Evaluation of non-additive genetic variation in feed-related traits of broiler chickens.

Genome-wide association mapping and genomic predictions of phenotype of individuals in livestock are predominately based on the detection and estimation of additive genetic effects. Non-additive genetic effects are largely ignored. Studies in animals, plants, and humans to assess the impact of non-additive genetic effects in genetic analyses have led to differing conclusions. In this paper, we examined the consequences of including non-additive genetic effects in genome-wide association mapping and genomic prediction of total genetic values in a commercial population of 5,658 broiler chickens genotyped for 45,176 single nucleotide polymorphism (SNP) markers. We employed mixed-model equations and restricted maximum likelihood to analyze 7 feed related traits (TRT1 - TRT7). Dominance variance accounted for a significant proportion of the total genetic variance in all 7 traits, ranging from 29.5% for TRT1 to 58.4% for TRT7. Using a 5-fold cross-validation schema, we found that in spite of the large dominance component, including the estimated dominance effects in the prediction of total genetic values did not improve the accuracy of the predictions for any of the phenotypes. We offer some possible explanations for this counter-intuitive result including the possible confounding of dominance deviations with common environmental effects such as hatch, different directional effects of SNP additive and dominance variations, and the gene-gene interactions' failure to contribute to the level of variance.

Numerical analysis of intensity signals resulting from genotyping pooled DNA samples in beef cattle and broiler chicken.

Pooled genomic DNA has been proposed as a cost-effective approach in genomewide association studies (GWAS). However, algorithms for genotype calling of biallelic SNP are not adequate with pooled DNA samples because they assume the presence of 2 fluorescent signals, 1 for each allele, and operate under the expectation that at most 2 copies of the variant allele can be found for any given SNP and DNA sample. We adapt analytical methodology from 2-channel gene expression microarray technology to SNP genotyping of pooled DNA samples. Using 5 datasets from beef cattle and broiler chicken of varying degrees of complexity in terms of design and phenotype, continuous and dichotomous, we show that both differential hybridization (M = green minus red intensity signal) and abundance (A = average of red and green intensities) provide useful information in the prediction of SNP allele frequencies. This is predominantly true when making inference about extreme SNP that are either nearly fixed or highly polymorphic. We propose the use of model-based clustering via mixtures of bivariate normal distributions as an optimal framework to capture the relationship between hybridization intensity and allele frequency from pooled DNA samples. The range of M and A values observed here are in agreement with those reported within the context of gene expression microarray and also with those from SNP array data within the context of analytical methodology for the identification of copy number variants. In particular, we confirm that highly polymorphic SNP yield a strong signal from both channels (red and green) while lowly or nonpolymorphic SNP yield a strong signal from 1 channel only. We further confirm that when the SNP allele frequencies are known, either because the individuals in the pools or from a closely related population are themselves genotyped, a multiple regression model with linear and quadratic components can be developed with high prediction accuracy. We conclude that when these approaches are applied to the estimation of allele frequencies, the resulting estimates allow for the development of cost-effective and reliable GWAS.

A single nucleotide polymorphism on chromosome 10 is highly predictive for the polled phenotype in Australian Merino sheep.

The aim of this study was to fine map the genomic location of the Horns locus in the Australian Merino sheep population and to identify markers that can be used to predict the horn phenotype. A linkage disequilibrium analysis of horn data from Australian Merino sheep mapped the Horns locus to a small region on chromosome 10. A single nucleotide polymorphism in the region was found to be highly predictive for the polled phenotype in an experimental population of Merino sheep. This was owing to a dominance effect of one of the alleles when inherited maternally. It was suggested that a genetic test would provide a good predictor of the polled phenotype. Finally, an evaluation of industry data showed that the SNP is at very different frequencies in Poll Merino sheep that have been bred for polledness (based on phenotype alone) compared with the Merino sheep breed.

Evaluation of a new approach for the estimation of the time of the LH surge in dairy cows using vaginal temperature and electrodeless conductivity measurements.

The objective of the study was to test the effectiveness of a new type of conductivity sensor, along with vaginal temperature, at identifying the LH peak associated with estrus in dairy cows. Twelve mature non-lactating Holstein-Friesian cows had their estrous cycles synchronized on two occasions, and then data were collected for the following spontaneous cycles. An indwelling electrodeless plastic-coated toroidal conductivity sensor, which also recorded temperature, was placed in the vagina throughout the cycle. Blood samples were collected for LH measurement, and ultrasound scanning used to confirm ovulation. Although there was a relationship between vaginal mucus conductivity measured by the toroidal sensor and the timing of the LH surge, it was not sufficiently robust in individual cows to be able to identify the time of the LH surge. The mean increase in vaginal temperature at estrus was 0.48 degrees C. An algorithm was developed which used the detected individual cow temperature peak to test the relationship with the LH peak. In 16 out of 21 cases where ovulation was confirmed and data existed, the estimated individual peak was within 4h of the LH surge, in three cases it was +/-6h, and in two instances it was early. In conclusion, the temperature algorithm was able to identify the time of the LH surge and thus predict time of ovulation in a way that would allow effective AI, although this result needs to be tested in lactating cows. However, the toroidal conductivity sensing method was not able to produce data of sufficient quality to develop a predictive relationship in individual cows.

Behavioral aspects of electronic bull separation and mate allocation in multiple-sire mating paddocks.

Controlling spatial positioning of cattle through use of electronic collars could provide new ways to farm under extensive conditions. This study examined the potential for bulls to be controlled during mating using mild electric shocks delivered through radio-controlled collars. Eighteen Belmont Red bulls were fitted with collars containing the Global Positioning System and that were able to emit a mild electric shock (500 mW) at the top of the neck behind the poll. Eighteen Belmont Red cows were fitted with Global Positioning System collars only. The experiment was replicated 3 times in 3 paddocks. Each paddock contained 2 bulls and 1 cow in induced estrus. On d 1, the bulls were either assigned to the cow or not assigned to the cow, and on d 2, the assignments were reversed, and bulls received the other treatment using a new cow. Treatments were applied for 2 h on each day. The nonassigned bull received a mild electric shock on approach to either the cow or to a bull, whereas the assigned bull received a mild electric shock on approach to the other bull only. The electric shock was applied when the bulls were within approximately 10 m and moving toward the nonallowed animal. The electric shock was terminated when the animal responded by stopping movement toward the nonallowed animal. In the first 10 min, nonassigned bulls spent less time within 5 m of the cow (P = 0.03) than assigned bulls. Assigned bulls spent more time close to the cow during the entire 120 min on d 1 than on d 2 (P = 0.014). On d 1, the assigned bulls moved more toward the cow and the nonassigned bull than they did on d 2 (P = 0.02). Assigned bulls displayed more sexual behaviors than nonassigned bulls (P = 0.004). Nonassigned bulls were sometimes observed not to approach the cow despite a change in its location. This suggests that the bull associated the electric shock with the cow and not with the location in which it received the electric shock. Instances were observed in which the cow pursued the nonassigned bull, in which case the bull did not receive an electric shock, and this may reflect the preference of the cow. This study demonstrated that bulls can be separated and prevented from approaching a cow in estrus using a mild electric shock. However, mate allocation was not completely successful due to the potential for cow preference for certain bulls.

Estimation of maternal variance components considering cow-calf contacts under extensive pastoral systems.

Traditional methods of variance component estimation for traits under maternal influence consist of partitioning the variance into direct additive genetic, maternal additive genetic, permanent maternal environmental, and error variance components. This partitioning is based on the assumption that each calf is nurtured and fed exclusively by its own dam. However, under extensive pastoral systems, voluntary cross-suckling may occur and could be quantified by using contact loggers recording cow-calf affiliations. A simulation study was conducted to test several variance models for partitioning maternal variation by including information on cow-calf contacts. The results indicated that weighting maternal genetic and permanent maternal environmental effects by the relative time calves spent with particular cows, including their own mothers, is feasible and significantly increased the log-likelihood of the models. However, the interpretation of the variance components in terms of traditional direct and maternal heritability is no longer straightforward. The need for further research and implications for the industry are discussed.

Adjusting worm egg counts for faecal moisture in sheep.

The number of eggs from gastrointestinal nematodes per gram of faeces (worm egg count WEC) is commonly used to determine the need for anti-parasite treatments and the breeding value of animals when selecting for worm resistance. Diarrhoea increases faecal moisture and may dilute the number of worm eggs observed. To quantify this effect, egg counts in sheep at pasture were simulated by dosing 15 animals with chromic oxide particles. The simulated WEC diminished as faecal moisture increased. When faeces were dried, simulated WEC per unit dry matter was not influenced by the amount of faecal moisture present prior to drying. The results suggest that adjustment for faecal moisture may provide an improved estimate of FEC. Drying faeces to calculate the WEC per unit dry matter would provide such an adjustment but may not be practical for industry application. In the past, the CSIRO McMaster Laboratory has used an adjustment factor developed by Gordon based on the classification of faecal consistency derived from the morphology of faeces. To examine the utility of an adjustment factor based on faecal consistency score (FCS), the relationships between FCS and simulated WEC and dry matter were examined. Dry matter and simulated WEC exhibited an exponential decline as FCS increased. The relationship between FCS and dry matter was further examined in 368 samples collected over 12 months from sheep at pasture, where it was observed that dry matter showed a linear decline as FCS increased. Adjustment factors based on dry matter were similar to those proposed by Gordon however adjustment factors predicted from simulated WEC diverged from the remainder for FCS>4. As no samples scored FCS 5 in the study of simulated FEC, the adjustment factors based on the larger study that included samples with FCS 5 was therefore considered more robust. Adjustment factors were given by the equation: WEC(estimated)=(WEC(observed)/(34.21-5.15 FCS))x29.06. This equation estimates for samples with FCS>1 the WEC that would be expected if the samples were FCS 1, the faecal consistency score for normal faeces. The impact of adjustment of observed WEC for faecal moisture predicted by FCS on decision points for treatment and on estimated breeding values requires further examination.

Use of the EM algorithm to detect QTL affecting multiple-traits in an across half-sib family analysis.

QTL detection experiments in livestock species commonly use the half-sib design. Each male is mated to a number of females, each female producing a limited number of progeny. Analysis consists of attempting to detect associations between phenotype and genotype measured on the progeny. When family sizes are limiting experimenters may wish to incorporate as much information as possible into a single analysis. However, combining information across sires is problematic because of incomplete linkage disequilibrium between the markers and the QTL in the population. This study describes formulae for obtaining MLEs via the expectation maximization (EM) algorithm for use in a multiple-trait, multiple-family analysis. A model specifying a QTL with only two alleles, and a common within sire error variance is assumed. Compared to single-family analyses, power can be improved up to fourfold with multi-family analyses. The accuracy and precision of QTL location estimates are also substantially improved. With small family sizes, the multi-family, multi-trait analyses reduce substantially, but not totally remove, biases in QTL effect estimates. In situations where multiple QTL alleles are segregating the multi-family analysis will average out the effects of the different QTL alleles.

Estimating genotypes with independently sampled descent graphs.

A method for estimating genotypic and identity-by-descent probabilities in complex pedigrees is described. The method consists of an algorithm for drawing independent genotype samples which are consistent with the pedigree and observed genotype. The probability distribution function for samples obtained using the algorithm can be evaluated up to a normalizing constant, and combined with the likelihood to produce a weight for each sample. Importance sampling is then used to estimate genotypic and identity-by-descent probabilities. On small but complex pedigrees, the genotypic probability estimates are demonstrated to be empirically unbiased. On large complex pedigrees, while the algorithm for obtaining genotype samples is feasible, importance sampling may require an infeasible number of samples to estimate genotypic probabilities with accuracy.

Multiple-trait mapping of quantitative trait loci after selective genotyping using logistic regression.

Experiments to map QTL usually measure several traits, and not uncommonly genotype only those animals that are extreme for some trait(s). Analysis of selectively genotyped, multiple-trait data presents special problems, and most simple methods lead to biased estimates of the QTL effects. The use of logistic regression to estimate QTL effects is described, where the genotype is treated as the dependent variable and the phenotype as the independent variable. In this way selection on phenotype does not bias the results. If normally distributed errors are assumed, the logistic-regression analysis is almost equivalent to a maximum-likelihood analysis, but can be carried out with standard statistical packages. Analysis of a simulated half-sib experiment shows that logistic regression can estimate the effect and position of a QTL without bias and confirms the increased power achieved by multiple-trait analysis.

Effects of Cordyceps sinensis on murine T lymphocyte subsets.

It was shown by flow cytometry analysis that crystalized preparation of Cordyceps sinensis (Cs-Cr) caused significant elevation of the number of T helper cells and Lyt-1/Lyt-2 (T helper to T suppressor cell) ratio both in peripheral blood and the treated mice spleen. The spleen weight, phagocyte counts and phagocytic activity were also elevated in the treated group. In addition, Cs-Cr could protect T helper cells from the immunosuppressive effects of prednisolone acetate and cyclophosphamide. These results further substantiate the fact that Cs-Cr is an immunoregulator/biological response modifier of cellular immunity and may be potentially useful in handling immunodeficient or immunosuppressed patients.