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.     

Experimental Neospora Caninum Infection in Pregnant Dairy Heifers Raises Concentrations of Pregnancy‐Associated Glycoproteins 1 and 2 in Foetal Fluids

Plasma concentrations of PAG‐1 are used for pregnancy diagnosis and as a marker of placental/foetal well‐being, while those of PAG‐2 may be an indicator of abortion risk in Neospora caninum‐infected cows. Studies have shown that N. caninum infection modifies PAG‐1 and PAG‐2 patterns in maternal blood plasma. However, no prior work has examined the effects of N. caninum infection on concentrations of PAGs in foetal fluids. In this study, PAG‐1, PAG‐2 and pH levels were determined in the amniotic and allantoic fluids of foetuses collected at 152 days of gestation from control uninfected dams and from dams experimentally infected with N. caninum on Day 110 of gestation. Foetal fluids from infected foetuses had significantly higher PAG‐2 concentrations (p = 0.026) and pH values (p = 0.02) than fluids from non‐infected foetuses. In infected foetuses, significantly higher concentrations of PAG‐1 (p < 0.001) and PAG‐2 (p < 0.001) were detected in fluid samples showing antibodies against N. caninum than those without antibodies. Moreover, pH values were significantly higher (p = 0.011) in foetal fluid samples with antibodies than in samples from non‐infected foetuses. In conclusion, this is the first report on the effect of N. caninum infection on PAG levels in foetal fluids. Our results indicate that following the experimental infection of dams with N. caninum on Day 110 of gestation, foetal fluids collected from the infected foetuses of these dams featured higher PAG‐1 and PAG‐2 levels and pH values than fluids from non‐infected controls, provided that the samples tested showed the presence of antibodies. The clinical implications of these findings are that following infection with N. caninum, most cows will experience some level of placental damage and that this injury correlates with foetal fluid PAG levels and pH.     

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.     

Effects of irrigation regimes on the yield and water use of strawberry

Summary Strawberry plants (Fragaria x annanasa D. cv Chandler) were grown in field plots and in drainage lysimeters under controlled soil moisture regimes. Four irrigation treatments were established by watering the plants when soil water potential reached -0.01, -0.03,-0.05 and -0.07 MPa. The maximum yield was attained at -0.01 MPa soil water potential. Differences in yield were caused by both changes in the number of fruits per plant and in the fresh weight per fruit. Yield reductions were associated with reductions in total assimilation rate resulting from the decreased assimilatory surface area in plants irrigated at lower soil water potentials. The crop water production function calculated on a fruit fresh weight basis resulted in a yield response factor (K _y) of 1.01.     

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.     

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.     

1-methylcyclopropene increases storability and shelf life in climacteric and nonclimacteric plums

The effect of 1-methylcyclopropene (1-MCP) at three different doses (0.25, 0.50, and 0.75 microL L(-1)) on the ripening processes of a climacteric, cv. Santa Rosa, and a suppressed climacteric type, cv. Golden Japan, plum was studied. For both cultivars, positive effects were observed in terms of inhibition of ethylene production and delays of the physical, chemical, and biochemical changes associated with ripening. 1-MCP-treated plums were firmer with lower weight loss, reduced degrees Brix/titratable acidity ratios, and lower color changes during cold storage and subsequent shelf life at 20 degrees C than controls. For most factors, the effectiveness of 1-MCP was dose-dependent in Santa Rosa but dose-independent for Golden Japan.     

Use of Aloe vera gel coating preserves the functional properties of table grapes

Table grapes (Vitis vinifera L. cv. Crimson Seedless) were coated with Aloe vera gel according to our developed patent (SP Patent P200302937) and then stored for 35 days at 1 degrees C, and the subsequent shelf life (SL) was monitored at 20 degrees C. Uncoated clusters showed a rapid loss of functional compounds, such as total phenolics and ascorbic acid. These changes were accompanied by reduction of the total antioxidant activity (TAA) and increases in total anthocyanins, showing an accelerated ripening process. On the contrary, table grapes coated with Aloe vera gel significantly delayed the above changes, such as the retention of ascorbic acid during cold storage or SL. Consequently, Aloe vera gel coating, a simple and noncontaminating treatment, maintained the functional properties during postharvest storage of table grapes.