Comparison of alternative methods of handling contemporary group effects in animal model prediction

Sivarajasingam, S.

doi:10.1111/j.1439-0388.1993.tb00753.x

Cited by 3 publications

(1 citation statement)

References 8 publications

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“…The problem with the usual definition of CG is its arbitrary definition of periods of time that do not correspond to criteria for maximum accuracy and minimum bias (Schmitz et al ., 1991; Carabaño et al , 2004). In an attempt to resolve this problem several criteria to compare different definitions of CG that consider the estimated intra-CG variance, residual variance and accuracy of genetic evaluations have been proposed (Schmitz et al , 1991; Sivarajasingam, 1993; Van Bebber et al , 1997; Carabaño et al , 2004). …”

Section: Introductionmentioning

confidence: 99%

Relative contribution of effects included in contemporary groups for adjusted and actual 120-day and 210-day weights in Nelore cattle in Brazil

et al. 2011

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The objective of this research was to estimate the relative magnitude of effects included in contemporary groups (CG) and their interactions with adjusted and actual 120 d and 210 d weights in 72,731 male and female Nelore calves born from 1985 to 2005 in 40 herds from PMGRN (Genetic Improvement Program of Nelore). Ten models with different CG structures were compared. The analyses were done using the general linear models (GLM) procedure run in SAS software. All of the effects included in the CG for each model were significant (p < 0.001) for the four traits analyzed. Inclusion of semester or trimester of birth as part of a CG was more appropriate than its use as an independent effect in the model because it accounted for interactions with the other effects in the CG. Calf sex (CS) and dam age at calving (DAC) had similar effects across the models, which suggested independence from other effects in these models. The corresponding age deviation effect had a larger impact on actual weight at 120 d than any other effect in all of the models tested. The use of actual weights in models with no CS effect in CG provides an alternative that would allow better genetic connectedness among CGs and greater accuracy in genetic evaluations.

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Section: Introductionmentioning

confidence: 99%

Relative contribution of effects included in contemporary groups for adjusted and actual 120-day and 210-day weights in Nelore cattle in Brazil

et al. 2011

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Comparing alternative definitions of the contemporary group effect in Avileña Negra Ibérica beef cattle using classical and Bayesian criteria1

Carabaño¹,

Mínguez²,

López-Romero

et al. 2004

Journal of Animal Science

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Data on weaning weight from 12,740 animals were used to compare different definitions of contemporary groups (CG) for the genetic evaluation of the Avilena Negra Iberica beef cattle breed. Six alternative definitions for the CG effect were considered: herd-year-season of calving (HYS), with seasons defined according to the four natural seasons; herd-year-month of calving (HYM); herd clusters of 30 d (HC30-30) or 90 d (HC90-90); and adaptive herd clusters with two time limits, 30 and 90 d (HC30-90), and 30 and 180 d (HC30-180). A minimum of five observations in each CG class was required. This rendered substantial differences in loss of information, ranging from 0.7% of the total number of records for HC30-180 to 14% for HYM. Several classical statistics and Bayesian criteria for statistical model comparison were used. The use of classical criteria, such as the between- and within-CG variation and the accuracy of prediction, can be controversial because of their dependency on the unknown variance components. Residual variance decreased with the decrease in time span associated with the definition of CG. This was expected in this population because environmental conditions are highly variable throughout the year. However, estimates of the additive genetic variance for direct effects, which should not be affected by the definition of CG, were substantially larger for definitions involving larger time periods (HYS, HC90-90). When parameters used in the current evaluation procedure were used with all data sets, CG involving 30 d (HYM and HC30-30) were optimal in terms of providing the lowest/largest within-/between-CG variation. On the other hand, CG involving 90 d (HYS and HC90-90) yielded the poorest within-/between CG variation, with only a slight improvement of accuracy of prediction of direct genetic values over the other definitions. Bayes factors and cross-validation predictive densities allowed for improved discrimination among models. Models including CG spanning 30 d were more plausible and showed better predicting ability than models spanning 90 d. Adaptive CG showed intermediate results. Overall, it seems that average time span rendered by the different definitions had a major effect on the ranking of models. However, from the breeder's point of view, the loss of information associated with definitions involving shorter periods of time, such as HYM or HC30-30, might be unacceptable.

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Semiparametric animal models via penalized splines as alternatives to models with contemporary groups1

Cantet

Birchmeier

Cayo

et al. 2005

Journal of Animal Science

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Contemporary groups (CG) are used in genetic evaluation to account for systematic environmental effects of management, nutritional level, or any other differentially expressed group effect; however, because the functional form of the distribution of those effects is unknown, CG serve as an approximation to a time-varying mean. Conversely, in semiparametric models, there is no need to assume any functional form for the time-varying effects. In this research, we present a semiparametric animal model (AMS) using the covariate day of birth (DOB) by means of penalized splines (P-splines), as an alternative to fitting CG. In the AMS, the functionality of the data on DOB is expressed by means of a Basic segmented polynomial line (B-spline) basis, and proper covariance matrices are used to reflect the serial correlation among the points of support (or knots) at different times. Three different covariance matrices that reflect either short- or long-range dependences among knots are discussed. Different models were fitted to birth weight data from Polled Hereford calves. Models compared were an animal model with CG, an animal model with CG and the covariate DOB nested within CG (CG + DOB), and P-splines with the first difference penalty matrix and three different AMS with 20, 40, 60, 80, or 120 knots. Models were compared using a modified Akaike information criterion (AICC), which was calculated as a byproduct of the estimation of variance components by REML using the expectation maximization algorithm. All three AMS had smaller (better) values of AICC than the regular model with CG, while producing almost the same ranking of predicted breeding values and similar average predicted error variance. In all AMS, the inference and all measures of comparison were similar when the number of knots was equal > or = 40. The model CG + DOB had analogous performance to the AMS, but at the expense of using more parameters. It is concluded that the use of penalized regression splines using a B-spline basis with proper covariance matrices is a competitive method to the fitting of CG into animal models for genetic evaluation, without having to assume any functional form for the covariate DOB.

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Comparison of alternative methods of handling contemporary group effects in animal model prediction

Cited by 3 publications

References 8 publications

Relative contribution of effects included in contemporary groups for adjusted and actual 120-day and 210-day weights in Nelore cattle in Brazil

Relative contribution of effects included in contemporary groups for adjusted and actual 120-day and 210-day weights in Nelore cattle in Brazil

Comparing alternative definitions of the contemporary group effect in Avileña Negra Ibérica beef cattle using classical and Bayesian criteria1

Semiparametric animal models via penalized splines as alternatives to models with contemporary groups1

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