Genomic evaluations for crossbred dairy cattle.

This short review discusses genomic evaluations for crossbreed dairy cattle from a New Zealand perspective. I briefly introduce the cow population and farm systems that have resulted in high crossbreeding rates and provide a short history of across-breed genetic and genomic evaluations used in New Zealand since 1996. I provide implementation details for the current across-breed single-step marker model (SSMM), including data sizes, solving methods, and how to account for multiple breed and breed crosses, along with a summary of the validation results. Finally, I outline future research areas that are being undertaken to improve our across-breed genomic evaluation.

Pregnancy status predicted using milk mid-infrared spectra from dairy cattle.

Accurate and timely pregnancy diagnosis is an important component of effective herd management in dairy cattle. Predicting pregnancy from Fourier-transform mid-infrared (FT-MIR) spectroscopy data is of particular interest because the data are often already available from routine milk testing. The purpose of this study was to evaluate how well pregnancy status could be predicted in a large data set of 1,161,436 FT-MIR milk spectra records from 863,982 mixed-breed pasture-based New Zealand dairy cattle managed within seasonal calving systems. Three strategies were assessed for defining the nonpregnant cows when partitioning the records according to pregnancy status in the training population. Two of these used records for cows with a subsequent calving only, whereas the third also included records for cows without a subsequent calving. For each partitioning strategy, partial least squares discriminant analysis models were developed, whereby spectra from all the cows in 80% of herds were used to train the models, and predictions on cows in the remaining herds were used for validation. A separate data set was also used as a secondary validation, whereby pregnancy diagnosis had been assigned according to the presence of pregnancy-associated glycoproteins (PAG) in the milk samples. We examined different ways of accounting for stage of lactation in the prediction models, either by including it as an effect in the prediction model, or by pre-adjusting spectra before fitting the model. For a subset of strategies, we also assessed prediction accuracies from deep learning approaches, utilizing either the raw spectra or images of spectra. Across all strategies, prediction accuracies were highest for models using the unadjusted spectra as model predictors. Strategies for cows with a subsequent calving performed well in herd-independent validation with sensitivities above 0.79, specificities above 0.91 and area under the receiver operating characteristic curve (AUC) values over 0.91. However, for these strategies, the specificity to predict nonpregnant cows in the external PAG data set was poor (0.002-0.04). The best performing models were those that included records for cows without a subsequent calving, and used unadjusted spectra and days in milk as predictors, with consistent results observed across the training, herd-independent validation and PAG data sets. For the partial least squares discriminant analysis model, sensitivity was 0.71, specificity was 0.54 and AUC values were 0.68 in the PAG data set; and for an image-based deep learning model, the sensitivity was 0.74, specificity was 0.52 and the AUC value was 0.69. Our results demonstrate that in pasture-based seasonal calving herds, confounding between pregnancy status and spectral changes associated with stage of lactation can inflate prediction accuracies. When the effect of this confounding was reduced, prediction accuracies were not sufficiently high enough to use as a sole indicator of pregnancy status.

Strategies for noise reduction and standardization of milk mid-infrared spectra from dairy cattle.

The use of Fourier-transform mid-infrared (FTIR) spectroscopy is of interest to the dairy industry worldwide for predicting milk composition and other novel traits that are difficult or expensive to measure directly. Although there are many valuable applications for FTIR spectra, noise from differences in spectral responses between instruments is problematic because it reduces prediction accuracy if ignored. The purpose of this study was to develop strategies to reduce the impact of noise and to compare methods for standardizing FTIR spectra in order to reduce between-instrument variability in multiple-instrument networks. Noise levels in bands of the infrared spectrum caused by the water content of milk were characterized, and a method for identifying and removing outliers was developed. Two standardization methods were assessed and compared: piecewise direct standardization (PDS), which related spectra on a primary instrument to spectra on 5 other (secondary) instruments using identical milk-based reference samples (n = 918) analyzed across the 6 instruments; and retroactive percentile standardization (RPS), whereby percentiles of observed spectra from routine milk test samples (n = 2,044,094) were used to map and exploit primary- and secondary-instrument relationships. Different applications of each method were studied to determine the optimal way to implement each method across time. Industry-standard predictions of milk components from 2,044,094 spectra records were regressed against predictions from spectra before and after standardization using PDS or RPS. The PDS approach resulted in an overall decrease in root mean square error between industry-standard predictions and predictions from spectra from 0.190 to 0.071 g/100 mL for fat, from 0.129 to 0.055 g/100 mL for protein, and from 0.143 to 0.088 g/100 mL for lactose. Reductions in prediction error for RPS were similar but less consistent than those for PDS across time, but similar reductions were achieved when PDS coefficients were updated monthly and separate primary instruments were assigned for the North and South Islands of New Zealand. We demonstrated that the PDS approach is the most consistent method to reduce prediction errors across time. We also showed that the RPS approach is sensitive to shifts in milk composition but can be used to reduce prediction errors, provided that secondary-instrument spectra are standardized to a primary instrument with samples of broadly equivalent milk composition. Appropriate implementation of either of these approaches will improve the quality of predictions based on FTIR spectra for various downstream applications.

Application of genomic evaluation to dairy cattle in New Zealand.

A hybrid method of estimating genomically enhanced breeding values (GEBV) that uses features of a single-step approach and traditional national estimated breeding value (EBV), based on pedigree, as the starting point was developed and assessed. The method uses deregressed EBV from the traditional EBV estimation procedures and a pedigree matrix that is augmented by a genomic relationship matrix based on a Euclidean distance (EDM) in a Gaussian kernel. Genotypes were obtained using the Illumina BovineSNP50 BeadChip (Illumina Inc., San Diego, CA). The pedigree information is restricted to animals with genotypes, as well as all of their ancestors, resulting in a system of equations that is considerably smaller than that of the national evaluation. Genome-wide association studies were used to identify regions of the genome that had high association with the traits in the New Zealand national breeding objective. The EDM were created for each selected region. The amount of variance accounted for by each region was estimated, and the variances, relative to the EDM excluding these areas, were used to create trait-specific weighted EDM that were used for the evaluations. The evaluation is done on the restricted data set and is a reversal of the deregression procedure using the augmented pedigree-based relationship matrix. The method was tested using data on 7,204 progeny-tested sires, in which the daughter records for the 3 youngest cohorts (i.e., validation data; n=1,410) were excluded. Evaluations were done for the 7 traits (3 production, 4 nonproduction) in the New Zealand national breeding objective. Regression of the traditional EBV based on daughter information on the GEBV for validation sires had an average slope of 0.99 (range 0.93 to 1.06); the average correlation between the EBV was 0.79 (range 0.56 to 0.84). The average slope and correlation for the previously used blended GEBV were 0.64 and 0.61, respectively. The method was applied to all genotyped animals that included approximately 13,000 genotyped males and 47,000 genotyped females and their ancestors. The correlation between the traditional EBV and GEBV of the proven bulls was 0.99; the correlations obtained from the previously used blended GEBV were 0.88 (no inflation adjustment) and 0.94 (following inflation adjustment). The values for the unproven bulls were 0.95 (parent average EBV and GEBV), 0.56 (blended GEBV, no inflation adjustment), and 0.88 (blended GEBV, following inflation adjustment). The use of trait-specific weighted EDM provided a 1 to 2% improvement in the accuracy of the genomic evaluations of the production traits and no improvement in the nonproduction traits. The hybrid method of estimating GEBV was found to be considerably less biased and generally more accurate than the previously used blended genomic breeding value.

Understanding cohort differences in appraisals of reconstruction priorities of mental health systems in postconflict Liberia.

OBJECTIVE: This study analyzes the relationship between informants' age and their assessment of mental health needs in postconflict society and examines if mental health needs assessment priorities differ depending upon whether or not the informant was exposed to the Liberian civil war. METHODS: cross-sectional survey was conducted in March 2009 to obtain data on mental health needs of Liberian children, adolescents and young adults. A total of 171 individuals were interviewed. The data were analyzed using a two- way ANOVA. RESULTS: Elder respondents expressed a preference for young adults to receive services in a church/mosque (F = 4.020, p < .05); for adolescents in volunteer programs (F = 3.987, p < .05) and for children in sports programs (F = 4.396, p < .05). Experiencing conflict did exert some influence on treatment setting preferences. Those who resided outside Liberia during the conflict cited a preference for traditional healers and medical clinics. However, this preference was for the children and young adult age categories. Those who experienced the civil war reported significantly higher preferences for adolescent services to be located in medical clinics, with traditional healers, and in churches/mosques. CONCLUSION: This study provides additional support for the premise that the utilization of psychiatric services needs to be viewed from the perspective of Liberians and that there are differences in preferences across groups. Our results suggest that service providers and policy makers take into account the age of the patient when deciding where to locate treatment settings for the population.

Assessment of the needs of vulnerable youth populations in post-conflict Liberia.

OBJECTIVE: The study examined key informants' perceptions of the emotional impact of traumatic events, major problems, functional limitations and appropriate treatment settings for children, adolescents, and young adults in post-conflict Liberia. METHOD: This research is a based on cross-sectional survey conducted between March 30, 2009 and April 30, 2009 in Liberia with 171 local key Liberian informants. Analysis was conducted using mixed methods. The findings we will report were collected in the qualitative portion of the survey. RESULTS: We found that while different interventions were preferred for different types of young people, some interventions were mentioned for all youth and by all age and gender groups of key informants. These included counseling, education, and skills training. Also frequently chosen were housing, community reintegration, recreation, and medical care. In general, key informants reported similar concerns regardless of their ages or genders. Notable exceptions to this were in interventions for youth who joined fighting forces. Men over 50 were the only ones to recommend apology and reparations. Similarly, in recommendations for criminals and violent youth, a number of men mentioned prison, whereas the women did not. CONCLUSION: Our findings suggest that the needs of post-conflict Liberian youth span a variety of domains, including physical, emotional, medical, psychological, and educational. These findings can be used to guide the development of treatment programs for these young people.

Genomic predictions for New Zealand dairy bulls and integration with national genetic evaluation.

A method is described for the prediction of breeding values incorporating genomic information. The first stage involves the prediction of genomic breeding values for genotyped individuals. A novel component of this is the estimation of the genomic relationship matrix in the context of a multi-breed population. Because not all ancestors of genotyped animals are genotyped, a selection index procedure is used to blend genomic predictions with traditional ancestral information that is lost between the process of deregression of the national breeding values and subsequent re-estimation using the genomic relationship matrix. Finally, the genomically enhanced predictions are filtered through to nongenotyped descendants using a regression procedure.

Estimation of test-day model (co)variance components across breeds using New Zealand dairy cattle data.

In New Zealand, a large proportion of cows are currently crossbreds, mostly Holstein-Friesians (HF) x Jersey (JE). The genetic evaluation system for milk yields is considering the same additive genetic effects for all breeds. The objective was to model different additive effects according to parental breeds to obtain first estimates of correlations among breed-specific effects and to study the usefulness of this type of random regression test-day model. Estimates of (co)variance components for purebred HF and JE cattle in purebred herds were computed by using a single-breed model. This analysis showed differences between the 2 breeds, with a greater variability in the HF breed. (Co)variance components for purebred HF and JE and crossbred HF x JE cattle were then estimated by using a complete multibreed model in which computations of complete across-breed (co)variances were simplified by correlating only eigenvectors for HF and JE random regressions of the same order as obtained from the single-breed analysis. Parameter estimates differed more strongly than expected between the single-breed and multibreed analyses, especially for JE. This could be due to differences between animals and management in purebred and non-purebred herds. In addition, the model used only partially accounted for heterosis. The multibreed analysis showed additive genetic differences between the HF and JE breeds, expressed as genetic correlations of additive effects in both breeds, especially in linear and quadratic Legendre polynomials (respectively, 0.807 and 0.604). The differences were small for overall milk production (0.926). Results showed that permanent environmental lactation curves were highly correlated across breeds; however, intraherd lactation curves were also affected by the breed-environment interaction. This result may indicate the existence of breed-specific competition effects that vary through the different lactation stages. In conclusion, a multibreed model similar to the one presented could optimally use the environmental and genetic parameters and provide breed-dependent additive breeding values. This model could also be a useful tool to evaluate crossbred dairy cattle populations like those in New Zealand. However, a routine evaluation would still require the development of an improved methodology. It would also be computationally very challenging because of the simultaneous presence of a large number of breeds.

Genetics of body condition score in New Zealand dairy cows.

Body condition score (BCS) data were collected on 169,661 first-parity cows from herds participating in progeny testing schemes and linear type assessment. Genetic and residual variances for BCS estimated across time using a quadratic random regression model were found to be largest at the start of lactation. Heritability estimates ranged from 0.32 to 0.23 from d 1 to 200 of lactation, with a mean of 0.26. Genetic correlations between BCS and other traits were estimated using 2 approaches: 1) a multivariate analysis that included BCS and live weight, both adjusted for stage of lactation; 270-d cumulative yields of milk, fat, and protein; average somatic cell score; and 2 measures of fertility; and 2) a bivariate random regression analysis in which BCS was considered to be a longitudinal trait across time, with the same measurements as in approach 1 for all other traits. Genetic correlations of BCS with the 2 fertility traits were 0.43 and 0.50 using the multivariate analysis; the corresponding random regression estimates between BCS as a longitudinal trait across time and 2 measures of fertility were 0.35 to 0.44 and 0.40 to 0.49, and tended to increase with stage of lactation. Genetic correlations estimated using the random regression model fluctuated around the multivariate estimates for live weight and somatic cell score, which were 0.50 and -0.12, respectively. Genetic correlations estimated using the multivariate analysis of BCS with fat and protein yields were close to zero. With the random regression model, genetic correlations between BCS and fat and protein yields were positive at d 1 of lactation (0.16 and 0.08, respectively) and were negative by d 200 of lactation (-0.25 and -0.20, respectively). In pastoral production systems, such as those typical in New Zealand, there appears to be an advantage in the total lactation yields of fat and protein for cows of higher BCS in early lactation, which is likely to be because these cows have body reserves that are available to be mobilized in later lactation, when feed resources are sometimes limited.

Breeding dairy cows for the future in New Zealand.

A brief history of the breeding of dairy cattle in New Zealand is provided. Dairy farming in New Zealand is unique compared with the majority of dairy systems in the developed world. New Zealand has a dependence on grass-based diets and a strict requirement for a 365-day calving interval. Four main areas are discussed: future traits to evaluate, advances in genetic evaluation technologies, impacts of crossbreeding, and future progeny testing schemes. These areas are not independent, e.g. the trend of increasing numbers of crossbred cattle in the national herd will have major impacts on the design of breeding schemes. It is foreseeable that in the future there will be improvements in the national breeding goal to better reflect on-farm profitability, and in the definition of traits and methods of data capture within the national breeding goal. Methods of selection and genetic evaluation that are currently feasible for a small population will become feasible for large populations as computing power improves. Genetic improvement of cows in New Zealand will continue to be a critical component of the increased economic efficiency achieved on dairy farms in this country.

Phenotypic associations between traits other than production and longevity in New Zealand dairy cattle.

A proportional hazards model was used to investigate the phenotypic effect of traits other than production (TOP) on true and functional longevity across purebred and crossbred Holstein-Friesian and Jersey dairy cattle in registered and commercial herds in New Zealand. The hazard function was described as the product of a baseline hazard function and the time-independent effects of age at first calving, heterosis, proportion of breed, period of last calving relative to herdmates, and TOP; a time-dependent effect of herd-year was also included. The influence of TOP on functional longevity was assessed by adjusting true longevity for the time-independent effects of production values as well as the time-dependent effects of deviation of milk, fat, and protein yield within contemporary group. All analyses were stratified by breed, and separate analyses were carried out for registered or commercial herds. All TOP were significantly related to true and functional longevity. Obvious differences existed in the relative influence of individual TOP on longevity in registered or commercial herds. Of the individual TOP describing the physical characteristics of the cow, the udder-related TOP exhibited the largest influence on functional longevity. Farmer opinion explained the largest proportion of variation in true and functional longevity among cows. In commercial herds, the risk of culling in cows with very low farmer opinion was 1.5 to 2.0 times that in cows with average or high farmer opinion.

Factors affecting commercial application of embryo technologies in New Zealand: a modelling approach.

New reproductive technologies include sexed sperm and embryo-based technologies. The technology of sperm sexing, for various reasons, is not available in New Zealand and its use has not been modelled. Embryo technologies are however already in use on a limited scale and various scenarios for their use in both the dairy and beef industries in New Zealand have been modelled. This review briefly discusses the various technologies available and some of their potential strengths and weaknesses. In the dairy industry, modelling has been used to simulate the production of breeding bulls for large breeding companies and the production of replacement heifers in dairy herds. For the beef industry, similar modelling has been carried out to determine the opportunities for more efficient beef production. All the models confirmed that at current levels of performance, embryo-based reproductive technologies are usually not profitable in New Zealand except in niche market situations where the returns from the resulting offspring are significantly greater than can be obtained from natural mating or artificial insemination (AI) reproduction systems. This is confirmed by the low uptake of these technologies in this country to date. Even if performance lifts to levels similar to AI, profitability is likely to occur only if the costs of pregnancies to embryo-based reproductive technologies can occur at prices less than two to four times greater than AI or natural mating. This break-even requirement depends on the returns that can be achieved and the advantages that can be captured by the technology over and above those available from AI or natural mating. Two new uses for reproductive technologies in dairy cattle could be the proliferation of novel or rare genotypes from gene discovery programs and improving the female reproductive rate for optimal marker assisted selection. In both these uses the technology is not at present competing with AI or natural mating. The challenge exists therefore for the biological scientists to satisfy these requirements, coupled with the ethical and human factors involved in the introduction of any new technology. Potential end users of the technologies have been surveyed. They are quite positive about the technologies provided they can use them profitably and are keen to obtain more information about them.

Genetic and phenotypic parameters for type and production in Guernsey dairy cows.

Heritabilities; genetic and phenotypic correlations for milk, fat, and protein production; and linear type traits were estimated from a sire model including sire relationships using multiple-trait REML. For the milk production traits, 68,109 first parity records were analyzed. Heritabilities ranged from .31 to .37, genetic correlations between the milk production traits ranged from .80 to .92, and phenotypic correlations ranged from .86 to .94. Linear type traits from 12,996 cows on 15 traits were used to estimate heritabilities and genetic and phenotypic correlations between linear type traits. The heritabilities ranged from .53 for stature to .09 for foot angle. Rear udder height and rear udder width had the highest positive genetic correlation (.85), whereas dairy form and udder depth had the highest negative genetic correlation (-.41). When the first parity production records were merged with type records for cows, 9867 records on 18 traits were obtained. Dairy form, rear udder height, and rear udder width had strong to moderate positive genetic correlations with the three production traits. Fore udder attachment and udder depth had moderate negative genetic correlations with the three milk production traits. These results suggest that selection for improvement of milk production will lead to correlated increases in dairy form, rear udder height, rear udder width, and udder depth and to correlated decreases in the strength of fore udder attachment.

Prediction of response with overlapping generations accounting for multistage selection.

A generalization of Hill's equations predicting response to selection is developed that accounts for multiple stage selection in either or both sexes. The method accounts for the flow of genes for animals selected at later stages. This allows for the use of genetic gains from later stages, which explains the reduction in variance due to previous selection. Genetic gains from different selection differentials in each reproductive pathway are incorporated into the equations. The asymptotic response to a single cycle of selection is shown to agree with classical selection theory.The method is applied to a dairy progeny testing scheme representative of an artificial insemination organization in the USA. Two models were compared: (1) the first model accounted for two-stage selection of males, the first stage being based on pedigree information and the second stage on both pedigree and progeny test information; and (2) the second model assumed single-stage male selection. Selection was based on milk volume, milk fat, and milk protein yields. The predicted asymptotic rates for a single cycle of selection were overestimated by 6% and the cumulative response to continuous selection over 20 years was overestimated by 8% by assuming singlestage male selection.

Becoming deprofessionalized: one aspect of the staff nurse's perspective on computer-mediated nursing care plans.

Negative impacts on the professionalization of staff nurses by the development and use of computerized nursing care plans are presented as a selected finding of a qualitative study. A symbolic interaction framework, using nurses' stories as communicated in semi-structured interviews, yielded meaning and behavior in metaphorical form. The computerized system for patient care planning, and the larger system in which it is embedded, contribute to loss of autonomy, loss of individualization of care, and loss of nursing expertise. Some questions that should be addressed now are identified.

The effect of drug co-payments on utilization and cost of pharmaceuticals in a health maintenance organization.

This study analyzed how the use and cost of pharmaceuticals varied by level of drug co-payment in a staff model health maintenance organization (HMO). An historical cohort design was used to study changes in drug utilization and drug costs in 19,982 continuously enrolled beneficiaries less than the age of 65. The beneficiaries initially had no drug co-payments, but experienced co-payment rates of $1.50, $3.00, and $3.00 plus other benefit changes during a three-year period. A comparison cohort of 23,164 beneficiaries was selected from the same setting who were subject to no drug co-payment during the same time period. Data on the use and cost of medications were obtained from an automated data system. Adjusted analyses for each time period controlled for age, sex, years in the Group Health Cooperative (GHC), and prior year utilization (or cost). The initial $1.50 drug co-payment was associated with a drop of 10.7% in the number of prescriptions filled relative to change in the comparison cohort. The decrease was greatest for discretionary drugs at each level of co-payment. The implementation of progressively greater levels of co-payments continued to have a significant effect on drug utilization since each co-payment level resulted in an additional reduction in drug utilization; 10.6% with the $3 co-payment and 12.0% when the $3 drug co-payment was combined with other cost-sharing provisions. Co-payments were associated with lower per capita drug costs and higher per prescription unit costs.

Cross-cultural conflict: the American nurse manager and a culturally mixed staff.

Many hospitals have employed nurses from other countries in order to cope with the problems of the nursing shortage in the United States. Mixing nurses from different cultures may create cross-cultural conflicts related to differing hierarchies of needs and to differences in language, decision making, viewing conflicts, behavioral norms, and role expectations. Nursing managers can develop feasible and effective means for solving cross-cultural conflicts if they are aware of these cultural differences, encourage the nurses involved to discuss their differences, and expand their own ability to listen.