Biomedical subjects

L R Schaeffer

Publications and source records attributed to L R Schaeffer.

At least 37 records · Page 2Linked to original sources

PubMed1997

Comparison of possible covariates for use in a random regression model for analyses of test day yields.

Random regression models have been proposed for the genetic evaluation of dairy cattle using test day records. Random regression models contain linear functions of fixed and random coefficients and a set of covariates to describe the shapes of lactation curves for groups of cows and for individual cows. Previous work has used a linear function of five covariates to describe lactation shape. This study compared the function of five covariates with a function of only three covariates in three random regression models. Comparisons of estimates of components of variances and covariances, as well as comparisons of EBV and their prediction errors for milk yield, were made among models. Small practical differences existed between models in all respects. The model using regressions with five covariates had a slight advantage for comparison of prediction error variances of daily yields.

Animals↗

PubMed1996

Factors influencing international comparisons of dairy sires.

A method of dairy sire evaluation across multiple countries is described. Factors influencing this method are overestimation of genetic trends within countries, inclusion of evaluations of imported bulls, years of birth of the bulls included in the analysis, and estimates of genetic correlations between countries. Fall 1994 evaluations for milk, fat, and protein yields from Canada (4559 bulls), Germany (5894 bulls), and France (8419 bulls) were used to study the effect of these factors. After inclusion of ancestors there were 21,555 bulls in total. Eight data files were created based on combinations of three factors: 1) bulls born from 1970 to present versus bulls born from 1979 to present, 2) all bulls included versus imported bulls omitted, and 3) official Canadian evaluations for all lactations versus Canadian evaluations for first lactation only. Separate evaluations for two of the data files assumed a uniform genetic correlation of 0.995 between countries. Rankings of top bulls from analyses were affected by all factors to various degrees, depending on the country. Evaluations of imported bulls have an effect on bull rankings and probably should not be included. An assumed uniform genetic correlation between countries of 0.995 may not be appropriate. Proper methods and data for estimation of the genetic correlation between countries should be sought.

Animals↗

PubMed1996

Multiple-trait prediction of lactation yields for dairy cows.

A multiple-trait procedure is described for predicting 305-d lactation yields for milk, fat, and protein that incorporates information about standard lactation curves and covariances between yields for milk, fat, and protein. Test day yields are weighted by their relative variances, and standard lactation curves of cows from similar breed, region, lactation number, age, and season of calving are used for the estimation of lactation curve parameters for each cow. Accuracies of the test interval method and the multiple-trait procedure were comparable. In addition, the multiple-trait procedure can handle long intervals between test days as well as test days with milk only recorded and can make 305-d predictions on the basis of just one test day record per cow. The procedure also lends itself to the calculation of peak yield, day of peak yield, yield persistency, and expected test-day yields, which could be useful management tools for a producer on a milk recording program.

Animals↗

PubMed1995

Estimation of genetic parameters for test day records of somatic cell score.

The present study estimated variance components for test day records of somatic cell score and production traits. Data consisted of 235,100 test day observations recorded between 1986 and 1994 on lactations 1 to 3 of 15,922 Holstein cows from 143 herds. Records were considered as repeated observations within a lactation and as different traits across lactations. The multiple-trait animal model for analysis included random animal additive genetic and permanent environment effects by lactation. Fixed effects included herd test date and a set of four covariables for days in lactation, estimated by parity, age, and season, which accounted for the shape of the lactation curve. Gibbs sampling chains were carried out separately for somatic cell score and milk production and fat and protein yields. Heritabilities of somatic cell score for lactations 1 to 3 were .09, .09, and .11, respectively. Genetic correlations between lactations were high (.88, .79, and .95 between lactations 1 and 2, 1 and 3, and 2 and 3, respectively). Correlations between permanent environment effects were smaller (.29, .19, and .46 between lactations 1 and 2, 1 and 3, and 2 and 3, respectively). Heritabilities and correlations between permanent environment effects were higher for production traits than for somatic cell score. Genetic correlations between lactations for production traits were similar to those for somatic cell score. Variances between lactations differed significantly, indicating that observations from different lactations should no be considered as repeated observations of the same trait.

Animals↗

PubMed1995

Genetic evaluation for somatic cell score with a test day model for multiple lactations.

A multiple lactation model for test day data was applied to predict genetic merit for somatic cell scores of Canadian Holsteins. The model for genetic evaluation included a fixed effect for herd test date, fixed regressions on functions of days of lactation, random effects of permanent environment within lactation, random genetic effects on animal, and residual effects. Records from the first three lactations were used and treated as different traits. Procedures for this model, developed for national genetic evaluation for somatic cell score in Canada, were found to be practical. Use of starting values from the previous genetic evaluation reduced the number of rounds necessary to reach convergence. Test day models were compared with several single-trait models based on lactation average of somatic cell score in terms of computing efficiency and ranking of animals. Differences between EBV from the test day model and EBV from a repeatability model for lactation average were small for bulls with many daughters, but differences were large with EBV from a single-trait model for first lactation average of somatic cell count. Association were desirable for EBV for somatic cell score with EBV for some udder conformation traits, but undesirable for EBV for milk and protein yield.

Animals↗

PubMed1994

Inclusion of semen price of the sire in an animal model to account for preferential treatment.

Histories of semen price for AI bulls used from 1970 to 1991 were collected and merged with first lactation milk and fat records of Ontario Holstein cows calving from 1970 through 1990. Data were analyzed with two animal models, both of which included herd-year-season and animal additive genetic effects. The second model included a fixed effect for semen price group. Cows that did not have a semen price for their sire were assigned to a separate group. Both models were used for milk and fat yields, and the second model was used separately for the semen price group of the sire at the time of daughter's conception, birth, and first calving. Hypothesis testing of group differences for semen price (excluding the group without a price match) resulted in significant effects of price group at first calving for milk and fat yields. The changes in estimated breeding values for cows and sires were summarized for cows by year of calving and for sires by Canadian versus US. Very few animals were affected by the inclusion of semen price groups in the model. Inclusion of effects of semen price group in an animal model did not significantly improve the accuracy of animal evaluations.

Animal Husbandry↗

PubMed1994

Multiple-country comparison of dairy sires.

A multiple-trait sire model was described in which yields of daughters in different countries were considered to be different traits. Such a model required estimates of genetic correlations among sire genetic effects in different countries. Observations were average daughter yield deviations, which were yields adjusted for all fixed effects within a country and for mate and animal permanent environmental effects. The methodology was described through a small example. Methods for estimating genetic covariances between countries as well as the advantages and disadvantages of the multiple-country approach to international comparisons were discussed. The proposed method appears to be better theoretically than methods in which the genetic correlations among countries are assumed to be 1. The relationships of estimated transmitting abilities of sires from the multiple-country analysis with international conversion formulas were discussed.

Animals↗

PubMed1993

Interaction of age and month of calving with year of calving for production traits of Ontario Holsteins.

Production records of 835,789 Ontario Holsteins calving between 1958 and 1990 were used to determine the presence of an interaction of the age and month of calving of cows with the year of calving for production of milk and fat and fat percentage. An animal model was employed including the effects of herd-year-season of calving, interaction of age and month of calving with year of calving, animal additive genetic effects, and permanent environmental effects. Tests for interactions of age with year within months of calving were significant for production of milk and fat, but not for fat percentage. Tests for interactions of month with year within age groups were significant for only a few age groups in the second and third parties. The implication of these findings on genetic evaluation is that an interaction of age and month of calving with year of calving should be included in the animal model for genetic evaluations rather than preadjusting production for age and month of calving.

Aging↗

PubMed1992

Reduced animal model with differential genetic grouping for direct and maternal effects.

Mixed-model equations for the reduced animal model with maternal effects and different genetic grouping of unknown parents for additive direct and maternal effects are derived. The matrices that relate the expected value and the variance of the breeding values of non-parents to the parents, as well as the different contributions of parental and non-parental breeding values, to the resulting mixed-model equations are presented. Mis-specification of additive maternal variance and the additive covariance between direct and maternal effects, arising from missing information on the dams of known individuals with records, is discussed. To avoid an incorrect specification of the variance-covariance matrix of the records without having to invert a nondiagonal variance of the residual terms, the breeding values of the unknown dams of individuals with records are included in the equations. Breeding values of non-parents are back-solved after the solutions for genetic groups and breeding values of parents are computed as simply as in cases in which maternal effects are absent. A numerical example is included to illustrate the derivations.

Animals↗

PubMed1991

Threshold models applied to Holstein conformation traits.

Threshold animal models were applied to five conformation traits of Canadian Holsteins. The estimated breeding values for sires from the threshold model allowed the calculation of predicted percentages of daughters in the desirable categories. Results were compared with those from a linear animal model in terms of their ability to predict future percentages of daughters in the desirable categories using an independent set of data. There was no advantage in a threshold model compared with a conventional linear animal model in its ability to predict future daughter performance. This was likely due to the 18 categories used in the classification of major type traits in Canada and the nearly normal distribution of observations across categories.

Animals↗

PubMed1991

C. R. Henderson: contributions to predicting genetic merit.

The contributions of C. R. Henderson to the genetic evaluation of livestock have been widely accepted, utilized, and enhanced by animal breeders and statisticians. Not well known are the possible alternatives to BLUP that have been suggested by Henderson, such as biased predictors and Bayesian methodology to incorporate prior information. A search for rapid methods of inverting dominance and additive by additive genetic relationship matrices has taken place since Henderson first described his method for computing the inverse of the additive genetic relationship matrix. Accounting for inbreeding and selected base populations continues to be a problem. There is a need to derive accurate descriptions of selection processes and the appropriate selection model in order to solve the problems of cow culling, nonrandom association of sires with herd-year-seasons, and preferential treatment. Henderson solved many animal breeding problems and left hints for solving others, but there are still many difficult problems to be tackled that will have to be resolved without the availability of his generous advice.

Animals↗

PubMed1991

Estimated genetic correlations between disease and yield traits in dairy cattle.

Data included observations on more than 200,000 first lactations of Norwegian cattle. Milk yield, fat and protein percentages, and observations on mastitis, ketosis, and presence of disease (binary coding of 0 or 1) were analyzed. Following Bayesian principles and applying the threshold concept, dispersion parameters for the binary traits (on the underlying scale) with continuous production traits were estimated. Heritabilities were .27, .34, and .43 for milk yield, fat percentage, and protein percentage, respectively. Heritabilities for the disease traits were .05 to .13 but may be inconsistent because of methodology problems with small sire by herd-year-season subclass size. Genetic correlations between milk yield and all three disease traits were above .5, indicating an undesirable relationship. Genetic correlations between ketosis and the content traits were -.38 to -.65; low component percentages were associated with high ketosis frequencies. Ignoring diseases in breeding programs may lead to undesirable correlated selection responses when selecting on milk yield.

Animals↗

PubMed1990

Feed intake, weaning weight and net returns comparisons for four breeding systems.

Feed intake, weaning weight and direct and maternal contributions to weaning weight were estimated for four breeding systems using data collected between 1979 and 1986 from 773 cow-calf pairs at the Elora Beef Research Centre. Breeding systems included purebred Hereford (HE), small rotational dual purpose (SR) (a four-way rotational crossing system utilizing Tarentaise, Angus, Gelbvieh and Pinzgauer breeds), large rotational beef (LR) (composed of Maine-Anjou, Simmental and Charolais) and Angus-sired large rotational beef (AL) utilizing Angus as the sire breed and LR as the maternal breed. Large rotational dams had the highest feed intakes for both dry (8.9 kg DM/d) and lactation (11.5 kg DM/d) periods. Conversely, HE calves consumed the greatest amounts of creep feed (309 kg DM), followed by AL, SR and LR. The large rotational system had the highest weaning weights (265 kg) and direct (12.3 kg greater than average of observations) and maternal (9.6 kg greater than average of observations) contributions to weaning weight, followed by AL, SR and HE for all three traits. An equation was derived for net returns that included parameters for feed intake and direct and maternal weaning weight. A linear programming model was designed to incorporate this equation as the objective function and determine the breeding system(s) that maximized net returns under various production conditions. In general, LR produced the greatest net returns, followed by SR and either AL or HE, depending on specific resource constraints (limited feed supply or herd size) included in the model.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗

PubMed1990

Influence of variations in biological and economical parameters on beef production net returns.

Net returns were defined as a function of the monetary returns (revenue) generated by the outputs less the monetary costs generated by the variable inputs. Outputs included total weaning weights of steers and heifers, weight of cull cows and weight of open heifers. Inputs included both feed and nonfeed costs. The net returns equation was incorporated as the objective function in a linear programming model. By maximizing the objective function, the breeding system that generated the highest net returns could be identified considering certain resource constraints. Breeding systems included purebred Herefords; small rotational dual purpose (SR), utilizing the breeds Angus, Pinzgauer, Gelbvieh and Tarentaise; large rotational (LR), a three-way rotational cross with the breeds Charolais, Simmental and Maine-Anjou; and Angus-sired terminal (AL) utilizing Angus as the sire breed and LR heifers as the maternal breed. Large rotational generally produced the greatest net returns, followed by SR and either AL or HE, depending on specific resource constraints (limited feed supply or herd size), calving rates, management systems, environment, beef to feed price ratios and purchased or farm-produced (inexpensive) feed utilized. Only under the conditions of a herd size constraint and farm-produced feed did AL exceed SR in net returns. Hereford had larger net returns than LR only when the two breeding systems were evaluated in an environment assumed to be reproductively stressful to LR. Ranking of breeding systems were dependent on specific conditions and indicated that one must consider each resource constraint and environment in which cattle are expected to produce before making breeding system recommendations.

Animal Feed↗

PubMed1990

Relationships between reproduction traits, age and body weight at calving, and days dry in first lactation Ayrshires and Holsteins.

Individual cow test day records collected between December 1979 and June 1986 were used to calculate measures of reproductive performance, age and weight at calving, and days dry for 7824 Ayrshire and 79,755 Holstein cows in first lactation. Separate analyses by breed were carried out according to a multiple-trait mixed model. Sixty-two Ayrshire and 369 Holstein sires were treated as random in the analyses. Ayrshires were, on average, older and lighter at calving than Holsteins, but the breeds differed little in reproduction measures and days dry. Heritabilities of fertility traits, days to first breeding, days open, and services per conception were all less than .015 in the multi-trait analyses. With the exception of body weight, heritability estimates for the other traits were less than .05. Phenotypic correlations between traits were almost identical for the two breeds, and genetic correlations tended to be similar. Exceptions involved the trait days to first breeding and services per conception, but heritabilities of these traits were close to zero (p less than .008) in Ayrshires. Fertility traits were positively correlated genetically. Genetic correlations between days open and both age and body weight at calving were small. The genetic correlation between age and weight at calving was -.90 and -.68 in Ayrshires and Holsteins, respectively. Genetic correlations between days dry and all traits except body weight were moderate and positive.

Aging↗

PubMed1989

Effects of embryo transfer in beef cattle on genetic evaluation methodology.

Because female cattle may be superovulated and their embryos dispersed to many surrogate dams, both the recording system and the models for genetic evaluation need to be modified. The recording system must keep track of the breed of the surrogate dams as well as their age and registration numbers. The model for evaluation of beef cattle for traits in which maternal effects are important, for example, must distinguish between natural and surrogate dams. The potential for interactions of breed and age of surrogate dam with sex of calf and the possibility that these may differ from age of natural dam x sex of calf interactions needs further study. A discussion of these issues is given. An example is given to illustrate how surrogate dams might be modeled. Assuming that only the breed of surrogate dam is known and that each surrogate dam gives birth to only one progeny, the mixed model equations for genetic evaluations can be simplified. These are illustrated.

Analysis of Variance↗

PubMed1989

Heifer fertility and its relationship with cow fertility and production traits in Holstein dairy cattle.

Breeding receipts from three AI units were merged with Ontario Dairy Herd Improvement Corporation and Record of Performance production records. Data comprised 53,705 heifer, 41,253 lactation 1, 14,688 lactation 2, and 3054 lactation 3 records by daughters of 2150 sires represented in 15,877 herd-year-seasons of birth. Three measures of heifer fertility, three measures of cow fertility, and three measures of production were investigated. Measures of heifer fertility were ages at first and last breeding and number of inseminations per conception. Cow fertility traits were days from calving to first breeding, days open, and number of inseminations per conception. Production traits were breed class average milk, breed class average fat, and fat percentage. Relationships among these nine traits for the first three lactations were estimated using a maximum likelihood multiple-trait procedure. The linear mixed model for each trait included fixed effects of herd-year-season of birth and genetic groups of sire and the random effect of sire. Transformations of the data for nonnormality had no influence on the estimates of genetic and phenotypic parameters. The heritability of .12 for age at first insemination, which was higher than other heifer fertility traits, indicated that selection would result in genetic response. Genetic and phenotypic correlations between heifer fertility and cow fertility and production traits in all three lactations were not different from zero. There was no genetic antagonism between fertility and subsequent production traits.

Animals↗

PubMed1989

Relationships between fertility and production in Holstein dairy cattle in different lactations.

Record of Performance and Dairy Herd Improvement Corporation production records of Ontario Holstein cows were merged with breeding receipts of three Ontario AI units from September 1981 through December 1985. Relationships between fertility and production in the first three lactations were investigated for 97,368 daughters of 3806 sires in 22,768 herd-hear-seasons of calving. Fertility traits were days from calving to first insemination, number of inseminations per conception, and days open. Production traits were age and month of calving adjusted 305-d milk and fat yields and fat percentage. Multiple-trait maximum likelihood was used to estimate variances and covariances. Heritabilities for the first three lactations were .18, .18, and .19 for milk yield; .20, .19, and .19 for fat yield; and .58, .52, and .48 for fat percentage. Heritabilities of fertility traits ranged from .03 to .06. Genetic and phenotypic correlations between fertility and production traits in all three lactations were essentially 0. Genetic correlations between different lactation production traits ranged from .2 to .65. Repeatabilities of fertility traits ranged from .05 to .16 in different lactations. Repeatabilities for production traits in different lactations ranged from .51 to .77. Genetic and phenotypic correlations between fertility and production in the subsequent lactation and between production and subsequent lactation fertility were also very low or zero.

Animals↗