Bias, dispersion, and accuracy of genomic predictions for feedlot and carcase traits in Australian Angus steers.

BACKGROUND: Improving feedlot performance, carcase weight and quality is a primary goal of the beef industry worldwide. Here, we used data from 3408 Australian Angus steers from seven years of birth (YOB) cohorts (2011-2017) with a minimal level of sire linkage and that were genotyped for 45,152 SNPs. Phenotypic records included two feedlot and five carcase traits, namely average daily gain (ADG), average daily dry matter intake (DMI), carcase weight (CWT), carcase eye muscle area (EMA), carcase Meat Standard Australia marbling score (MBL), carcase ossification score (OSS) and carcase subcutaneous rib fat depth (RIB). Using a 7-way cross-validation based on YOB cohorts, we tested the quality of genomic predictions using the linear regression (LR) method compared to the traditional method (Pearson's correlation between the genomic estimated breeding value (GEBV) and its associated adjusted phenotype divided by the square root of heritability); explored the factors, such as heritability, validation cohort, and phenotype that affect estimates of accuracy, bias, and dispersion calculated with the LR method; and suggested a novel interpretation for translating differences in accuracy into phenotypic differences, based on GEBV quartiles (Q1Q4). RESULTS: Heritability (h2) estimates were generally moderate to high (from 0.29 for ADG to 0.53 for CWT). We found a strong correlation (0.73, P-value < 0.001) between accuracies using the traditional method and those using the LR method, although the LR method was less affected by random variation within and across years and showed a better ability to discriminate between extreme GEBV quartiles. We confirmed that bias of GEBV was not significantly affected by h2, validation cohort or trait. Similarly, validation cohort was not a significant source of variation for any of the GEBV quality metrics. Finally, we observed that the phenotypic differences were larger for higher accuracies. CONCLUSIONS: Our estimates of h2 and GEBV quality metrics suggest a potential for accurate genomic selection of Australian Angus for feedlot performance and carcase traits. In addition, the Q1Q4 measure presented here easily translates into possible gains of genomic selection in terms of phenotypic differences and thus provides a more tangible output for commercial beef cattle producers.

ImmuneDEX: a strategy for the genetic improvement of immune competence in Australian Angus cattle.

In animal breeding and genetics, the ability to cope with disease, here defined as immune competence (IC), with minimal detriment to growth and fertility is a desired objective which addresses both animal production and welfare considerations. However, defining and objectively measuring IC phenotypes using testing methods which are practical to apply on-farm has been challenging. Based on previously described protocols, we measured both cell-mediated immune response (Cell-IR) and antibody-mediated immune response (Ab-IR) and combined these measures to determine an animal's IC. Using a population of 2,853 Australian Angus steers and heifers, we compared 2 alternative methods to combine both metrics into a single phenotype to be used as a tool for the genetic improvement of IC. The first method, named ZMEAN, is obtained by taking the average of the individual metrics after subjecting each to a Z-score standardization. The second, ImmuneDEX (IDEX), is a weighted average that considers the correlation between Cell-IR and Ab-IR, as well as the difference in ranking of individuals by each metric, and uses these as weights in the averaging. Both simulation and real data were used to understand the behavior of ZMEAN and IDEX. To further ascertain the relationship between IDEX and other traits of economic importance, we evaluated a range of traits related to growth, feedlot performance, and carcass characteristics. We report estimates of heritability of 0.31 ± 0.06 for Cell-IR, 0.42 ± 0.06 for Ab-IR, 0.42 ± 0.06 for ZMEAN and 0.370 ± 0.06 for IDEX, as well as a unity genetic correlation (rg) between ZMEAN and IDEX. While a moderately positive rg was estimated between Cell-IR and Ab-IR (rg = 0.33 ± 0.12), strongly positive estimates were obtained between IDEX and Cell-IR (rg = 0.80 ± 0.05) and between IDEX and Ab-IR (rg = 0.85 ± 0.04). We obtained a moderately negative rg between IC traits and growth including an rg = -0.38 ± 0.14 between IDEX and weaning weight, and negligible with carcass fat measurements, including an rg = -0.03 ± 0.12 between IDEX and marbling. Given that breeding with a sole focus on production might inadvertently increase susceptibility to disease and associated antibiotic use, our analyses suggest that ImmuneDEX will provide a basis to breed animals that are both highly productive and with an enhanced ability to resist disease.

Associations between immune competence phenotype and feedlot health and productivity in Angus cattle.

Genetic strategies aimed at improving general immune competence (IC) have the potential to reduce the incidence and severity of disease in beef production systems, with resulting benefits of improved animal health and welfare and reduced reliance on antibiotics to prevent and treat disease. Implementation of such strategies first requires that methodologies be developed to phenotype animals for IC and demonstration that these phenotypes are associated with health outcomes. We have developed a methodology to identify IC phenotypes in beef steers during the yard weaning period, which is both practical to apply on-farm and does not restrict the future sale of tested animals. In the current study, a total of 838 Angus steers, previously IC phenotyped at weaning, were categorized as low (n = 98), average (n = 653), or high (n = 88) for the IC phenotype. Detailed health and productivity data were collected on all steers during feedlot finishing, and associations between IC phenotype, health outcomes, and productivity were investigated. A favorable association between IC phenotype and number of mortalities during feedlot finishing was observed with higher mortalities recorded in low IC steers (6.1%) as compared with average (1.2%, P < 0.001) or high (0%, P = 0.018) IC steers. Disease incidence was numerically highest in low IC steers (15.3 cases/100 animals) and similar in average IC steers (10.1 cases/100 animals) and high IC steers (10.2 cases/100 animals); however, differences between groups were not significant. No significant influence of IC phenotype on average daily gain was observed, suggesting that selection for improved IC is unlikely to incur a significant penalty to production. The potential economic benefits of selecting for IC in the feedlot production environment were calculated. Health-associated costs were calculated as the sum of lost production costs, lost capital investment costs, and disease treatment costs. Based on these calculations, health-associated costs were estimated at AUS$103/head in low IC steers, AUS$25/head in average IC steers, and AUS$4/head in high IC steers, respectively. These findings suggest that selection for IC has the potential to reduce mortalities during feedlot finishing and, as a consequence, improve the health and welfare of cattle in the feedlot production environment and reduce health-associated costs incurred by feedlot operators.

Immune competence traits assessed during the stress of weaning are heritable and favorably genetically correlated with temperament traits in Angus cattle1.

Selection for production traits with little or no emphasis on health-related traits has the potential to increase susceptibility to disease in food-producing animals. A possible genetic strategy to mitigate such effects is to include both production and health traits in the breeding objective when selecting animals. For this to occur, reliable methodologies are required to assess beneficial health traits, such as the immune capacity of animals. We describe here a methodology to assess the immune competence of beef cattle which is both practical to apply on farm and does not restrict the future sale of tested animals. The methodology also accommodates variation in prior vaccination history of cohorts of animals being tested. In the present study, the immune competence phenotype of 1,100 Angus calves was assessed during yard weaning. Genetic parameters associated with immune competence traits were estimated and associations between immune competence, temperament, and stress-coping ability traits were investigated. Results suggested that immune competence traits, related to an animal's ability to mount both antibody and cell-mediated immune responses, are moderately heritable (h2 = 0.32 ± 0.09 and 0.27 ± 0.08, respectively) and favorably genetically correlated with the temperament trait, flight time (r = 0.63 ± 0.31 and 0.60 ± 0.29 with antibody and cell-mediated immune responses, respectively). Development of methodologies to assess the immune competence phenotype of beef cattle is a critical first step in the establishment of genetic selection strategies aimed at improving the general disease resistance of beef herds. Strategies aimed at reducing the incidence of disease in beef cattle are expected to significantly improve animal health and welfare, reduce reliance on the use of antibiotics to treat disease, and reduce disease-associated costs incurred by producers.

The impacts of Ascaridia galli on performance, health, and immune responses of laying hens: new insights into an old problem.

Gastrointestinal nematodes are re-emerging in countries where the popularity of free-range poultry production systems is increasing. Amongst all gastrointestinal nematodes, Ascaridia galli is of significant concern due to the parasite's direct life cycle and ability to survive extreme environmental conditions. In laying hens, A. galli parasites have been associated with reduced health, welfare, immunity, and egg production. Direct losses are caused by obstruction and damage of the intestinal tract in hens when high worm burdens are present. These result in reduction in egg production and body weight of infected laying hens, consequently leading to significant economic losses for farmers. Furthermore, heavy infections with A. galli may lead to increased mortality within the flock. Indirect losses are due to suppression of immune system function which can increase susceptibility to secondary infections. Infection with A. galli can also alter nutrient utilization and absorption. Levels of anti- A. galli serum and egg yolk antibodies increase following A. galli infection. Elevated antibodies can be used as an indicator of current or previous infections and therefore can be used as a diagnostic tool. The impact of A. galli on hen health and welfare manifests through the depletion of liver lipid reserves and increased use of energy reserves to mount immune responses against the parasite. This review highlights the variable effects of A. galli infection on the performance, health, egg quality, and emphasizes especially on immune responses of free-range laying hens as well as it evaluates various potential detection methods and preventive and control measures of this parasitic disease.

Production and active transport of immunoglobulins within the ruminant mammary gland.

The primary function of the mammary gland is to produce milk to feed the suckling young. In ruminants, ingestion of maternal antibodies in mammary secretions facilitates the transfer of passive immunity from mother to young, providing antibody-mediated immunity to protect the neonate against disease while their own immune system develops. Antibodies in mammary secretions also play a role in protecting the gland itself against infection. Here we provide a brief history of studies on immunoglobulins in ruminant mammary secretions and review recent findings describing the mechanisms by which antibody-producing plasmablasts are recruited to the gland and immunoglobulins are transported into ruminant mammary secretions. An improved understanding of the complex interaction of factors which regulate immunoglobulin production and transfer to the ruminant mammary gland may provide opportunities to enhance antibody concentrations in mammary secretions during normal lactation and in response to immunisation. Strategies aimed at increasing antibody concentrations in ruminant mammary secretions have the potential to improve the ability of animals to resist mammary infections, enhance the transfer of passive immunity from mother to young and increase the feasibility of harvesting antibodies from the mammary secretions for use in commercial therapeutic applications for humans and domesticated animals.

Detection of Ascaridia galli infection in free-range laying hens.

Reliable methods for detection of A. galli infection using excreta egg count (EEC) and ELISA assays to determine A. galli specific IgY levels in serum and yolk samples were compared from hens infected naturally and artificially. Artificially infected hens were used to generate samples for analysis of preferred detection methods and to generate contaminated ranges for use in the naturally acquired infection study in which Lohmann Brown hens (n = 200) at 16 weeks of age were randomly assigned to four treatments with five replicate pens. Hens of negative control (NC) ranged on a decontaminated area, hens of low infection, medium infection and positive control (PC) ranged on the areas previously contaminated by hens artificially infected with 250, 1000 and 2500 A. galli eggs/hen, respectively. Additionally, hens of PC were orally infected with 1000 A. galli eggs/hen. Anti A. galli antibody levels in hen serum (SIgY) and yolk (YIgY) were measured before range access, and 2, 7 and 12 weeks after access to the contaminated ranges. In a natural infection study, eggs were detected in the excreta of all hens 4 weeks after range access, with the exception of NC in which no eggs were detected. EEC increased to reach maximum value (2204 ±â€¯307 eggs/g) after 11 weeks of range access and then declined at 12 weeks (905 ±â€¯307eggs/g) (p < 0.01). While SIgY OD values were not different in hens between any groups before range access, after 2 weeks, both SIgY and YIgY gradually increased in hens of PC (1.17 ±â€¯0.03 and 0.88 ±â€¯0.04) and medium infection (1.07 ±â€¯0.03 and 0.96 ±â€¯0.04) compared to low infection (0.38 ±â€¯0.03 and 0.29 ±â€¯0.04) (p < 0.01) and NC. After 12 weeks, SIgY were similar in hens of PC, medium and low groups whereas YIgY was higher in hens of low infection group (p < 0.01). Sensitivity of the serum and egg yolk antibody levels assay to detect A. galli infection was 100% and 96%, respectively, whereas the pooled EEC method yielded a sensitivity of 93%. The results of this study suggest that hens naturally infected with A. galli produce both SIgY and YIgY at different levels depending on the infection intensity and duration of exposure which allows the diagnosis of prior infection or early diagnosis of current infection. Use of the practical and non-invasive method of yolk sample analysis for detecting IgY can be just as informative as using serum samples to detect A. galli infection.

A Novel Protocol to Assess Acclimation Rate in Bos taurus Heifers during Yard Weaning.

The speed with which animals acclimate to a new environment could be an important measure of ability to cope with management induced stress. This study developed a measure of acclimation rate in a group of 50 Bos taurus heifers during yard weaning over nine days. We recorded the time and order in which heifers moved through a novel funnel structure into a feeding yard daily. We hypothesised that addition of an obstacle at the entrance would increase the time it took heifers to move through the funnel, but that they would acclimate to the obstacle over a three-day period. The change in latency to move through could then be used as a measure of acclimation rate. We hypothesised that individuals which acclimated to obstacles at a faster rate might display favourable temperament as assessed by flight time. All heifers took longer to move through the funnel after a novel object was introduced, then latency decreased over the following two days while the object was present. This indicates the protocol could be useful for measuring acclimation rate at a group level. Individual acclimation rate variables, measured as change in times and orders of heifers between test days, did not appear to have any consistent relationships with flight time or weight change during or post-weaning (p > 0.05). We concluded that the protocol was inappropriate for assessing acclimation rate at an individual level, due to social effects while testing heifers as a group. Heifers which were consistently one of the first 20 to move through the funnel had a significantly greater average weight 5 and 10 months post-weaning (345 ± 9 kg and 518 ± 10 kg respectively) than heifers which were consistently one of the last 20 through the funnel (311 ± 8 kg and 484 ± 8 kg respectively; p < 0.001). This may indicate order of movement through the funnel was related to feeding motivation or another aspect of temperament not reflected by flight time.

Keratin and S100 calcium-binding proteins are major constituents of the bovine teat canal lining.

The bovine teat canal provides the first-line of defence against pathogenic bacteria infecting the mammary gland, yet the protein composition and host-defence functionality of the teat canal lining (TCL) are not well characterised. In this study, TCL collected from six healthy lactating dairy cows was subjected to two-dimensional electrophoresis (2-DE) and mass spectrometry. The abundance and location of selected identified proteins were determined by western blotting and fluorescence immunohistochemistry. The variability of abundance among individual cows was also investigated. Two dominant clusters of proteins were detected in the TCL, comprising members of the keratin and S100 families of proteins. The S100 proteins were localised to the teat canal keratinocytes and were particularly predominant in the cornified outermost layer of the teat canal epithelium. Significant between-animal variation in the abundance of the S100 proteins in the TCL was demonstrated. Four of the six identified S100 proteins have been reported to have antimicrobial activity, suggesting that the TCL has additional functionality beyond being a physical barrier to invading microorganisms. These findings provide new insights into understanding host-defence of the teat canal and resistance of cows to mastitis.

Transfer of intestinal bacterial components to mammary secretions in the cow.

Results from large multicentre epidemiological studies suggest an association between the consumption of raw milk and a reduced incidence of allergy and asthma in children. Although the underlying mechanisms for this association are yet to be confirmed, researchers have investigated whether bacteria or bacterial components that naturally occur in cow's milk are responsible for modulating the immune system to reduce the risk of allergic diseases. Previous research in human and mice suggests that bacterial components derived from the maternal intestine are transported to breast milk through the bloodstream. The aim of our study was to assess whether a similar mechanism of bacterial trafficking could occur in the cow. Through the application of culture-independent methodology, we investigated the microbial composition and diversity of milk, blood and feces of healthy lactating cows. We found that a small number of bacterial OTUs belonging to the genera Ruminococcus and Bifidobacterium, and the Peptostreptococcaceae family were present in all three samples from the same individual animals. Although these results do not confirm the hypothesis that trafficking of intestinal bacteria into mammary secretions does occur in the cow, they support the existence of an endogenous entero-mammary pathway for some bacterial components during lactation in the cow. Further research is required to define the specific mechanisms by which gut bacteria are transported into the mammary gland of the cow, and the health implications of such bacteria being present in milk.

Analysis of leukocyte populations in Canadian Holsteins classified as high or low immune responders for antibody- or cell-mediated immune response.

Selection of dairy cattle for increased milk production with little or no emphasis on health traits leads to an increased prevalence of disease. A possible genetic solution to this problem is to combine production and immune response traits in a weighted selection index. In the current study, leukocyte populations in heifers identified as having a high antibody-mediated immune response (HiAMIR) or high cell-mediated immune response (HiCMIR) phenotype were compared before and after immunization in order to identify leukocyte population profiles associated with these phenotypes. The results demonstrated that the HiCMIR-phenotype animals had a higher baseline proportion of gamma-delta T-cells in peripheral blood. Also, the observed increase in the proportion of B-cells in peripheral blood in response to immunization was greater in the HiAMIR-phenotype animals. It is expected that identifying leukocyte population profiles associated with immune response phenotypes will improve our ability to identify animals with enhanced overall immune responsiveness.