Correction to: A bivariate genomic model with additive, dominance and inbreeding depression effects for sire line and three-way crossbred pigs.

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A bivariate genomic model with additive, dominance and inbreeding depression effects for sire line and three-way crossbred pigs.

BACKGROUND: Crossbreeding is widely used in pig production because of the benefits of heterosis effects and breed complementarity. Commonly, sire lines are bred for traits such as feed efficiency, growth and meat content, whereas maternal lines are also bred for reproduction and longevity traits, and the resulting three-way crossbred pigs are used for production of meat. The most important genetic basis for heterosis is dominance effects, e.g. removal of inbreeding depression. The aims of this study were to (1) present a modification of a previously developed model with additive, dominance and inbreeding depression genetic effects for analysis of data from a purebred sire line and three-way crossbred pigs; (2) based on this model, present equations for additive genetic variances, additive genetic covariance, and estimated breeding values (EBV) with associated accuracies for purebred and crossbred performances; (3) use the model to analyse four production traits, i.e. ultra-sound recorded backfat thickness (BF), conformation score (CONF), average daily gain (ADG), and feed conversion ratio (FCR), recorded on Danbred Duroc and Danbred Duroc-Landrace-Yorkshire crossbred pigs reared in the same environment; and (4) obtain estimates of genetic parameters, additive genetic correlations between purebred and crossbred performances, and EBV with associated accuracies for purebred and crossbred performances for this data set. RESULTS: Additive genetic correlations (with associated standard errors) between purebred and crossbred performances were equal to 0.96 (0.07), 0.83 (0.16), 0.75 (0.17), and 0.87 (0.18) for BF, CONF, ADG, and FCR, respectively. For BF, ADG, and FCR, the additive genetic variance was smaller for purebred performance than for crossbred performance, but for CONF the reverse was observed. EBV on Duroc boars were more accurate for purebred performance than for crossbred performance for BF, CONF and FCR, but not for ADG. CONCLUSIONS: Methodological developments led to equations for genetic (co)variances and EBV with associated accuracies for purebred and crossbred performances in a three-way crossbreeding system. As illustrated by the data analysis, these equations may be useful for implementation of genomic selection in this system.

Genome-wide association and pathway analysis of feed efficiency in pigs reveal candidate genes and pathways for residual feed intake.

Residual feed intake (RFI) is a complex trait that is economically important for livestock production; however, the genetic and biological mechanisms regulating RFI are largely unknown in pigs. Therefore, the study aimed to identify single nucleotide polymorphisms (SNPs), candidate genes and biological pathways involved in regulating RFI using Genome-wide association (GWA) and pathway analyses. A total of 596 Yorkshire boars with phenotypes for two different measures of RFI (RFI1 and 2) and 60k genotypic data was used. GWA analysis was performed using a univariate mixed model and 12 and 7 SNPs were found to be significantly associated with RFI1 and RFI2, respectively. Several genes such as xin actin-binding repeat-containing protein 2 (XIRP2),tetratricopeptide repeat domain 29 (TTC29),suppressor of glucose, autophagy associated 1 (SOGA1),MAS1,G-protein-coupled receptor (GPCR) kinase 5 (GRK5),prospero-homeobox protein 1 (PROX1),GPCR 155 (GPR155), and FYVE domain containing the 26 (ZFYVE26) were identified as putative candidates for RFI based on their genomic location in the vicinity of these SNPs. Genes located within 50 kbp of SNPs significantly associated with RFI and RFI2 (q-value ≤ 0.2) were subsequently used for pathway analyses. These analyses were performed by assigning genes to biological pathways and then testing the association of individual pathways with RFI using a Fisher's exact test. Metabolic pathway was significantly associated with both RFIs. Other biological pathways regulating phagosome, tight junctions, olfactory transduction, and insulin secretion were significantly associated with both RFI traits when relaxed threshold for cut-off p-value was used (p ≤ 0.05). These results implied porcine RFI is regulated by multiple biological mechanisms, although the metabolic processes might be the most important. Olfactory transduction pathway controlling the perception of feed via smell, insulin pathway controlling food intake might be important pathways for RFI. Furthermore, our study revealed key genes and genetic variants that control feed efficiency that could potentially be useful for genetic selection of more feed efficient pigs.

Prediction of enteric methane emissions from cattle.

Agriculture has a key role in food production worldwide and it is a major component of the gross domestic product of several countries. Livestock production is essential for the generation of high quality protein foods and the delivery of foods in regions where animal products are the main food source. Environmental impacts of livestock production have been examined for decades, but recently emission of methane from enteric fermentation has been targeted as a substantial greenhouse gas source. The quantification of methane emissions from livestock on a global scale relies on prediction models because measurements require specialized equipment and may be expensive. The predictive ability of current methane emission models remains poor. Moreover, the availability of information on livestock production systems has increased substantially over the years enabling the development of more detailed methane prediction models. In this study, we have developed and evaluated prediction models based on a large database of enteric methane emissions from North American dairy and beef cattle. Most probable models of various complexity levels were identified using a Bayesian model selection procedure and were fitted under a hierarchical setting. Energy intake, dietary fiber and lipid proportions, animal body weight and milk fat proportion were identified as key explanatory variables for predicting emissions. Models here developed substantially outperformed models currently used in national greenhouse gas inventories. Additionally, estimates of repeatability of methane emissions were lower than the ones from the literature and multicollinearity diagnostics suggested that prediction models are stable. In this context, we propose various enteric methane prediction models which require different levels of information availability and can be readily implemented in national greenhouse gas inventories of different complexity levels. The utilization of such models may reduce errors associated with prediction of methane and allow a better examination and representation of policies regulating emissions from cattle.

Animal production for efficient phosphate utilization: from optimized feed to high efficiency livestock.

Phosphorus (P) is an essential nutrient for livestock but its efficiency of utilization is below 40%, contributing to environmental issues. In this review, we summarize recent approaches to optimize P availability in livestock diets and improve its utilization efficiency. Phase feeding could potentially reduce P excretion by 20%. Addition of phytase enzymes to diets increased P availability from 42 to 95%. Low phytate transgenic plants and transgenic animals increased P availability by 14% and 52-99%, respectively. In practice, a combination of phase feeding and enzymes has the highest potential for P reduction but legislation and ethics implications will prevent using transgenic animals in the short term. Functional and nutritional genomics may provide tools to improve efficiency in the future.

Evaluation of coronary band temperatures in healthy horses.

OBJECTIVE: To measure coronary band temperature (CBT) in healthy horses fed high-fructan or low-carbohydrate diets and to analyze the association of CBT with diet, time of day, and ambient temperature. ANIMALS: 6 healthy horses. PROCEDURES: Horses were fed 3 diets (treatment 1, 1 g of fructan/kg fed daily in the morning; treatment 2, 1 g of fructan/kg fed daily in the afternoon; and treatment 3, a low-carbohydrate [7.2%] diet) in a 3 × 3 Latin square study design. For each horse, the CBT of all 4 limbs as well as rectal and ambient temperatures were recorded by use of infrared thermometry and standard thermometers hourly from 8 am to 10 pm for 4 consecutive days after the initiation of each diet. Each horse received each diet, and there was a 10-day washout period between each diet change. Data were analyzed by use of a mixed linear model. RESULTS: 4,320 CBTs were obtained from the 6 horses. The CBT ranged from 9.6° to 35.5°C. Coronary band temperature followed a diurnal pattern and was positively associated with ambient temperature but was not associated with diet. CONCLUSIONS AND CLINICAL RELEVANCE: CBT of healthy horses varied significantly during the day and among limbs. These results should be considered whenever increased CBT is used as an indication of incipient laminitis or in other clinical investigations.

Quantitative computed tomography evaluation of pulmonary disease.

Objective assessment of pulmonary disease from computed tomography (CT) examinations is desirable but difficult. When such assessments can be made, it is important that they are related to some part of the pathophysiologic process present. Herein we propose that automated volume histogram analysis can yield data that allow differentiation of normal from abnormal lung, and that the magnitude of disease will have an association with objective CT indices. Data from pulmonary CT images from 34 foxes (six uninfected controls and 28 infected with Angiostrongylus vasorum, subdivided by age and infective dose) were available. Lung tissue was segmented from surrounding tissue using an automated segmentation method. A volume histogram showing voxel frequency for each CT number in the range -1024 to -250 HU was created from the entire image stack from each fox. Using these data, the inter-quartile range and the CT number at the 95th percentile were determined. The results showed that segmentation could be readily achieved but that areas of severely diseased lung were excluded. Based on two-way analysis of variance for both the inter-quartile range and the CT number at the 95th percentile, both quantities were significantly affected by the infection status of the animal and were related to worm burden (P < 0.001). The study shows that this form of analysis is readily achieved and provides quantitative data that can be used to assess disease severity, progression, and response to treatment.

Hounsfield Unit dynamics of adipose tissue and non-adipose soft tissues in growing pigs.

Changes in the Hounsfield Unit value of adipose tissue and of non-adipose soft tissue during growth are poorly documented. This study examines the HU of these tissues in growing pigs. Computer tomography scans were made in nine growing pigs on three occasions, approximately four weeks apart. Average body weight was 51, 94, and 121 kg for each successive scan. Images from the level of the diaphragm to the hips were analyzed. The mean HU and its standard deviation, for adipose tissue and for non-adipose soft tissues was determined for each pig. The mean adipose tissue HU for all pigs was -90, -98 and -101 on the first, middle and last scans, respectively. Corresponding HU values for non-adipose soft tissues were, 52, 51 and 49. There was a significant difference (p<0.01) between HU at each scan time for each set of tissues.

Changes in the relative thickness of individual subcutaneous adipose tissue layers in growing pigs.

BACKGROUND: The thickness of the subcutaneous fat layer is an important parameter at all stages of pig production. It is used to inform decisions on dietary requirements to optimize growth, in gilts to promote longevity and finally to assist in the calculation of payments to producers that allow for general adiposity. Currently for reasons of tradition and ease, total adipose thickness measurements are made at one or multiple sites although it has been long recognized that up to three well defined layers (outer (L1), middle (L2), and inner (L3)) may be present to make up the total. Various features and properties of these layers have been described. This paper examines the contribution of each layer to total adipose thickness at three time points and describes the change in thickness of each layer per unit change in body weight in normal growing pigs. METHODS: A group of nine pigs was examined using 14 MHz linear array transducer on three separate occasions. The average weight was 51, 94 and 124 kg for each successive scan. The time between scanning was approximately 4 weeks. The proportion of each layer to total thickness was modeled statistically with scan session as a variable and the change in absolute thickness of each layer per unit change in body weight was modeled in a random regression model. RESULTS: There was a significant change in ratios between scans for the middle and inner layers (P < 0.001). The significant changes were seen between the first and second, and between the first and final, scan sessions. The change in thickness per unit change in body weight was greatest for L2, followed by L1 and L3. CONCLUSION: These results demonstrate that subcutaneous adipose layers grow at different rates relative to each other and to change in body weight and indicate that ultrasound can be used to track these differences.