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.     

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.     

Disturbance to a foraging seabird by sea-based tourism: Implications for reserve management in marine protected areas

The provision of recreational opportunities is one of the important human goals of marine protected areas. However, as levels of recreational use increase, human disturbance is likely to cause significant detrimental effects upon wildlife. Here we evaluate the best managing options to mitigate the impact of sea-based tourism on the foraging activity of an endangered population of European shags, Phalacrocorax aristotelis, in a coastal marine protected area (Cíes islands, north-western Iberia). Boat disturbance elicited a characteristic avoidance behavior that resulted in a substantial reduction in foraging activity as levels of boat use increased. Moreover, boats excluded shags from the best feeding areas, resulting in higher densities of foragers in areas of little boat traffic. We used a behavioral model to explore the effects of managing strategies aimed at reducing the impact of boats on the foraging activity of shags. Our model suggested that in low boat disturbance scenarios limiting the number of boats using the reserve would be a better management option than habitat protection (i.e. the establishment of set-aside areas free of boat traffic). On the contrary, when boat disturbance levels are high the protection of habitat is recommendable, even if spatial variation in habitat quality is unknown or poorly assessed. Our study stresses the point that management strategies to minimize disturbance to foraging seabirds may depend on the spatial overlap between sea-based recreational activities and foraging seabirds and the spatial variation in marine habitat quality for seabirds.     

Accumulation and depletion kinetics of erythromycin in rainbow trout (Oncorhynchus mykiss)

Erythromycin is an antimicrobial agent recommended for the control and treatment of diseases caused by gram-positive bacteria. Few studies, however, have determined the metabolic and pharmacokinetic aspects of this antimicrobial agent in fish. The aim of the present study, therefore, was to determine the accumulation and depletion time of erythromycin after administration of medicated feed containing 52 mg kg(-1) body weight day(-1) for 8 days in rainbow trout (Oncorhynchus mykiss). Results were analyzed following the European Agency for Evaluation of Medicinal Products guidelines. We measured a withdrawal time of 187°C-day (°C-day=water temperature×days), lower than the value (500°C-day) recommended by Council Directive 2004/28/EC for veterinary medicinal products. Our results provide data to establish therapeutic regimens for the use of erythromycin in aquaculture.     

Pathogenicity of plant and soil isolates of <Emphasis Type="Italic">Phytophthora parasitica</Emphasis> on tomato and pepper

Crown and root rot of tomato and sweet pepper can be caused by Phytophthora parasitica. In this work, 23 P. parasitica isolates from diseased pepper or tomato plants as well as 54 isolates from 23 monocrop tomato soils (from Spain and Chile) and one from a pepper soil were studied for their host–pathogen response. Results show significant host specificity for the isolates from tomato plants and tomato soils (63 of 64 isolates were unable to cause disease in pepper). None of the pepper plant/soil isolates showed pathogenicity on tomato, and only four of 14 reproduced their pathogenicity on pepper. Only one tomato isolate was pathogenic to both Solanaceae species. Two different inoculation protocols were evaluated (substrate irrigation and stem cutting). All isolates which expressed pathogenicity when stem inoculated also did it when root inoculated, but not vice-versa. Therefore, the recommended test protocol for tomato and pepper breeding programmes is that based on root inoculation by irrigation.     

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.     

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.     

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.     

Polyunsaturated Aldehydes from Large Phytoplankton of the Atlantic Ocean Surface (42°N to 33°S)

Polyunsaturated aldehydes (PUAs) are organic compounds mainly produced by diatoms, after cell wounding. These compounds are increasingly reported as teratogenic for species of grazers and deleterious for phytoplanktonic species, but there is still scarce information regarding concentration ranges and the composition of PUAs in the open ocean. In this study, we analyzed the spatial distribution and the type of aldehydes produced by the large-sized (>10 μm) phytoplankton in the Atlantic Ocean surface. Analyses were conducted on PUAs released after mechanical disruption of the phytoplankton cells, referred to here as potential PUAs (pPUAs). Results show the ubiquitous presence of pPUA in the open ocean, including upwelling areas, as well as oligotrophic gyres. Total pPUA concentrations ranged from zero to 4.18 pmol from cells in 1 L. Identified PUAs were heptadienal, octadienal and decadienal, with heptadienal being the most common (79% of total stations). PUA amount and composition across the Atlantic Ocean was mainly related to the nitrogen:phosphorus ratio, suggesting nutrient-driven mechanisms of PUA production. Extending the range of trophic conditions considered by adding data reported for productive coastal waters, we found a pattern of PUA variation in relation to trophic status.