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.     

Composition and fatty acid profile of milk from cows supplemented with pressed oilseed cake

This study compared the productive and nutritional parameters of milk from crossbred lactating cows managed on Panicum maximum Jacq. cv. Tanzania and with a diet supplemented with different pressed oilseed cakes. The supplements used were as follows: peanut cake, sunflower cake and palm kernel cake for replacement of soybean meal. Sixteen cows with an average weight of 544 ± 57 kg and producing 8 ± 1.4 L of milk per day were used in this study. The animals were randomly assigned to the treatments according to a Latin square design repeated over time, with four treatments, 16 animals and four experimental periods. Supplementation of the diet with peanut cake, sunflower cake and palm kernel cake compared with soybean meal in the diet of cows did not affect the average daily production or composition of the milk. The palm kernel cake promoted an increase in lauric fatty acids (C_12:0) and palmitoleic acids (C_16:1) (5.02 and 1.65%, respectively) compared with peanut cake and sunflower cake (4.13 and 4.01%, respectively). The levels of oleic fatty acids (C_18:1) were higher for the sunflower cake and palm kernel cake supplements (26.01 and 25.01%, respectively) compared with peanut cake (23.11%). The replacement of soybean meal with sunflower cake and palm kernel cake improved the nutritional quality of the milk, with lower concentrations of saturated fatty acids and higher concentrations of unsaturated fatty acids, without compromising the production or nutritional composition of the milk. © 2015 Japanese Society of Animal Science     

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.     

Fate of phosphorus in soil during a long‐term fertilization experiment in Finland

Accumulation and depletion of soil phosphorus (P) was studied in a long‐term (37 y) field experiment in Southern Finland. The loam soil had a high pH (7.5–7.7) due to an earlier liming. Spring barley, spring wheat, oat, and ryegrass, grown in rotation, were annually fertilized with 0, 32, or 67 kg P ha^?1 y^?1 (P₀, P₁, and P₂K) and sufficient N. The average dry matter grain yield 2,600 kg ha^?1 of the P₀ plots increased by about 500 kg ha^?1 at P₁ treatment and another 600 kg ha^?1 by P₂K. Soil samples were collected in 1978 (beginning), 1995, 2005, and 2015. According to the Chang and Jackson sequential extraction, the P₂K and P₁ treatments increased the inorganic soil P by 732 and 32 kg P ha ^?1 in 37 years, respectively, while the P₀ plots were depleted by –459 kg P ha ^?1. The P₂K treatment increased all four P fractions, extracted with NH₄Cl (easily soluble), NH₄F (Al‐P), NaOH (Fe‐P), and H₂SO₄ (Ca‐P). Continuous depletion (P₀) decreased the NH₄Cl‐P and NH₄F‐P pools, NaOH‐P and H₂SO₄‐P pools remaining stable. None of the P pools changed significantly at P₁. The remarkable gap between the measured change and the balance for the P₂K and P₁ treatments cannot be explained solely by lateral soil movement, meaning that a significant proportion of the applied P was lost either in surface runoff or transported below the investigated depth of 40 cm. Despite large P applications, the degree of P saturation reached only 20% in the P₂K topsoil, assuming a 50% reactivity of Fe and Al oxides. As derived from sorption isotherms, a high EPC₀ (i.e., equilibrium P concentration at zero net P sorption or desorption) of 1.30 mg L^?1 had been built up in the P₂K treatment, while in the P₁ treatment EPC₀ (0.33 mg L^?1) had remained unchanged and P depletion (P₀) had caused a decrease to 0.12 mg L^?1. These results demonstrate that P sorption and desorption properties respond strongly to both P fertilization and null fertilization treatments and that in a long‐term field experiment only a low proportion of the residual fertilizer P can be recovered from soil.     

Sodicity and salinity in a Brazilian Oxisol cultivated with sugarcane irrigated with wastewater

Changes in soil sodicity-salinity parameters are one of the most characteristic alterations after treated sewage effluent (TSE) irrigation in agro-systems. Considering the importance of these parameters for agricultural management, as well as the economical value of sugarcane for Brazil, the present study aimed at evaluating effects on soil sodicity and salinity under tropical conditions over 16 months of TSE irrigation in a sugarcane plantation at Lins, São Paulo State, Brazil. Soil samplings were carried out in February 2005 (before planting), December 2005 (after 8 months of TSE irrigation) and September 2006 (after 16 months of TSE irrigation) following a complete block design with four treatments and four replicates. Treatments consisted of: (i) control, without TSE irrigation; (ii) T100, T150 and T200, with TSE irrigation supplying 100% (0% surplus, total of 2524 mm), 150% (50% surplus, total of 3832 mm) and 200% (100% surplus, total of 5092 mm) of crop water demand, respectively. Compared to initial soil conditions, at the end of the experiment increases of exchangeable sodium (from 2.4 to 5.9 mmol_c kg⁻¹), exchangeable sodium percentage (ESP) (from 8 to 18%), soluble Na (from 1.4 to 4.7 mmol L⁻¹) and sodium adsorption ratio (SAR) of soil solution (from 3.6 to 12.6 (mmol L⁻¹)^0.5) were found in the soil profile (0-100 cm) as an average for the irrigated plots due to high SAR of TSE. Associated with the increments were mostly significant increases in clay dispersion rates at depths 0-10, 10-20 and 20-40 cm. Electrical conductivity (EC) of soil solution increased during the TSE irrigation period whereas at the end of the experiment, after short term discontinuation of irrigation and harvest, EC in the topsoil (0-10 and 10-20 cm) decreased compared to the previous samplings. Moreover, despite increasing sodicity over time mainly insignificant differences within the different irrigated treatments were found in December 2005 and September 2006. This suggests that independent of varying irrigation amounts the increasing soil sodicity over time were rather caused by the continuous use of TSE than by its quantity applied. Moreover, also plant productivity showed no significant differences within the TSE irrigated plots. The study indicates that monitoring as well as remediation of soil after TSE irrigation is required for a sustainable TSE use in order to maintain agricultural quality parameters.     

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.