Accuracy of genomic prediction using imputed whole‐genome sequence data in white layers

There is an increasing interest in using whole‐genome sequence data in genomic selection breeding programmes. Prediction of breeding values is expected to be more accurate when whole‐genome sequence is used, because the causal mutations are assumed to be in the data. We performed genomic prediction for the number of eggs in white layers using imputed whole‐genome resequence data including ~4.6 million SNPs. The prediction accuracies based on sequence data were compared with the accuracies from the 60 K SNP panel. Predictions were based on genomic best linear unbiased prediction (GBLUP) as well as a Bayesian variable selection model (BayesC). Moreover, the prediction accuracy from using different types of variants (synonymous, non‐synonymous and non‐coding SNPs) was evaluated. Genomic prediction using the 60 K SNP panel resulted in a prediction accuracy of 0.74 when GBLUP was applied. With sequence data, there was a small increase (~1%) in prediction accuracy over the 60 K genotypes. With both 60 K SNP panel and sequence data, GBLUP slightly outperformed BayesC in predicting the breeding values. Selection of SNPs more likely to affect the phenotype (i.e. non‐synonymous SNPs) did not improve the accuracy of genomic prediction. The fact that sequence data were based on imputation from a small number of sequenced animals may have limited the potential to improve the prediction accuracy. A small reference population (n = 1004) and possible exclusion of many causal SNPs during quality control can be other possible reasons for limited benefit of sequence data. We expect, however, that the limited improvement is because the 60 K SNP panel was already sufficiently dense to accurately determine the relationships between animals in our data.     

Profile of Steroid Receptors and Increased Aromatase Immunoexpression in Canine Inflammatory Mammary Cancer as a Potential Therapeutic Target

Canine inflammatory mammary cancer (IMC) has been proposed as a model for the study of human inflammatory breast cancer (IBC). The aims of this study were to compare the immunohistochemical expression of aromatase (Arom) and several hormone receptors [estrogen receptor α (ERα), estrogen receptor β (ERβ), progesterone receptor (PR) and androgen receptor (AR)], in 21 IMC cases vs 19 non‐IMC; and to study the possible effect of letrozole on canine IMC and human inflammatory breast cancer (IBC) in vitro using IPC‐366 and SUM‐149 cell lines. Significant elevations of the means of Arom Total Score (TS), ERβ TS and PR TS were found in the IMC group (p = 0.025, p = 0.038 and p = 0.037, respectively). Secondary IMC tumours expressed higher levels of Arom than primary IMC (p = 0.029). Non‐IMC PR‐ tumours contained higher levels of Arom than non‐IMC PR+ tumours (p = 0.007). After the addition of letrozole, the number of IMC and IBC cells dropped drastically. The overexpression of Arom found and the results obtained in vitro further support canine IMC as a model for the study of IBC and future approaches to the treatment of dogs with mammary cancer, and especially IMC, using Arom inhibitors.     

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.     

Response of healthy dogs to infusions of human serum albumin

OBJECTIVE: To evaluate the clinical and immunologic response in healthy dogs to infusions of human serum albumin (HSA). ANIMALS: 9 healthy purpose-bred mixed-breed dogs. PROCEDURES: Each dog was administered a 25% HSA solution once or twice. Various physical examination and laboratory variables were serially evaluated. Antibody against HSA was assayed before and after infusion by use of an ELISA. Intradermal testing was also conducted. A repeated-measures ANOVA or Friedman repeated-measures ANOVA on ranks was used to compare results for the variables. RESULTS: Adverse clinical reactions were observed after the first or second infusion in 3 dogs. Anaphylactoid reactions were observed in 1 of 9 dogs during the first infusion and in 2 of 2 dogs administered a second infusion. Two dogs developed severe edema and urticaria 6 or 7 days after an initial infusion. All dogs developed anti-HSA antibodies. Positive responses for ID tests were observed in 8 of 9 dogs. Short-term increases were detected in blood protein, total bilirubin, and calcium concentrations after HSA infusion. Serum cholesterol concentrations and platelet counts decreased after HSA infusion. CONCLUSIONS AND CLINICAL RELEVANCE: Administration of HSA resulted in profound reactions in 2 of 9 dogs administered a single infusion and in 2 of 2 dogs administered a second infusion. This indicates that there is risk of life-threatening adverse reactions to HSA infusion in healthy dogs.     

Comparison of three methods of temperature measurement in hypothermic, euthermic, and hyperthermic dogs

OBJECTIVE: To assess the reliability and accuracy of a predictive rectal thermometer, an infrared auricular thermometer designed for veterinary use, and a subcutaneous temperature-sensing microchip for measurement of core body temperature over various temperature conditions in dogs. DESIGN: Prospective study. ANIMALS: 8 purpose-bred dogs. PROCEDURES: A minimum of 7 days prior to study commencement, a subcutaneous temperature-sensing microchip was implanted in 1 of 3 locations (interscapular, lateral aspect of shoulder, or sacral region) in each dog. For comparison with temperatures measured via rectal thermometer, infrared auricular thermometer, and microchip, core body temperature was measured via a thermistor-tipped pulmonary artery (TTPA) catheter. Hypothermia was induced during anesthesia at the time of TTPA catheter placement; on 3 occasions after placement of the catheter, hyperthermia was induced via administration of a low dose of endotoxin. Near-simultaneous duplicate temperature measurements were recorded from the TTPA catheter, the rectal thermometer, auricular thermometer, and subcutaneous microchips during hypothermia, euthermia, and hyperthermia. Reliability (variability) of temperature measurement for each device and agreement between each device measurement and core body temperature were assessed. RESULTS: Variability between duplicate near-simultaneous temperature measurements was greatest for the auricular thermometer and least for the TTPA catheter. Measurements obtained by use of the rectal thermometer were in closest agreement with core body temperature; for all other devices, temperature readings typically underestimated core body temperature. CONCLUSIONS AND CLINICAL RELEVANCE: Among the 3 methods of temperature measurement, rectal thermometry provided the most accurate estimation of core body temperature in dogs.     

Applicability of ground‐penetrating radar as a tool for nondestructive soil‐depth mapping on Pleistocene periglacial slope deposits

Soil depth plays a decisive role in determining soil properties in mountainous regions for ecological site assessment. To evaluate the use of ground‐penetrating radar (GPR) for fast and high‐resolution mapping within mountainous regions, we examined the possibilities and limitations of GPR to determine soil depth over bedrock and to delineate individual substrate layers formed during the Pleistocene in a periglacial environment (Pleistocene periglacial slope deposits, PPSD). Selected catenae in representative subregions of the study area (Dill catchment, SE Rhenish Massif, Germany) have been successfully mapped using GPR. A practicable method was developed using a 400 MHz antenna to reach a mean penetration depth of 1.5 m and to map different substrates and layers of PPSD based on calibrations of the GPR at soil pits along 12 catenae. Colluvium, the three types of PPSD layers, as well as the in situ bedrock could be distinguished in most sections of the GPR surveys. Characteristic GPR facies caused by intrinsic material properties of the different substrates, such as stone content and soil moisture content, could be distinguished in different geomorphologic and lithological settings. A layer‐based velocity distribution was determined for characteristic substrate layers at soil pits enabling us to considerably enhance the accuracy of soil‐depth prediction. Compared to traditionally surveyed soil profiles, our results demonstrate an accuracy of layer thickness surveying within a standard deviation of approx. 0.1 m. It is demonstrated that the combination of GPR with conventional soil‐pit mapping is an efficient and valid method to produce high‐resolution data of substrate distribution.     

Short‐term degradation of semiarid grasslands—results from a controlled‐grazing experiment in Northern China

The assessment of grassland degradation due to overgrazing is a global challenge in semiarid environments. In particular, investigations of beginning steppe degradation after a change or intensification of the land use are needed in order to detect and adjust detrimental land‐use management rapidly and thus prevent severe damages in these sensitive ecosystems. A controlled‐grazing experiment was established in Inner Mongolia (China) in 2005 that included ungrazed (UG) and heavily grazed plots with grazing intensities of 4.5 (HG4.5) and 7.5 (HG7.5) sheep per hectare. Several soil and vegetation parameters were investigated at all sites before the start of the experiment. Topsoil samples were analyzed for soil organic C (SOC), total N (N_tot), total S (S_tot), and bulk density (BD). As vegetation parameters, aboveground net primary productivity (ANPP), tiller density (TD), and leaf‐area index (LAI) were determined. After 3 y of the grazing experiment, BD increased and SOC, N_tot, S_tot, ANPP, and LAI significantly decreased with increasing grazing intensity. These sensitive parameters can be regarded as early‐warning indicators for degradation of semiarid grasslands. Vegetation parameters were, however, more sensitive not only to grazing but also to temporal variation of precipitation between 2006 and 2008. Contrary, soil parameters were primarily affected by grazing and resistant against climatic variations. The assessment of starting conditions in the study area and the application of defined grazing intensities is essential for the investigation of short‐term degradation in semiarid environments.     

Relation between soil organic matter and yield levels of nonlegume crops in organic and conventional farming systems

The aim of this study was to evaluate the interaction between yield levels of nonleguminous crops and soil organic matter (SOM) under the specific conditions of organic and conventional farming, respectively, and to identify implications for SOM management in arable farming considering the farming system (organic vs. conventional). For that purpose, correlations between yield levels of nonlegume crops and actual SOM level (C_org, N_t, C_hwe, N_hwe) as well as SOM‐level development were examined including primary data from selected treatments of seven long‐term field experiments in Germany and Switzerland. Yield levels of nonlegume crops were positively correlated with SOM levels, but the correlation was significant only under conditions of organic farming, and not with conventional farming treatments. While absolute SOM levels had a positive impact on yield levels of nonlegumes, the yield levels of nonlegumes and SOM‐level development over time correlated negatively. Due to an increased demand of N from SOM mineralization, higher yield levels of nonlegumes obviously indicate an increased demand for OM supply to maintain SOM levels. Since this observation is highly significant for farming without mineral‐N fertilization but not for farming with such fertilization, we conclude that the demand of SOM‐level maintenance or enhancement and thus adequate SOM management is highly relevant for crop production in organic farming both from an agronomical and ecological point of view. Under conventional management, the agronomic relevance of SOM with regard to nutrient supply is much lower than under organic management. However, it has to be considered that we excluded other possible benefits of SOM in our survey that may be highly relevant for conventional farming as well.