Although good indicators of quantity of CH4 were obtained with respiration and eructation CH4, the method needed to separate the data into high and low levels of CH4 was not simple to apply in practice. Further assessment of the LMD should be performed in relation to animal feeding behavior and physiology to validate assumptions of eructation and respiration levels, and other sources of variation should be tested (i.e., micrometeorology) to better investigate its potential application for CH4 testing in outdoor conditions.

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.

Genetic associations between behavioral traits and direct-social effects of growth rate in pigs.

This study examined the behavioral consequences of selecting pigs using a social genetic model for growth. Calculations enable each member of a group of pigs to be given a direct breeding value (DBV) and a social breeding value (SBV), which can be summarized into a total breeding value (TBV) for growth. Selection for growth TBV could affect animal behavior because social effects account for within-group interactions. Data were recorded from 96 groups of Yorkshire and Yorkshire × Landrace pigs in a nucleus herd. Each group contained 15 pigs fed ad libitum from 2 feeders; the space allowance was 0.85 m2/pig. Average daily gain was quantified from 35 to 100 kg of BW. Fighting and bullying activity at mixing (period 1), lying frequency 3 wk after mixing (period 2), and counts of skin lesions in periods 1 and 2 were recorded. The DBV for these traits were estimated with a classic animal model. We simulated different correlations between the direct genetic effect and the social genetic effect on growth rate (r(DS)), 2 components that respectively determine a pig's genetic capacity to grow and its genetic influence on growth of group mates: r(DS) was successively assumed to be 0 and ±0.12, ±0.20, ±0.29, and ±0.58. Finally, the correlations between DBV, SBV, and TBV for ADG, as well as the DBV for behavior and skin lesions, were calculated and tested for a level of significance at P < 0.05. The gradient from negative to positive values of r(DS) refers to a progressive path running from genetic antagonism to genetic mutualism for growth. If rDS in the population truly ranged between -0.58 and -0.20, correlations for TBV for ADG with DBV for fighting and bullying progressively increased with rDS. Consequently, if rDS was low (between -0.12 and +0.12) or positive (>+0.12), pigs with high TBV for ADG had higher DBV for bullying other pigs in the group and for fighting than pigs with lower TBV for ADG. Pigs with high TBV for ADG did not differ from other pigs in their DBV for lesions to the anterior part of the body, but they had a lower DBV for posterior lesions, whereas in period 2, they had higher DBV for posterior lesions and lower DBV for lying. Under genetic mutualism for growth and in housing conditions similar to those in the present study, selection for growth TBV would promote the rapid establishment of the dominance relationships, with more aggressive contests among group mates at mixing. Pigs would subsequently be more active but, judging by skin lesions, less willing to fight in a more stable social situation.

A review of the development and use of video image analysis (VIA) for beef carcass evaluation as an alternative to the current EUROP system and other subjective systems.

The current EUROP beef carcass classification scheme is still largely dependent on visually assessed fatness and conformation and its purpose is to provide a common basis for the description of carcasses for use in trade, price reporting and intervention. The meat industry, however, aims for accurately predicted saleable meat yield (SMY%) to which the EUROP carcass classification shows highly variable correlations due in part to the variable distribution of fat throughout the carcass as affected by breed, sex, diet, and the level of fat trimming. Video image analysis (VIA) technology is capable of improving the precision and accuracy of SMY% prediction even for specific carcass joints and simultaneously mimics the visual assessment to comply with EU regulations on carcass classification. This review summarises the development and use of VIA for evaluation of beef carcasses and discusses the advantages and shortfalls of the technology and its application.

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.

Nitrogen excretion at different stages of growth and its association with production traits in growing pigs.

The objectives of this study were to determine nitrogen loss at different stages of growth and during the entire growing period and to investigate the associations between nitrogen excretion and production traits in growing pigs. Data from 315 pigs of an F(2) population which originated from crossing Pietrain sires with a commercial dam line were used. Nitrogen retention was derived from protein retention as measured using the deuterium dilution technique during different stages of growth (60 to 90 kg, 90 to 120 kg, and 120 to 140 kg). Pigs were fed ad libitum with 2 pelleted diets containing 17% (60 to 90 kg) and 16.5% (90 to 120 and 120 to 140 kg) CP. Average daily nitrogen excretion (ADNE) within each stage of growth was calculated on the basis of the accumulated difference between average daily nitrogen intake (ADNI) and average daily nitrogen retention (ADNR). Least ADNE, nitrogen excretion per BW gain (NEWG) and total nitrogen excretion (TNE) were observed during growth from 60 to 90 kg. In contrast, the greatest ADNE, NEWG, and TNE were found during growth from 120 to 140 kg. Statistical analyses indicated that gender, housing type, the ryanodine receptor 1 (RYR1) gene, and batch influenced nitrogen excretion (P < 0.05), but the degree and direction of influences differed between growth stages. Gender differences showed that gilts excreted less nitrogen than barrows (P < 0.05), which was associated with decreased feed conversion ratio (FCR; feed:gain) and lipid:protein gain ratio. Single-housed pigs showed reduced nitrogen excretion compared with group-housed pigs (P < 0.05). In comparison to other genotypes, pigs carrying genotype NN (homozygous normal) at the RYR1 locus had the least nitrogen excretion (P < 0.05) at all stages of growth except from 60 to 90 kg. The residual correlations indicated that NEWG and TNE have large positive correlations with FCR (r = 0.99 and 0.91, respectively) and moderate negative correlations with ADG (r = -0.53 and -0.48, respectively), for the entire growing period. Improvement in FCR, increase in ADG and reduction in lipid:protein gain ratio by 1 phenotypic SD reduced TNE per pig by 709 g, 307 g, and 211 g, respectively, over the entire growing period. The results indicate that nitrogen excretion changes substantially during growth, and it can be reduced most effectively by improvement of feed efficiency and to a lesser extent through the improvement of BW gain or body composition or both.

Associations between response to handling and growth and meat quality in frequently handled Bos taurus beef cattle.

Fearful behavioral responses to handling (temperament) are undesirably associated with ADG and meat quality in infrequently handled Bos indicus cattle. It has never been assessed whether these relationships exist in calmer Bos taurus breeds in systems where handling is more frequent. Such systems predominate in some countries where beef production is a major agricultural activity. During fattening, 144 crossbred cattle from Limousin and Aberdeen Angus sires were assessed for temperament using 4 approaches: response to movement along a race (race score; 4 occasions), restraint in a crush (crush score; 4 occasions), flight speed from the crush (flight speed; 4 occasions), and isolation in a pen with a human (isolation score; 1 occasion in yr 1, 2 occasions in yr 2). Measurements of ADG were made between birth and slaughter and between 16 and 18 mo of age during fattening. Fattening occurred indoors on a complete mixed diet fed for ad libitum intake. Meat quality was measured by pH, color, and Volodkevitch shear force and by a sensory panel. The repeatability of temperament traits was 0.17 (race score), 0.35 (crush score), 0.51 (flight speed), and 0.36 (isolation score). The proportion of the total variance of temperament traits attributable to the sire and the social group was low (0.003 to 0.402). However, the sire did affect behavior in all tests apart from the crush score (ranging from P = 0.02 to P < 0.001). Correlations between behavior in the different tests (ranging from r = 0.21 to 0.54, and P = 0.02 to P < 0.001) apart from between-flight speed and isolation score indicate that fearful behavior was consistently shown across assessment methods. A calm response in the crush score test was associated with a greater ADG during fattening (P = 0.05), whereas a calm response during the isolation test was associated with a greater ADG in cold carcass weight (P = 0.02). Animals with a calm isolation score had less tender meat as judged by the sensory panel (P = 0.03), but no other effects were apparent between temperament and meat quality measures, although several tendencies (0.06 ≤ P ≤ 0.10) were found. Temperament did not appear to relate to meat quality in this study of frequently handled Bos taurus genotypes, which is in contrast to other studies using different beef production systems. Genetic correlations between temperament and meat quality under these conditions could, although not measured in this study, still exist in the absence of phenotypic correlations.

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.

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.