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D Gianola

Publications and source records attributed to D Gianola.

At least 37 records · Page 2Linked to original sources

Comparison between a Weibull proportional hazards model and a linear model for predicting the genetic merit of US Jersey sires for daughter longevity.

Predicted transmitting abilities (PTA) of US Jersey sires for daughter longevity were calculated using a Weibull proportional hazards sire model and compared with predictions from a conventional linear animal model. Culling data from 268,008 Jersey cows with first calving from 1981 to 2000 were used. The proportional hazards model included time-dependent effects of herd-year-season contemporary group and parity by stage of lactation interaction, as well as time-independent effects of sire and age at first calving. Sire variances and parameters of the Weibull distribution were estimated, providing heritability estimates of 4.7% on the log scale and 18.0% on the original scale. The PTA of each sire was expressed as the expected risk of culling relative to daughters of an average sire. Risk ratios (RR) ranged from 0.7 to 1.3, indicating that the risk of culling for daughters of the best sires was 30% lower than for daughters of average sires and nearly 50% lower than than for daughters of the poorest sires. Sire PTA from the proportional hazards model were compared with PTA from a linear model similar to that used for routine national genetic evaluation of length of productive life (PL) using cross-validation in independent samples of herds. Models were compared using logistic regression of daughters' stayability to second, third, fourth, or fifth lactation on their sires' PTA values, with alternative approaches for weighting the contribution of each sire. Models were also compared using logistic regression of daughters' stayability to 36, 48, 60, 72, and 84 mo of life. The proportional hazards model generally yielded more accurate predictions according to these criteria, but differences in predictive ability between methods were smaller when using a Kullback-Leibler distance than with other approaches. Results of this study suggest that survival analysis methodology may provide more accurate predictions of genetic merit for longevity than conventional linear models.

Animals↗

Analysis of the relationship between type traits and functional survival in US Holstein cattle using a Weibull proportional hazards model.

Survival analysis with a Weibull proportional hazards model was used to evaluate the effects of 15 linear type traits, 5 composite traits, and final score on the functional longevity of US Holstein cows. Culling data and type classification scores (measured in first lactation) from 891,524 cows with first calving from 1993 to 2000 were used. The data were divided into 9 geographical regions to determine whether the relationship between type traits and longevity differed according to climate or management system. Functional survival was defined as the number of days from first calving until culling or censoring, after correction for 305-d mature equivalent combined fat and protein yield. The Weibull model included time-dependent effects of herd-year-season, parity-stage of lactation, and within herd-year quintile ranking for combined fat and protein yield (nested within biennium), as well as time-independent effects of age at first calving and type classification score (type traits were analyzed one at a time). Type classification scores were rounded to the nearest 5 points, and the impact of each type trait on functional survival in each region was evaluated. Mean failure time ranged from 694 d in the South to 758 d in the North East. Risk of culling differed by region for several linear type traits, and differences were greatest for regions that were most dissimilar in climate and herd management (e.g., South East, East North Central, and West). Udder depth, fore udder attachment, udder cleft, and rear legs side view were consistently associated with functional longevity, regardless of region, but, the importance of some secondary traits, such as stature or dairy form, differed by region. The survival model applied in this study easily described both linear and nonlinear relationships between type traits and longevity while accounting for important time-dependent and time-independent explanatory variables.

Animals↗

Multivariate threshold model analysis of clinical mastitis in multiparous norwegian dairy cattle.

A Bayesian multivariate threshold model was fitted to clinical mastitis (CM) records from 372,227 daughters of 2411 Norwegian Dairy Cattle (NRF) sires. All cases of veterinary-treated CM occurring from 30 d before first calving to culling or 300 d after third calving were included. Lactations were divided into 4 intervals: -30 to 0 d, 1 to 30 d, 31 to 120 d, and 121 to 300 d after calving. Within each interval, absence or presence of CM was scored as "0" or "1" based on the CM episodes. A 12-variate (3 lactations x 4 intervals) threshold model was used, assuming that CM was a different trait in each interval. Residuals were assumed correlated within lactation but independent between lactations. The model for liability to CM had interval-specific effects of month-year of calving, age at calving (first lactation), or calving interval (second and third lactations), herd-5-yr-period, sire of the cow, plus a residual. Posterior mean of heritability of liability to CM was 0.09 and 0.05 in the first and last intervals, respectively, and between 0.06 and 0.07 for other intervals. Posterior means of genetic correlations of liability to CM between intervals ranged from 0.24 (between intervals 1 and 12) to 0.73 (between intervals 1 and 2), suggesting interval-specific genetic control of resistance to mastitis. Residual correlations ranged from 0.08 to 0.17 for adjacent intervals, and between -0.01 and 0.03 for nonadjacent intervals. Trends of mean sire posterior means by birth year of daughters were used to assess genetic change. The 12 traits showed similar trends, with little or no genetic change from 1976 to 1986, and genetic improvement in resistance to mastitis thereafter. Annual genetic change was larger for intervals in first lactation when compared with second or third lactation. Within lactation, genetic change was larger for intervals early in lactation, and more so in the first lactation. This reflects that selection against mastitis in NRF has emphasized mainly CM in early first lactation, with favorable correlated selection responses in second and third lactations suggested.

Animals↗

Prediction of longevity breeding values for US Holstein sires using survival analysis methodology.

Breeding values of Holstein sires for daughter longevity in each of 9 geographical regions of the United States were predicted using a Weibull proportional hazards model. Longevity (also commonly referred to as herd life or length of productive life) was defined as the number of days from first calving until culling or censoring. Records from 2,322,389 Holstein cows with first calving from 1990 to 2000 were used. In addition to the sire's additive genetic merit, our failure time model included time-dependent effects of herd-year-season of calving, parity-stage of lactation, and within-herd-year quintiles for mature equivalent fat plus protein yield, as well as the time-independent effect of age at first calving. Sire variances and parameters of the Weibull distribution were estimated separately for each region. The relative risk of culling for daughters of each individual sire was expressed relative to that of daughters of an average sire (within a specific region). Predicted breeding values for functional longevity, expressed as relative risk ratios, ranged from 0.7 to 1.3. Sizable differences were observed between geographical regions in sire rankings, as well as estimated sire variances and gamma parameters (of the distribution of herd-year-season effects), suggesting that a single national ranking may not be appropriate for every region. Two random samples of herds were selected from the full national data set; these contained 375,086 records and 256,751 records, respectively. Predicted transmitting abilities (PTA) of sires for daughter longevity were calculated using the Weibull proportional hazards (sire) model described previously but without the correction for milk production. These were compared with predictions from a linear (animal) model, as currently used for routine genetic evaluation of length of productive life in the United States. Logistic regression of daughters' stayability to 36, 48, 60, 72, or 84 mo of life (among animals that had opportunity to stay that long) on sires' PTA indicated that the proportional hazards model yielded more accurate predictions of daughter longevity than the linear animal model, even though the latter relied on denser pedigree information.

Animals↗

Bayesian inference about parameters of a longitudinal trajectory when selection operates on a correlated trait.

A hierarchical model for inferring the parameters of the joint distribution of a trait measured longitudinally and another assessed cross-sectionally, when selection has been applied to the cross-sectional trait, is presented. Distributions and methods for a Bayesian implementation via Markov Chain Monte Carlo procedures are discussed for the case where information about the selection criterion is available for all the individuals, but longitudinal records are available only in the later generations. Alternative specifications of the residual covariance structure are suggested. The procedure is illustrated with an analysis of correlated responses in growth curve parameters in a population of rabbits selected for increased growth rate. Results agree with those obtained in a previous study using both selected and control populations. The high correlation between samples indicates slow mixing, resulting in small effective sample sizes and high Monte Carlo standard errors.

Animals↗

Bivariate analysis of liability to clinical mastitis and to culling in first-lactation cows.

Records taken on 13,070 first-lactation daughters of 250 Norwegian Cattle sires were used to examine associations between susceptibility to clinical mastitis and to culling. Clinical mastitis was defined as a binary trait, whereas culling was treated as either binary (culled or not culled) or continuous (length of opportunity period) for two sampling periods (120 or 300 d of lactation). Two Bayesian models were employed; 1) a bivariate threshold model with both mastitis and culling as binary traits, and 2) a bivariate model with mastitis as a threshold binary variable and time to culling as Gaussian. The heritability of liability to clinical mastitis was not affected by either the length of sampling period (120 vs. 300 d) or by whether culling (binary) or length of opportunity period was the second trait in the bivariate analysis. The posterior mean (standard deviation) of heritability of liability to clinical mastitis was 0.06 to 0.07 (0.02) in all analyses. The heritability estimate of length of opportunity period was less than 0.001. Culling (threshold trait) in first lactation had a low heritability, but a high genetic correlation with clinical mastitis. The posterior means (standard deviation) for heritability of liability to culling were 0.01 (0.006) for 120 d and 0.02 (0.009) for 300 d, and the posterior means (standard deviation) of the genetic correlation between liability to clinical mastitis and to culling were 0.48 (0.24) and 0.53 (0.21) for 120 and 300 d, respectively.

Analysis of Variance↗

Bayesian estimation of parameters of a structural model for genetic covariances between milk yield in five regions of the United States.

Inference about genetic covariance matrices using multiple-trait models is often hindered by lack of information. This leads to imprecise estimates of genetic parameters and of breeding values. Patterns in a genetic covariance matrix can be exploited to reduce the number of parameters and to increase quality of inferences. A structural model for genetic covariances was developed and fitted to milk yield data in five regions of the United States. This was compared with a standard multiple-trait analysis using a deviance information criterion, a measure of quality of fit. Data consisted of 3,465,334 Holstein first-lactation records from daughters of 43,755 sires in five regions of the United States (Midwest, Northeast, Northwest, Southeast, Southwest). Parameters of the structural model included an intercept and effects of measures of genetic and of management similarity on genetic covariances. Genetic similarity depended on the number of records contributed by sires that were common to a pair of regions. Management similarity was a function of the quantity of concentrate used to produce 1000 kg of milk in each pair of regions. The structural and the multiple-trait models gave similar estimates of genetic covariances, but the number of parameters was 8 in the former vs. 15 in the latter. Hence, estimates of genetic covariances were more precise with the structural model. A deviance information criterion suggested a slight superiority of the multiple-trait model, although probably within sampling error. For both models, genetic correlations between milk yield in five regions of the United States were larger than 0.93.

Analysis of Variance↗

Genetic analysis of longitudinal trajectory of clinical mastitis in first-lactation Norwegian cattle.

Clinical mastitis records for 36,178 first-lactation daughters of 245 Norwegian Cattle (NRF) sires were analyzed with a Bayesian longitudinal threshold model. For each cow, the period going from 30 d before calving to 300 d after calving was divided into 11 intervals of 30 d length each. Absence or presence of clinical mastitis within each interval was scored as "0" or "1", respectively. A Bayesian threshold model consisting of a set of explanatory variables plus Legendre polynomials on time of order four was used to describe the trajectory of liability to clinical mastitis. Heritability ranged between 0.07 and 0.13 before calving, from 0.04 to 0.15 during the first 270 d after calving, and increased sharply thereafter, as a consequence of the form of the polynomial. Genetic correlations between adjacent days were close to 1, and decreased when days were further apart. Most genetic correlations were moderate to high. A measure of probability of future daughters contracting clinical mastitis during lactation was computed for each sire. A typical curve had a peak near calving followed by a decrease thereafter. The best sires had a low peak around calving and a low expected probability of mastitis among daughters throughout lactation. Expected fraction of days without mastitis was derived from the probability curves and used for ranking of sires. Rank correlations with genetic evaluations of sires obtained from cross-sectional models were high. However, sire selection was affected markedly, especially at high selection intensity. An advantage of the longitudinal model for clinical mastitis is its ability to take multiple treatments and time aspects into account.

Animals↗

Analysis of the relationship between type traits, inbreeding, and functional survival in Jersey cattle using a Weibull proportional hazards model.

A Weibull proportional hazards model was used to analyze the effects of 13 linear type traits, final score, and inbreeding on the functional survival of 268,008 US Jersey cows in 2416 herds with first calving from 1981 to 2000. Functional survival was defined as the number of days from first calving until involuntary culling or censoring. The statistical model included the time-dependent effects of herd-year-season of calving, parity by stage of lactation interaction, and within-herd-year quintile for mature equivalent milk yield, as well as the time-independent effects of inbreeding, age at first calving, and linear type traits or final score (analyzed one at a time). Each type trait was divided into 10 classes, and the relative risk of involuntary culling was calculated for animals in each class after accounting for the aforementioned management factors. Type traits with the greatest contribution to the likelihood function were udder depth, fore udder attachment, front teat placement, and udder support. Cows with low scores for these traits had a risk of culling that was 1.3 to 1.8 times that of cows with intermediate scores. Cows with high scores for udder depth and udder support had a risk of culling only 0.7 to 0.85 as great as that of cows with intermediate scores. Intermediate scores were desirable for rear leg set, dairy form, and strength, but stature, rump angle, and rump width had negligible effects on survival. Cows with low final scores had a risk of culling that was 1.35 times that of cows with intermediate scores, whereas cows with high final scores had a risk of culling that was 0.8 times that of cows with intermediate scores. Animals with inbreeding coefficients greater than 10% had a slightly higher risk of culling than animals with inbreeding coefficients less than 5%.

Animals↗

Bayesian estimates of covariance components between lactation curve parameters and disease liability in Danish Holstein cows.

In the present work, covariance components for milk yield and disease liability were estimated with bivariate random regression test-day sire models using a Bayesian approach and implemented via the Gibbs sampler. The data consist of 8075 first-parity Danish Holstein (DH) cows, from 1259 sires, performing in 57 herds from 1992 to 1997. Treatments associated with five different type of diseases were pooled into a single general disease liability for each cow. Two models were fitted to the data. First, using a bivariate model, milk yield is modeled via a random regression, and disease liability via a repeatablility model. Second, using a bivariate model, both milk yield and disease liability are modeled using random regressions. A comparison based on a Bayes factor provides very strong support for the bivariate random regression model. Posterior means of heritabilities for each of the traits were estimated for five different points in time throughout lactation. Across models, heritabilities for milk yield are lowest in the beginning of the lactation (0.19) and highest at the end of the lactation (0.35). Posterior means of heritabilities of disease liability range from 0.04 to 0.10 for test days, and is equal to 0.20 for the whole lactation. Heritability of persistency measures estimated from the two models are 0.20 and 0.21. Estimates of posterior means of genetic correlations between single test-day milk yield and single test-day disease liability are in the range of 0.31 to 0.57. The estimates of posterior mean and of the 95% posterior interval of the genetic correlation between persistency and (total) disease liability using the model with the highest posterior probability are -0.12 and (-0.44; 0.20), respectively. Even though the largest proportion of the posterior probability mass is spread along negative values of the correlation (indicating that individuals with a flatter lactation curve tend to have lower disease liability), a value of zero of the genetic correlation falls comfortably within the 95% posterior interval. Thus the prospects of reducing incidence of disease by manipulating persistency as defined in this work remain inconclusive.

Animals↗

Detection of mastitis in dairy cattle by use of mixture models for repeated somatic cell scores: a Bayesian approach via Gibbs sampling.

The distribution of somatic cell scores could be regarded as a mixture of at least two components depending on a cow's udder health status. A heteroscedastic two-component Bayesian normal mixture model with random effects was developed and implemented via Gibbs sampling. The model was evaluated using datasets consisting of simulated somatic cell score records. Somatic cell score was simulated as a mixture representing two alternative udder health statuses ("healthy" or "diseased"). Animals were assigned randomly to the two components according to the probability of group membership (Pm). Random effects (additive genetic and permanent environment), when included, had identical distributions across mixture components. Posterior probabilities of putative mastitis were estimated for all observations, and model adequacy was evaluated using measures of sensitivity, specificity, and posterior probability of misclassification. Fitting different residual variances in the two mixture components caused some bias in estimation of parameters. When the components were difficult to disentangle, so were their residual variances, causing bias in estimation of Pm and of location parameters of the two underlying distributions. When all variance components were identical across mixture components, the mixture model analyses returned parameter estimates essentially without bias and with a high degree of precision. Including random effects in the model increased the probability of correct classification substantially. No sizable differences in probability of correct classification were found between models in which a single cow effect (ignoring relationships) was fitted and models where this effect was split into genetic and permanent environmental components, utilizing relationship information. When genetic and permanent environmental effects were fitted, the between-replicate variance of estimates of posterior means was smaller because the model accounted for random genetic drift.

Animals↗

Inferring the trajectory of genetic variance in the course of artificial selection.

A method is proposed to infer genetic parameters within a cohort, using data from all individuals in an experiment. An application is the study of changes in additive genetic variance over generations, employing data from all generations. Inferences about the genetic variance in a given generation are based on its marginal posterior distribution, estimated via Markov chain Monte Carlo methods. As defined, the additive genetic variance within the group is directly related to the amount of selection response to be expected if parents are chosen within the group. Results from a simulated selection experiment are used to illustrate properties of the method. Four sets of data are analysed: directional selection with and without environmental trend, and random selection, with and without environmental trend. In all cases, posterior credibility intervals of size 95% assign relatively high density to values of the additive genetic variance and heritability in the neighbourhood of the true values. Properties and generalizations of the method are discussed.

Animals↗

Threshold model for misclassified binary responses with applications to animal breeding.

A Bayesian procedure for misclassified binary data was developed. An animal breeding simulation indicated that, when error of classification was ignored, the variance between clusters was inferred incorrectly. Data were reanalyzed assuming that the probability of misclassification was either known or unknown. In the first case, input parameter values were recovered in the analysis. When the probability was unknown, there was a slight bias; the true probability of misclassification and the true number of miscoded observations appeared within high credibility regions. An analysis of fertility in dairy cows is presented.

Animals↗

Application of a structural model for genetic covariances in international dairy sire evaluations.

A structural model for estimation of genetic covariances in international dairy sire evaluations was compared with a standard multiple-trait mixed model using milk yield data from 13 environments (Austria, Belgium, Czech Republic, Denmark, Estonia, Finland, Israel, Switzerland and five regions of the United States). Data consisted of 2,885,117 first-lactation records from daughters of 17,867 Holstein sires. Parameters of the structural model for genetic covariances included an intercept and measures of genetic, management, and climate similarity. Genetic similarity was defined as the ratio between the number of daughters of common bulls used in a given pair of regions and the total number of daughters of all bulls. The measure of management similarity was the ratio between the absolute value of the difference in average milk yield between two regions and the sum of these averages. Climate similarity was a function of the difference in heat indices between pairs of regions. Results showed that the structural model for the genetic covariances gave more precise estimates of the latter than the standard multivariate analysis because the number of parameters to be estimated in the genetic covariance matrix was reduced from 91 to 16. A comparison of the two models using a deviance information criterion (a measure of quality of fit) showed a slight superiority for the structural model. For the latter, the posterior means of the genetic correlations between environments ranged between 0.63 and 0.98.

Analysis of Variance↗

Bayesian analysis of liability of clinical mastitis in Norwegian cattle with a threshold model: effects of data sampling method and model specification.

First-lactation records of Norwegian Cattle were used to infer heritability of liability to clinical mastitis with a threshold sire model. Mastitis was defined as a binary response (presence or absence) in a defined period of first lactation (opportunity period). Length of opportunity period (from 30 d before calving up to 120 or 300 d of lactation) had less effect on heritability estimates than data sampling methods (include or exclude records of cows culled before the end of the opportunity period) whereas sire ranking was more affected by the former. Including all cows, whether culled before the end of the opportunity period or not, gave a sharper and more symmetric posterior distribution of heritability of liability to clinical mastitis. When we analyzed data for all cows, model specification had a small effect on heritability estimates, while sire ranking was affected markedly. Posterior means of heritability range from 0.058 to 0.074. A model regressing on the length of the opportunity period for culled cows without mastitis, was shown favorable for the two opportunity periods using Bayes factors and the deviance information criterion for model comparison. This model, in which liability of mastitis depends on time to culling, may allow utilizing information from all first lactations in genetic evaluation, irrespectively of duration and culling outcome.

Animals↗

Slow-release lanreotide in the treatment of acromegaly: a study in 66 patients.

OBJECTIVE: Slow-release (SR) lanreotide is a long-acting somatostatin analog that has been developed in order to overcome the inconvenience of multiple daily subcutaneous injections of octreotide, required for metabolic control in acromegaly. Lanreotide SR has been found to be well tolerated and effective in reducing GH and IGF-I levels but clinical data are still limited compared with those with subcutaneous octreotide treatment. DESIGN: Sixty-six unselected patients with active acromegaly were therefore evaluated in a multi-center, prospective, open label study. Lanreotide SR was given at a dose of 30mg intramuscular every 7-14 days. METHODS: At baseline and after 2, 4, 8, 12, 24, 36 and 48 weeks patients underwent a clinical examination with assessment of acromegaly related symptoms, and blood was sampled for serum GH, IGF-I, prolactin, glycosylated hemoglobin, fasting glucose, hematology, kidney function and liver function tests. Biliary ultrasonography and pituitary magnetic resonance imaging were performed at baseline and after one year. RESULTS: Treatment resulted in a significant improvement in the symptom score from 2.69+/-0.27 to 1.06+/-0.17 (P<0.0001). Serum IGF-I levels fell from 699+/-38microg/l at baseline to 399+/-26microg/l (P<0.0001, n=60) after one month, after which levels remained stable: 480+/-37microg/l after 6 months (n=54) and 363+/-32microg/l after one year (n=46). GH levels dropped from 13.8+/-3.2microg/l to 4.3+/-0.7microg/l after one month (P<0.0001, n=60) and remained stable thereafter: 3.9+/-0.4microg/l (n=54) after 6 months and 3.5+/-1.1microg/l after one year (n=46). Twenty-nine out of 66 patients (44%) attained a normal age-corrected IGF-I level and 30 patients (45%) attained a GH level below 2.5microg/l. Pituitary adenoma shrinkage of at least 25% was found in 5 of 14 patients (36%) after one year. Side effects were mainly transient gastrointestinal symptoms and pain at the injection site, resulting in drug discontinuation in only 6 patients (9%). Two patients developed new gall stones. No difference was found between subcutaneous octreotide and lanreotide SR in efficacy and almost all patients preferred the easier dose administration of lanreotide SR. CONCLUSIONS: Long-term treatment of acromegaly with SR-lanreotide is effective in controlling GH and IGF-I levels and symptoms and is well tolerated in the majority of patients. Compared with subcutaneous octreotide, lanreotide SR considerably improves patient's acceptance of therapy while having the same overall efficacy.

Acromegaly↗

Genetic analysis of fertility in dairy cattle using negative binomial mixed models.

Two negative binomial mixed models with different dispersion specifications were compared for analysis of dairy reproduction count data. The first model was developed previously and had heterogeneous overdispersion in an associated logarithmic scale, assigning greater uncertainty to observations with smaller conditional expectations. The second model postulated homogeneous overdispersion across all data. A simulation study was used to compare marginal modal estimates of additive genetic variance, based on these two negative binomial models, with analogous estimates computed by an overdispersed Poisson mixed model. Estimators from the second negative binomial and overdispersed Poisson models had better frequentist properties than did those from the first negative binomial model. Nevertheless, application to a data set of number of artificial inseminations until conception in Holstein heifers suggested a slightly better fit of the first negative binomial model. A marginal likelihood ratio test indicated that the additive genetic variance was significant. Cross-validation analyses suggested that the two negative binomial mixed models had slightly better predictive ability than a linear mixed model.

Animals↗

Impact of bovine somatotropin on genetic evaluation of dairy sires and cows.

Data for milk yield and bovine somatotropin (bST) injections were obtained for 92,463 lactations of 51,986 Holstein cows in 222 commercial dairy herds that had used bST during the previous 3 yr. The overall rate of bST usage in these herds was 29%, and little difference occurred across lactations. A slightly higher percentage of cows with a low pretreatment phenotypic milk yield received bST, but there was no relationship between bST usage rate and the genetic potential of the cows, as measured by the PTA for milk of the sire. The mean starting date of bST administration was 147 d of lactation. Breeding values were estimated using three different animal models. In the first model, all data regarding bST injection were ignored. The second model included a fixed effect of bST injection (0 or 1 for each lactation). In the third model, data for bST injection were used to define management groups such that cows within a particular herd, year, and season of calving that received bST during the lactation were in a different management group from their contemporaries that did not receive bST. Correlations for EBV between sire and cow either ignoring bST or treating bST as a fixed effect were > 0.999, and approximately 98% of selected individuals were chosen under both models. Use of bST information to define the management groups resulted in correlations > 0.99; the EBV from models that either ignored bST or treated bST as a fixed effect had 92 to 95% of the selected individuals chosen by the other two models. The genetic correlation between lactation milk yield with and without bST treatment, which was estimated using a multiple-trait model, was 0.98, which indicated minimal interaction of genotype and bST. In general, bST treatment had little impact on the genetic selection decisions in this study.

Animals↗