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.     

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).     

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.

     

Marketing of meat sheep with intensive finishing in southern state of Mexico

The objective of the present study was to quantify the marketing margins of cold sheep carcass and barbacoa meat in the southern state of Mexico. Data were obtained from the production chain links (production, industrialization, and marketing) where the marketing margins were calculated along with the benefit/cost (B/C) ratio. In the absolute marketing margin of the final consumer price per kilogram of carcass meat, the producer obtained US$2.7/kg (47 %) of the utilities, while the intermediaries obtained US$3.1/kg (53 %). Considering the final cooked product in barbacoa (typical dish), the margin was US$6.3/kg (29 %) for the producer and US$15.2/kg (71 %) for the intermediaries. The B/C ratio was 1.0, 1.1, 2, and 1.3 for the producer, stocker, butcher, and barbacoa seller, respectively. It is concluded that the best marketing channel for the producer was the producer-stocker-processor (butcher and barbacoa seller). The highest marketing margin was for the intermediaries followed by the producer. The order of importance of the B/C kilogram ratio of meat was for the butcher first, then barbacoa seller, and lastly stocker and producer.     

Mutants in the lipopolysaccharide of Brucella ovis are attenuated and protect against B. ovis infection in mice

Brucella spp. are Gram-negative bacteria that behave as facultative intracellular parasites of a variety of mammals. This genus includes smooth (S) and rough (R) species that carry S and R lipopolysaccharides (LPS), respectively. S-LPS is a virulence factor, and mutants affected in the S-LPS O-polysaccharide (R mutants), core oligosaccharide or both show attenuation. However, B. ovis is naturally R and is virulent in sheep. We studied the role of B. ovis LPS in virulence by mutating the orthologues of wadA, wadB and wadC, three genes known to encode LPS core glycosyltransferases in S brucellae. When mapped with antibodies to outer membrane proteins (Omps) and R-LPS, wadB and wadC mutants displayed defects in LPS structure and outer membrane topology but inactivation of wadA had little or no effect. Consistent with these observations, the wadB and wadC but not the wadA mutants were attenuated in mice. When tested as vaccines, the wadB and wadC mutants protected mice against B. ovis challenge. The results demonstrate that the LPS core is a structure essential for survival in vivo not only of S brucellae but also of a naturally R Brucella pathogenic species, and they confirm our previous hypothesis that the Brucella LPS core is a target for vaccine development. Since vaccine B. melitensis Rev 1 is S and thus interferes in serological testing for S brucellae, wadB mutant represents a candidate vaccine to be evaluated against B. ovis infection of sheep suitable for areas free of B. melitensis.     

Effect of increasing levels of seven tree species extracts added to a high concentrate diet on in vitro rumen gas output

This study was conducted to investigate the effects of increasing levels of extracts of Byrsonima crassifolia, Celtis pallida, Enterolobium cyclocarpum, Fraxinus excelsior, Ficus trigonata, Phoradendrom brevifolium and Prunus domestica on in vitro gas production (GP) and ruminal fermentation of a high concentrate diet. Plant extracts were prepared at 1 g dry matter (DM)/8 mL of solvent mixture (methanol : ethanol : water, 1:1:8) and added at levels of 0, 0.6, 1.2 and 1.8 mL/g DM of a high concentrate diet. In vitro GP was recorded at 2, 4, 6, 8, 10, 12, 24, 48 and 72 h of incubation. Increasing addition of extracts linearly increased (P < 0.001), the GP₂₄, GP₄₈ and GP₇₂ (mL/g DM), and linearly decreased (P < 0.001), the discrete GP lag time. Moreover, increasing extract doses linearly increased (P < 0.001) the asymptotic GP and decreased (P < 0.001) the rate of GP. GP₆ was not impacted by treatments and GP₁₂ increased linearly (P = 0.01) with increasing addition of extracts. Rumen pH declined linearly (P < 0.05) with increasing doses of extracts added. As no interactions (P > 0.05) occurred between the extracts and doses, it could be conclude that all extracts positively modified rumen fermentation at doses of 1.2 to 1.8 mL extract/g diet DM.