Emerging issues in genomic selection

Genomic selection (GS) is now practiced successfully across many species. However, many questions remain, such as long-term effects, estimations of genomic parameters, robustness of genome-wide association study (GWAS) with small and large datasets, and stability of genomic predictions. This study summarizes presentations from the authors at the 2020 American Society of Animal Science (ASAS) symposium. The focus of many studies until now is on linkage disequilibrium between two loci. Ignoring higher-level equilibrium may lead to phantom dominance and epistasis. The Bulmer effect leads to a reduction of the additive variance; however, the selection for increased recombination rate can release anew genetic variance. With genomic information, estimates of genetic parameters may be biased by genomic preselection, but costs of estimation can increase drastically due to the dense form of the genomic information. To make the computation of estimates feasible, genotypes could be retained only for the most important animals, and methods of estimation should use algorithms that can recognize dense blocks in sparse matrices. GWASs using small genomic datasets frequently find many marker-trait associations, whereas studies using much bigger datasets find only a few. Most of the current tools use very simple models for GWAS, possibly causing artifacts. These models are adequate for large datasets where pseudo-phenotypes such as deregressed proofs indirectly account for important effects for traits of interest. Artifacts arising in GWAS with small datasets can be minimized by using data from all animals (whether genotyped or not), realistic models, and methods that account for population structure. Recent developments permit the computation of P-values from genomic best linear unbiased prediction (GBLUP), where models can be arbitrarily complex but restricted to genotyped animals only, and single-step GBLUP that also uses phenotypes from ungenotyped animals. Stability was an important part of nongenomic evaluations, where genetic predictions were stable in the absence of new data even with low prediction accuracies. Unfortunately, genomic evaluations for such animals change because all animals with genotypes are connected. A top-ranked animal can easily drop in the next evaluation, causing a crisis of confidence in genomic evaluations. While correlations between consecutive genomic evaluations are high, outliers can have differences as high as 1 SD. A solution to fluctuating genomic evaluations is to base selection decisions on groups of animals. Although many issues in GS have been solved, many new issues that require additional research continue to surface.     

Comparative pharmacokinetics and pharmacokinetic/pharmacodynamic analysis by nonlinear mixed‐effects modeling of cefquinome in nonpregnant,pregnant, and lactating goats after intravenous and intramuscular administration

Cefquinome is a fourth‐generation cephalosporin that is used empirically in goats. Different physiologic factors like pregnancy or lactation could determine the pharmacokinetic behavior of drugs in the organism. The objectives of this study are to (a) compare the pharmacokinetics of cefquinome after intravenous and intramuscular administration in adult nonpregnant (n = 6), pregnant (n = 6), and lactating goats (n = 6), at a dose of 2 mg/kg, with rich sampling by nonlinear mixed‐effects modeling, (b) conduct a pharmacokinetic/pharmacodynamic analysis to evaluate the efficacy of the recommended posology in goats with different physiological states, and (c) determine the optimal posology that achieve a PTA value ≥ 90%, taking into account a T > MIC ≥ 60% of a MIC value ≤ 0.25 µg/ml, in the different subpopulations of goats for both routes. Gestation significantly increased Ka and V1, while reduced F0, Cl, and Q. On the other hand, lactation significantly increased V1 and reduced Tk0. Cefquinome concentrations achieved in placental cotyledon, amniotic fluid, and fetal serum indicate a minimal penetration across the placental barrier. Moreover, milk penetration of cefquinome was minimal. The total body clearance of cefquinome for goats was 0.29 L kg^?1 hr^?1, that is apparently higher than the reported for cows (0.13 L kg^?1 hr^?1) and pigs (0.16 L kg^?1 hr^?1). So, the optimal dose regimen for cefquinome after intravenous and intramuscular administration required higher dose and frequency of administration compared with recommendations for cows or pigs. Therefore, 2 mg kg^?1 8 hr^?1 and 5 mg kg^?1 12 hr^?1 could be used for IV and IM routes, respectively, for the treatment of respiratory infections caused by P. multocida and M. haemolytica, but only 5 mg kg^?1 12 hr^?1 by both routes should be recommended for Escherichia coli infections.     

Gastrointestinal parasitism reduces the plasma availability of doramectin in lambs

A study was undertaken to investigate the effect of parasitism on plasma availability and pharmacokinetic behaviour of doramectin (DRM) in lambs. Fourteen parasitised grey face Suffolk lambs (26.9 ± 1.5 kg bodyweight) were selected for the study. Seven pairs of lambs were allocated to two groups to obtain an approximately even weight distribution. Group I (non-parasitised) was pre-treated with three repeated administrations of 5 mg/kg fenbendazole to maintain a parasite free condition. In group II (parasitised), the lambs did not receive any anthelmintic treatment. After the 85-day pre-treatment period, both groups of animals were treated with DRM by subcutaneous (SC) injection in the shoulder area at 200 μg/kg. Throughout the experimental period, both groups were maintained together under similar feeding and management conditions. Blood samples were collected by jugular venepuncture at different set times between 0.5 h and 60 days post-treatment. After plasma extraction and derivatisation, samples were analysed by high performance liquid chromatography (HPLC) with fluorescence detection. A computerised kinetic analysis was performed and the data were compared using the Student’s paired t test.The parent molecule was detected in plasma between 30 min and either day 20 (parasitised) or day 35 (non-parasitised) post-DRM treatment. The AUC values of the parasitised group (143.0 ± 18 ng d/mL) were significantly lower (P < 0.05) than those observed in the parasitically naïve animals (229.6 ± 21.7 ng d/mL). The mean residence time (MRT) in the parasitised group (3.4 ± 0.3 days) was significantly shorter (P < 0.05) than in the healthy group (6.6 ± 0.6 days). Study results have shown that parasitic disease, through alteration in the body condition, can produce significant changes in the plasma disposition of DRM when administered SC to parasitised lambs.     

Evaluation of different doses of propofol in xylazine pre-medicated horses

Objective To characterize responses to different doses of propofol in horses pre‐medicated with xylazine. Animals Six adult horses (five females and one male). Methods Each horse was anaesthetized four times with either ketamine or propofol in random order at 1‐week intervals. Horses were pre‐medicated with xylazine (1.1 mg kg^?1 IV over a minute), and 5 minutes later anaesthesia was induced with either ketamine (2.2 mg kg^?1 IV) or propofol (1, 2 and 4 mg kg^?1 IV; low, medium and high doses, respectively). Data were collected continuously (electrocardiogram) or after xylazine administration and at 5, 10 and 15 minutes after anaesthetic induction (arterial pressure, respiratory rate, pH, PaO₂, PaCO₂ and O₂ saturation). Anaesthetic induction and recovery were qualitatively and quantitatively assessed. Results Differences in the quality of anaesthesia were observed; the low dose of propofol resulted in a poorer anaesthetic induction that was insufficient to allow intubation, whereas the high dose produced an excellent quality of induction, free of excitement. Recorded anaesthesia times were similar between propofol at 2 mg kg^?1 and ketamine with prolonged and shorter recovery times after the high and low dose of propofol, respectively (p < 0.05; ketamine, 38 ± 7 minutes; propofol 1 mg kg^?1, 29 ± 4 minutes; propofol 2 mg kg^?1, 37 ± 5 minutes; propofol 4 mg kg^?1, 50 ± 7 minutes). Times to regain sternal and standing position were longest with the highest dose of propofol (32 ± 5 and 39 ± 7 minutes, respectively). Both ketamine and propofol reversed bradycardia, sinoatrial, and atrioventricular blocks produced by xylazine. There were no significant alterations in blood pressure but respiratory rate, and PaO₂ and O₂ saturation were significantly decreased in all groups (p < 0.05). Conclusion The anaesthetic quality produced by the three propofol doses varied; the most desirable effects, which were comparable to those of ketamine, were produced by 2 mg kg^?1 propofol.     

Effect of two thermal regimes on the muscle growth dynamics of sea bass larvae,Dicentrarchus labrax L

Muscle growth was studied in larvae of sea bass, Dicentrarchus labrax L., reared at two temperatures: real ambient temperature ( congruent with 15 degrees C during vitelline phase and increased gradually) and 19 degrees C from fertilization until the end of larval development. Muscle cellularity, body length and body weight were measured. Early temperature influenced larval development and so, pre-larval phase finished earlier at 19 degrees C than at ambient temperature (4 and 6 days, respectively). Temperature also affected muscle growth such that at hatching and at mouth opening hypertrophy of muscle fibres was greater at 19 degrees C (P < 0.05), whereas hyperplasia was similar in both groups. After 25 days, the cross-sectional area of the white muscle was greater at 19 degrees C (P < 0.05), which was mainly associated with a higher proliferation of new white muscle fibres. At this stage the body length was also higher at 19 degrees C. Metamorphosis finished earlier in fish reared at 19 degrees C (52 days) than at natural temperature (82 days). At this developmental stage body length and cross-sectional area of the myotome were similar in both groups. However, muscle cellularity differed between groups. Thus, hypertrophy of muscle fibres was higher in fish reared at ambient temperature (P < 0.05), whereas proliferation of new muscle fibres was higher at 19 degrees C (P > 0.05).     

Isolation and characterization of immortalized porcine aortic endothelial cell lines

Primary porcine endothelial cells have a limited life span in culture. After four to five passages, they tend to de-differentiate and eventually reach senescence. The aim of this work was to establish immortalized porcine aortic endothelial cell lines (AOCs) to facilitate in vitro studies of different pathological process involving the endothelium. Primary porcine aortic endothelial cells (PAECs) were transfected with a plasmid containing the SV40 genome and selected on the basis of morphological and phenotypical features. Flow cytometry analysis demonstrated uptake of acetylated low density lipoproteins (Ac-LDL) and constitutive expression of SLA class I, CD29, CD31, CD41/61, CD80/86, CD46, SWC3, and LAMP-1 antigens by all analyzed lines and showed little differences to primary cells. The functional similarity between primary and immortalized endothelial cells was demonstrated in a cytotoxicity assay using a human natural killer cell line (NKL) as effector. The AOCs cell lines should be valuable tools for in vitro study of the human immune response against pig endothelial cells. In addition, they would be very useful to gain insight in the pathogenesis of some viral haemorrhagic diseases of pig such as African swine fever (ASF) or classical swine fever (CSF).     

Morphology and amplitude values of the electrocardiogram of Spanish-bred horses of different ages in the Dubois leads system

The aim of this work was to record the modifications of the form and amplitude of the electrocardiographic tracings during growth using the Dubois system and to study its sensibility to these physiological changes. This work was carried out on 179 healthy, young and adult Spanish-bred horses (98 females and 81 males). One electrocardiogram (ECG) was obtained from each horse using the Dubois leads system. The bifid shape deflection of the P wave was generally more frequent than the simple one in animals at 4 months of age or older. Amplitudes of the P2 component and of the simple positive wave presented significant differences (p < 0.01) between the age groups studied: animals up to 3 months in age and older than 2 years of age (highest amplitudes), and the rest of the animals (lowest amplitudes). Significant variations (p < 0.05) were found for the QS amplitude between animals of 1 month of age, and all the other groups. The multiple range analysis did not define a clear distribution of age groups for the amplitude of the T wave. It may therefore be concluded, that in the Spanish-bred horse up to 1 month of age, the form and amplitude of the QRS complex in the Dubois leads system differ from those of older animals. Thus, this study shows the sensibility of the Dubois leads system for detecting the electrocardiographic changes related to the growing process in the Spanish-bred horse. In addition, it provides standard values of electrocardiographic parameters in the Spanish-bred horse at different stages of growth.     

Temperature effect on muscle growth of the axial musculature of the sea bass (Dicentrarchus labrax L.)

In order to determine the temperature effect on the axial muscle growth of sea bass, a stock of larvae was subjected to the following incubation and cultivation temperatures, respectively: 15 degrees C/ambient, 15/17 degrees C, 17 degrees C/ambient and 17/17 degrees C. In all groups the cross-sectional area of white and red muscles and the number and average area of the white and red muscle fibres were quantified. Results showed that the embryonic period, pre-larval phase and the end of metamorphosis were accelerated at higher temperatures. During the endogenous feeding period, muscle growth took place by fibrillar hypertrophy, and was not influenced by the temperature. Thereafter (external feeding) muscular hyperplasia began, and growth of all the muscular parameters was favoured by the effect of high incubation and cultivation temperatures, with the latter having higher influence. High incubation temperature had an slight effect on muscle growth and body length, which was only observed from 15 days. Metamorphosis finished at 3 +/- 0.4 cm in all the larvae, but this length was earlier reached at higher temperatures. At 120 days, the largest growth was obtained in the larvae maintained at a higher temperature.     

Channels and ditches as the last shelter for freshwater mussels: the case of Margaritifera auricularia and other naiads inhabiting the mid Ebro River Basin,Spain

• 1. Freshwater mussels or naiads are generally considered to thrive in river habitats, provided the ecological conditions are good. The presence of populations of these bivalves in artificial channels and ditches with natural bottoms has only scarcely been reported. The aim of this paper was to present the idea that these ‘channel’ and ‘ditch’ habitats could in fact be a sanctuary for naiads.
• 2. Approximately 80 km of several of these waterways fed by the mid Ebro River were sampled in Spain to monitor their naiad populations. Observations indicate that these habitats harbour substantial colonies of freshwater mussels (including two populations of adult specimens of the endangered species Margaritifera auricularia), much more so than the corresponding river.
• 3. The authors wish to alert conservation authorities and freshwater mussel experts to the extreme fragility and importance of this kind of habitat for the long‐term conservation of these imperilled molluscs.

Copyright © 2008 John Wiley & Sons, Ltd.     

Influence of diet and feeding strategy on the performance of nitrifying trickling filter,oxygen consumption and ammonia excretion of gilthead sea bream (Sparus aurata) raised in recirculating aquaculture systems

Gilthead sea bream (Sparus aurata) was raised in six individual recirculating aquaculture systems (RAS) whose biofilters’ performance was analyzed. Fish were fed with three different diets (a control diet, a fishmeal-based diet (FM), and a plant meal-based diet (VM)) and with three different feeding strategies (manual feeding to apparent satiation, automatic feeding with restricted ration, and auto-demand feeding). For every combination of diet and feeding strategy, the mean oxygen consumption, ammonia excretion, and ammonia removal rate were determined. Fish fed with the VM diet consumed the most oxygen (20.06?±?1.80 gO₂ consumed kg^?1 day^?1). There were significant differences in ammonia excretion depending on the protein content and protein efficiency of the diet, as well as depending on feeding strategy, which in turn affected ammonia removal rates. Fish fed by auto-demand feeders led to the highest mean ammonia removal rate (0.10 gN-TAN removed m^?2 biofiltration area day^?1), while not leading to peaks of high ammonia concentration in water, which preserve fish welfare and growth.