Estimation of genetic covariances with method R.

Method R is a simple and computationally inexpensive method for estimating (co)variances. The objective of the study was to investigate properties of Method R for estimation of (co)variance components with emphasis on covariance estimation. Theoretical Method R formulas were developed for simplified single-variate and bivariate models.

Comparison of threshold vs linear and animal vs sire models for predicting direct and maternal genetic effects on calving difficulty in beef cattle.

This study compared the accuracy of several models for obtaining genetic evaluations of calving difficulty. The models were univariate threshold animal (TAM), threshold sire-maternal grandsire (TSM), linear animal (LAM), and linear sire-maternal grandsire (LSM) models and bivariate threshold-linear animal (TLAM), threshold-linear sire-maternal grandsire (TLSM), linear-linear animal (LLAM), and linear-linear sire-maternal grandsire (LLSM) models for calving difficulty and birth weight. Data were obtained from the American Gelbvieh Association and included 84,420 first-parity records of both calving difficulty and birth weight.

Bias in genetic evaluations by records of cows treated with bovine somatotropin.

Records from Dairy Records Management Systems in Raleigh were used to estimate effects of bovine somatotropin (bST) treatment and to predict breeding values for milk production traits. The data comprised 5245 test-day records of bST-treated cows and 126,223 test-day records of untreated cows in first lactation for milk, fat, and protein yields. Fixed effects of bST treatment were estimated from test-day animal models with herd-test-date as another fixed factor.

Genetic component of heat stress in dairy cattle, parameter estimation.

Our data included 119,205 first-parity, test-day records from 15,002 Holsteins in 134 Georgia farms with temperature and humidity data from 21 weather stations throughout Georgia. The test-day model included the effects of herd test date, days-in-milk (DIM) classes, age, milking frequency, general additive effect, random regression on the heat-humidity index for heat-tolerance additive effect, general permanent environment, and the random regression on the heat-humidity index for a permanent environment. The general effects, which corresponded to effects in the current repeatability models, were assumed to be correlated with the heat-tolerance effects.

Genetic Component of Heat Stress in Dairy Cattle, Development of Heat Index Function.

Production data obtained from AIPL USDA included 119,337 first-parity, test-day records of 15,012 Holsteins from 134 Georgia farms collected in 1990 to 1997. Weather information was obtained from the Georgia Automated Environmental Monitoring Network and included daily minimum, average, and maximum temperatures and humidity for 21 stations throughout the state. Each test-day record was augmented with weather information from the closest weather station.

Method R estimates of additive genetic, dominance genetic, and permanent environmental fraction of variance for yield and health traits of Holsteins.

Fractions of variance accounted for by additive genetic, dominance genetic, and permanent environmental effects for milk, fat, and protein yields; somatic cell score; and productive life were estimated from Holstein data used for national genetic evaluations. Contemporary group assignments were determined using the national procedure. Data included 1,973,317 milk and fat records for 812,659 cows, 1,019,421 protein records for 462,067 cows, 468,374 lactation average somatic cell score (SCS) records for 232,909 cows, and 735,256 cows with productive-life records.

Investigation of genotype x environment interactions for weaning weight for Herefords in three countries.

The objective of this study was to investigate the possibility of genotype x environment interactions for weaning weight (WWT) between different regions of the United States (US) and between Canada (CA), Uruguay (UY), and US for populations of Hereford cattle. Original data were composed of 487,661, 102,986, and 2,322,722 edited weaning weight records from CA, UY, and US, respectively. A total of 359 sires were identified as having progeny across all three countries; 240 of them had at least one progeny with a record in each environment.

Strategies for estimating the parameters needed for different test-day models.

Currently, most analyses of parameters in test-day models involve two types of models: random regression, where various functions describe variability of (co)variances with regard to days in milk, and multiple traits, where observations in adjacent days in milk are treated as one trait. The methodologies used for estimation of parameters included Bayesian via Gibbs sampling, and REML in the form of derivative-free, expectation-maximization, or average-information algorithms. The first method is simpler and uses less memory but may need many rounds to produce posterior samples.

Variance and covariance components for weaning weight for Herefords in three countries.

Records from the Hereford Associations of the United States (USA), Canada, and Uruguay were used to estimate genetic and phenotypic variances and covariances for weaning weight. Estimation was done using a complete animal model, relatively large data sets, and the same methodology for the three countries in order to determine whether genetic parameters for weaning weight were homogeneous across environments. Data were composed of 2,322,722, 487,661, and 102,986 edited weaning weight records for USA, Canada, and Uruguay, respectively.

Genetic parameters for first and second lactation milk yields of Polish black and white cattle with random regression test-day models.

Single- and two-trait random regression models were applied to estimate variance components of test-day records of milk, fat, and protein yields in the first and second lactation of Polish Black and White cattle. The model included fixed herd test-day effect, three covariates to describe lactation curve nested within age-season classes, and random regressions for additive genetic and permanent environmental effects. In two-parity models, each parity was treated as a separate trait.

Prediction of parental dominance combinations for planned matings, methodology, and simulation results.

Optimal use of dominance information requires a mating system and predictions of specific combining abilities for each set of prospective parents. Current evaluation procedures provide such predictions only for a limited number of parents. A procedure is described that predicts the specific combining ability for any parents.

Threshold-linear versus linear-linear analysis of birth weight and calving ease using an animal model: II. Comparison of models.

Several models were evaluated in terms of predictive ability for calving difficulty. Data included birth weight and calving difficulty scores provided by the American Gelbvieh Association from 26,006 calves born to first-parity cows and five simulated populations of 6,200 animals each. Included in the model were fixed age of dam x sex interaction effects, random herd-year-season effects, and random animal direct and maternal effects.

Threshold-linear versus linear-linear analysis of birth weight and calving ease using an animal model: I. Variance component estimation.

Birth weight and calving difficulty were analyzed with Bayesian methodology using univariate linear models, a bivariate linear model, a threshold model for calving difficulty, and a joint threshold-linear model using a probit approach. Field data included 26,006 records of Gelbvieh cattle. Simulated populations were generated using parameters estimated from the field data.

Supply of genetic information--amount, format, and frequency.

The volume and complexity of genetic information is increasing because of new traits and better models. New traits may include reproduction, health, and carcass. More comprehensive models include the test day model in dairy cattle or a growth model in beef cattle.

Genetic parameter estimates for carcass and yearling ultrasound measurements in Brangus cattle.

Carcass measurements of 12th-rib fat thickness (CARCFAT), longissimus muscle area (CARCLMA), and weight (CARCWT) on 2,028 Brangus and Brangus-sired fed steers and heifers, as well as yearling weights (YWT) and ultrasound measures of 12th-rib fat thickness (USFAT) and longissimus muscle area (USLMA) on 3,583 Brangus bulls and heifers were analyzed to estimate genetic parameters. Data were analyzed using a six-trait animal model and an average information REML algorithm. The model included fixed effects for contemporary group and breed of dam, covariates for age at slaughter or measurement, and random animal and residual effects.

Estimation of the dominance variance for postweaning gain in the U.S. Limousin population.

The objective of this study was to estimate the dominance variance for postweaning gain in Limousin cattle. Data included 215,326 records of postweaning gain from 205 to 365 d, provided by the North American Limousin Foundation. Parental dominance subclasses were formed and related using the method of Hoeschele and VanRaden.

Effect of full sibs on additive breeding values under the dominance model for stature in United States Holsteins.

Differences in breeding values between dominance and additive models were examined theoretically and with field data. Data included 5.2 million records on stature from 3.

Estimation of dominance variance in purebred Yorkshire swine.

We used 179,485 Yorkshire reproductive and 239,354 Yorkshire growth records to estimate additive and dominance variances by Method Fraktur R. Estimates were obtained for number born alive (NBA), 21-d litter weight (LWT), days to 104.5 kg (DAYS), and backfat at 104.

Influence of dominance relationships on the estimation of dominance variance with sire-dam subclass effects.

Two data sets from the USDA Livestock and Range Research Laboratory were analyzed to study dominance variance and the influence of dominance relationships. The first consisted of 4,155 birth weight (3,884 weaning weight) records of inbred USDA Line 1 Herefords. The second consisted of 8,065 birth weight (7,380 weaning weight) records from a line-cross experiment with five lines.

Dominance models with method R for stature of Holsteins.

Estimates of variance components were obtained with method R for several additive and dominance models. The data included 301,960 records for first parity and 280,040 records for later parities of Holsteins. The single-record model included effects of management, regression on inbreeding percentage, age at calving, stage of lactation, and additive and dominance effects.

Comparison of computing properties of derivative and derivative-free algorithms in variance-component estimation by REML.

Computing properties of better derivative and derivative-free algorithms were compared both theoretically and practically. Assuming that the log-likelihood function is approximately quadratic, in a t-trait analysis the number of steps to achieve convergence increases as t(2) in 'better' derivative-free algorithms and is independent of that number in 'better' derivative algorithms. The cost of one step increases as t(3) .

Estimation of genetic parameters for somatic cell score in Holsteins.

Genetic parameters of somatic cell scores for Holstein cows were estimated using an animal model and REML for two data sets. Set 1, with 13,017 records from 5278 cows, was used to obtain variance components, heritability, and repeatability for two lactation measures: the simple average and the weighted average of test day data. Set 2, with 14,418 records from 4806 cows, was used to obtain genetic correlations for the simple average between lactations 1 and 2, between lactations 1 and 3, and between lactations 2 and 3.

Prediction error variance and restricted maximum likelihood estimation for animal model with relationship grouping.

Genetic evaluation using animal model with relationship grouping has been shown to be feasible. However, algorithms were unavailable for prediction error variance and REML estimation of variance components. This paper shows that prediction error variance of an estimable function of the total merit of additive genetic and group effects is a simple function of a generalized inverse of the coefficient matrix for a transformed mixed model equation or of the inverse of the coefficient matrix when it is restricted to full rank.

Genetic analysis of dystocia and calf mortality in Israeli-Holsteins by threshold and linear models.

Calvings of 106,751 Israeli Holstein heifers were analyzed for dystocia and calf mortality, scored dichotomously, and a composite trait, scored trichotomously. Dystocia was also studied with 146,973 second and third parity records. Models fitted included herd-year-season, sex of calf, calving age, calving month, sire of cow, sire of calf, and groups of sire of cow and of calf.

Genetic evaluation of dairy goats for milk and fat yield with an animal model.

An animal model was applied to evaluate 120,073 Alpine, LaMancha, Nubian, Saanen, and Toggenburg bucks and does. Parities higher than six were excluded. The model included fixed herd-year-season and random herd-sire interaction, permanent environmental breeding value, and residual effects.