Application of multiple shrinkage methods to genomic predictions

New challenges have arisen with the development of large marker panels for livestock species. Models easily become overparameterized when all available markers are included. Solutions have led to the development of shrinkage or regularization techniques. The objective of this study was the application and comparison of Bayesian LASSO (B-L), thick-tailed (Student-t), and semiparametric multiple shrinkage methods. The B-L and Student-t methods were also each analyzed within a single shrinkage and a multiple shrinkage framework. Simulated and real data were used to evaluate each method's performance. Real data consisted of SNP genotypes of 4,069 Holstein sires. Traits included in analysis of real data were milk, fat, protein yield, and somatic cell score. The performance of each model was compared based on correlations between true and predicted genomic predicted transmitting abilities. Model performance was also compared with the performance of routinely used methods such as Bayes-A and GBLUP through cross-validation techniques. When using simulated data regardless of shrinkage framework, shrinkage models outperformed genomic BLUP (GBLUP). The average advantage of shrinkage models ranged from 1% to approximately 8% depending on the prior specification. When analyzing real data, shrinkage models slightly outperformed GBLUP for most traits. Shrinkage models were better able to model traits for which 1 or more SNP of large effect have been identified. Overall, results suggested a relatively small advantage in multiple shrinkage models. Multiple shrinkage methods could represent a useful alternative to current methods of prediction; however, their performance in a variety of scenarios needs to be investigated further.     

Physiological Predictors in Calves of Dairy Breeds: Part 1. Genetic Parameters of Basal and Induced Growth Hormone Secretion

Abstract

Genetic variation in plasma growth hormone (GH) concentration before and after GRF (growth hormone releasing factor) stimulation was studied in young bulls (N=284) and heifers (N=212), the progeny of 53 sires of four dairy and dual-purpose breeds (Danish Jersey, Red Dane, Danish Friesian and Danish Red and White). Male and female calves were reared, fed and tested on separate experimental stations; thus sex, station and feeding were completely confounded effects. The animals were tested at about 9 months of age, after a 24 h fast. GH concentration was measured in serial plasma samples collected for 1 h before and 1 h following intravenous administration of 2.0 ug synthetic GRF(1–29)NH₂/kg live weight^>0.75. Prior to statistical analysis, concentrations were log_e-transformed. Response variables were BASELINE (mean GH in -15, -5 and 0 min samples) and PEAK (mean GH in 10, 15 and 20 min samples). A statistical model taking at least three generations of ancestral relationships into account was used to estimate variance and covariance components for traits in male and female calves by use of restricted maximum likelihood methods.

Heritability of BASELINE was low (0.04 ± 0.12) in males but high in females (0.60 ± 0.16). The heritability of PEAK was high in both sexes (males, 0.42 ± 0.16; females, 0.60 ± 0.16). Genetic correlations between the same trait measured in males and females were low for BASELINE (r _g = 0.32±0.55) but high for PEAK (r _g = 0.82±0.15). Within sex, BASELINE and PEAK were both highly genetically correlated (males, r _g=0.62 ± 0.40; females, r _g= 1.00 ± 0.07).

We conclude that growth hormone concentration is a highly heritable trait in juvenile cattle of both sexes, and that GRF stimulation is benificial to the uncovering of genetic differences among animals.     

Lack of detection of circulating skin-specific IgE autoantibodies in dogs with moderate or severe atopic dermatitis

Human patients with atopic dermatitis (AD) commonly exhibit IgE reactivity to cutaneous self-antigens. The presence of serum IgE autoantibodies appears to correlate with disease severity, and it is suspected to reflect or contribute to tissue damage. The objective of this study was to determine whether IgE autoantibodies specific for cutaneous antigens could be detected in the serum of dogs with AD. Serum was collected from 19 dogs with untreated moderate to severe AD and four specific-pathogen free (SPF) dogs. Indirect immunofluorescence was performed using normal canine skin collected at four different locations (concave ear, nose, medial thigh and lateral thorax), while Western immunoblotting was done using normal canine ear pinna epidermal and dermal extracts and reducing conditions. In both methods, IgE was detected using a monoclonal antibody specific for heat stable epitopes of canine IgE. At 1:10 dilution, specific IgE autoantibodies against cutaneous autoantigens were not detected, with either method, in AD and SPF canine sera. Either IgE autoreactivity is not associated with moderate to severe AD in dogs, or the methods employed herein were not sensitive enough to permit IgE autoantibody detection.     

Fishmeal alternative from renewable CO2 for rainbow trout feed

The rapid global growth in fish farming and limited supply of fish meal (FM) has consequently reduced FM inclusion levels in compound feeds leading to a higher reliance on alternative protein sources. Sasya is a single cell protein (SCP) product that has a similar amino acid profile as FM. The aim of this study was to evaluate the effects of replacing FM with SCP on in vivo digestibility, growth, feed efficiency, whole‐body proximate/amino acid composition and gene expression levels of various hepatic enzymes in rainbow trout (Oncorhynchus mykiss). Three isonitrogenous (470 g/kg crude protein) and isolipidic (18 g/kg crude lipid) diets were formulated as follows: Diet 1: control (30% FM); Diet 2:24% FM + 6% SCP and Diet 3:18% FM + 12% SCP. Each diet was hand‐fed to triplicate tanks containing 30 rainbow trout fingerlings (4.99 ± 0.20 g) for 9 weeks. Apparent digestibility coefficients of SCP for dry matter, crude protein, lipid and energy were 60, 80, 93 and 74% respectively. Growth performance (final weight: 69–71 g), feed conversion ratios (0.91–0.94) as well as whole‐body protein and amino acid composition were unaffected by diets. However, Diet 3 significantly increased whole‐body crude fat and energy. Fish fed the SCP‐based diets had significantly higher expression for carnitine palmitoyltransferase‐1b (CPT1b), fatty acid delta 6 desaturase (FADS6) and fatty acid elongase 5 compared to the control. Overall, the quality of the SCP was similar as FM. Therefore, this product could enlarge the portfolio of alternative protein sources that can be used in fish diets and thus open a new market opportunity for use of a new feed resource in the feed industry.     

Eumycetoma and disseminated phaeohyphomycosis in a Sumatran tiger

A 16-y-old female Sumatran tiger (Panthera tigris sumatrae) was evaluated for hyporexia. Examination revealed chronic kidney disease and a large subcutaneous axillary mass with draining tracts that contained numerous small black grains. Histologic examination revealed the presence of intralesional fungal hyphae. Persistent hyporexia and pyogranulomatous disease, as well as progressive cachexia and azotemia occurred despite treatment, and euthanasia was performed. Disseminated phaeohyphomycosis was diagnosed on postmortem examination, additionally affecting various lymph nodes, the nasal cavity, mesenteric adipose tissue, abdominal aorta, pericardium, and kidney. Fungal culture from a deep-tissue sample isolated a pure growth of Curvularia sp., a dematiaceous opportunistic fungus able to cause eumycetomas and/or phaeohyphomycosis. Phaeohyphomycosis is a rare but emerging condition, not previously reported as disseminated disease in an exotic carnivore, to our knowledge. Aggressive systemic antifungal treatment was unsuccessful, likely complicated by diagnostic challenges and concurrent renal disease. The presence of a swelling with abundant grains exiting draining tracts should direct clinicians to the diagnosis of a mycetoma, warranting early and aggressive treatment.