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.     

The effect of stocking rate and calving date on grass production,utilization and nutritive value of the sward during the grazing season

A 2‐year whole‐farm system study compared the accumulation, utilization and nutritive value of grass in spring‐calving grass‐based systems differing in stocking rate (SR) and calving date (CD). Six treatments (systems) were compared over two complete grazing seasons. Stocking rates used in the study were low (2·5 cows ha^?1), medium (2·9 cows ha^?1) and high (3·3 cows ha^?1), respectively, and mean CDs were 12 February (early) and 25 February (late). Each system had its own farmlet of eighteen paddocks and one herd that remained on the same farmlet area for the duration of the study. Stocking rate had a small effect on total herbage accumulation (11 860 kg DM ha^?1 year^?1), but had no effect on total herbage utilization (11 700 kg DM ha^?1 year^?1). Milk and milk solids (MS; fat + protein) production per ha increased by 2580 and 196 kg ha^?1 as SR increased from 2·5 to 3·3 cows ha^?1. Milk production per ha and net herbage accumulation and utilization were unaffected by CD. Winter feed production was reduced as SR increased. Increased SR, associated with increased grazing severity, resulted in swards of increased leaf content and nutritive value. The results indicate that, although associated with increased milk production per ha, grazed grass utilization and improved sward nutritive value, the potential benefits of increased SR on Irish dairy farms can only be realized if the average level of herbage production and utilization is increased.     

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.     

Winter movement activity patterns of anadromous Arctic charr in two Labrador lakes

Anadromous Arctic charr, Salvelinus alpinus, feed in the marine environment for several months during the summer and migrate back to fresh water in late summer to spawn and/or overwinter. While overwintering, anadromous Arctic charr are generally believed to reduce or cease feeding, and they are poorly described in their winter movement activity. This study used telemetry data collected from two locations to describe overwintering movement activity, including interindividual variation. Movement activity declined markedly during the ice‐covered period, suggesting opportunistic maintenance feeding was used as an energy conservation strategy. Fall and spring movement was correlated with daylight hours, and ice break‐up had a significant effect on the timing of outmigration. Movement activity was negatively correlated with body length, with smaller individuals being more active than larger fish. Although general activity patterns were evident, there were significant differences among individuals, particularly during spring immediately prior to lake departure. Lake size and individual differences in metabolic rate may account for some of this variation.     

Laparoscopic‐assisted splenectomy in a horse with splenomegaly

This reports describes the surgical management of a horse evaluated for recurrent colic. These frequent colic episodes were attributed by exclusion to an abnormally enlarged spleen (idiopathic splenomegaly). Splenectomy was elected and performed with a laparoscopic assisted technique. The advantages observed by using this surgical approach were a clear view of the visceral aspect of the spleen and consequently an accurate dissection of the hilus of the spleen and associated vasculature. Ultimately the laparoscopic technique allowed the surgeons to reduce the size of the laparotomy incision required to remove the spleen and the overall invasiveness of the procedure. The horse recovered well from the procedure and ultimately returned to the previous level of competitiveness.     

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.     

Studies on effects of nutritional factors on bone structure and osteoporosis in laying hens

1. A modern hybrid strain of laying hen (Hisex) was fed from point of lay to 68 weeks on a control diet and diets containing oystershell, fluoride, 1,25‐dihydroxycholecalciferol, ascorbic acid, a lower concentration of phosphorus and a combination of a lower concentration of crude protein and higher concentration of vitamin K. Hens from a much older strain (Brown Leghorn J‐line) were fed on the control diet.

2. Plasma variables were measured during lay. End‐of‐lay trabecular and medullary bone volumes in the proximal tarsometatarsus and free thoracic vertebra were measured by histomorphometry.

3. The majority of Hisex hens were considered to be osteoporotic by the end of lay. In contrast, none of the J‐line were osteoporotic.

4. None of the nutritional treatments affected trabecular bone volumes. Medullary bone volumes were increased significantly by feeding oystershell or fluoride.

5. There was no phenotypic correlation between egg production and trabecular bone volume in the Hisex hens.

6. The experiment provided evidence that osteoporosis in laying hens, as assessed by trabecular bone volumes, is not caused by calcium deficiency and could not be prevented by any of the nutritional treatments studied.