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ANIMAL GENETICS |
,3

* Department of Agro-biology, Niigata University, Niigata 950-2181, Japan; and
and
Department of Animal and Dairy Science, University of Georgia, Athens 30602-2771
| Abstract |
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Key Words: Beef Cattle Early Growth Genetic Parameters Linear Spline Function Random Regression
| Introduction |
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With applications in other livestock species (Schaeffer and Dekkers, 1994
; Huisman et al., 2002
), random regression models (RRM; Kirkpatrick et al., 1990
) have recently attracted the interest of beef cattle breeders for modeling the changes in growth in time. For RRM application in beef cattle, Legendre polynomials of age at recording have typically been used (Albuquerque and Meyer, 2001
; Nobre et al., 2003a
,b
). In contrast to MTM, RRM permits the calculation of (co)variances and EPD at any age between two growth points. However, it has been indicated that parameter estimates obtained by fitting polynomials could be affected by sparse data and extremes of trajectories, especially at later ages (Nobre et al., 2003a
,b
).
One alternative approach could be spline-fitting, which is expected to estimate parameters more smoothly, possibly free from sharp bends at extremes at later ages (Verbyla et al., 1999
), while still adequately modeling the features of longitudinal data (White et al., 1999
). However, no numerical comparison is available between genetic parameters from the application of MTM and RRM with spline functions to early growth data in beef cattle.
The objectives of this study were to estimate (co)variance components and genetic parameters for direct and maternal effects of birth, weaning, and yearling weights in Gelbvieh cattle by RRM with a linear spline function (SFM) and to numerically compare the resulting estimates with those estimated with MTM.
| Materials and Methods |
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where Fqr denotes a set of fixed effects, as stated below; dqh and pqh are the random regression coefficients for direct additive genetic and permanent environmental effects of animal q at knot h, respectively; mqh and pmrh are the random regression coefficients for maternal additive genetic and maternal permanent environmental effects of dam r at knot h, respectively; fh(aq) stands for the linear spline coefficient at knot h for age aq; and eqr is the random residual term.
Linear spline functions were used to explain fixed effects as follows:
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with cgih, aodjh, mockh, and sexlh representing the fixed regression coefficients for contemporary group i, age of dam class j, month of calving k, and sex l at knot h, respectively. In this model, knots were set to 1, 205, and 365 d, which were practically averages of the three growth points, so that two line segments were joined at 205 d of age.
The SFM above could be expressed in matrix notation as:
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where yS is the vector of observations for BWT, WWT, and YWT; bS is the vector of the fixed effects; dS is the random vector of direct additive genetic effects; mS is the random vector of maternal additive genetic effects; pS is the random vector of direct permanent environmental effects; pmS is the random vector of maternal permanent environmental effects; eS is the vector of random residuals; and XS, ZS, ZS2, ZS3, and ZS4 are incidence covariance matrices relating elements of yS to elements of bS, dS, mS, pS, pmS, and eS, respectively.
For the model, the covariance matrix was assumed to be:
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where GSd, GSm and GSdm were covariance matrices of random regression for direct additive genetic effect, maternal additive genetic effect, and their covariances, respectively; PS, PmS, and RS were covariance matrices of random regression for direct permanent environmental, maternal permanent environmental, and residual effects, respectively; A was the additive relationship matrix among all animals in the pedigree file, In, Ic, and Ik were identity matrices, whose orders are the numbers of animals, dams, and records, respectively, and
denotes the direct product operator. Heterogeneous residual variances were considered for ages of BWT, WWT, and YWT in SFM. The (co)variance matrix for target ages was defined as B'KB, where B is a matrix containing the random effects of the spline for the target ages, and K is the estimated covariance matrix of the spline coefficients.
Multitrait Analysis
The three-trait maternal animal model used was, in matrix notation, of the following form:
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where y is the vector of observations for BWT, WWT, and YWT; b is the vector of the fixed effects, or discrete variables for the fixed factors as considered in SFM, including age measurements as a linear covariate for WWT and YWT; d is the random vector of direct additive genetic effects; m is the random vector of maternal additive genetic effects; pm is the random vector of maternal permanent environmental effects; e is the vector of random residuals; and X, Z1, Z2, and Z3 are known incidence matrices relating elements of y to elements of b, d, m, and pm, respectively.
For this model, it was assumed that:
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where Gd and Gm are covariance matrices of random direct additive genetic effects and random maternal additive genetic effects, respectively; Gdm is a matrix of additive genetic covariances between direct and maternal effects; Pm is a covariance matrix of random maternal permanent environmental effects; R is a covariance matrix of random residual effects; A is the additive relationship matrix among all animals in the pedigree file; and Ic and In are identity matrices, whose orders were the numbers of dams and animals, respectively. Note that in MTM, the residual effect corresponded to the sum of the direct permanent environmental and the residual effects in the SFM.
Computation of (Co)variance Components
Estimates of (co)variance components from SFM and MTM were calculated by a Bayesian implementation via Gibbs sampling using flat improper priors for nuisance parameters and flat priors for (co)variance components. A total chain length of 100,000 rounds was run by a single long-chain algorithm. After discarding the initial 50,000 samples as the burn-in, one in every 10 samples was stored to generate the Gibbs samples that were used to compute the means and standard deviations of the posterior distribution. The means and the posterior distribution were used as the estimates of the (co)variance components, and their posterior standard deviations were considered to be a measure of their accuracy. Computations were carried out using the program GIBBSF90 (Misztal, 1999
).
| Results and Discussion |
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The results for maternal permanent environmental effects were more variable than those estimates for the direct and maternal genetic effects. Sampling variances were larger for all SFM estimates compared with MTM estimates, and some of the SFM estimates were larger. Approximately half the current data were represented by progeny of first-parity cows, and the proportion of missing data was high for YWT, which would not be an exception in the case of beef field weight data. Therefore, (co)variance estimates of maternal permanent environmental effects, especially for YWT could reasonably be susceptible to larger sampling variances, which should be taken into consideration when assessing these results.
The residual term in MTM would be, for the case of no missing data, approximately equivalent to the sum of direct permanent environmental and residual effects in SFM. Actually, the sums of permanent environmental and residual (co)variances obtained with SFM corresponded well to the appropriate residual (co)variances estimated with MTM, taking into account their posterior standard deviations. For BWT, with no missing data, estimated residual variances from both models were equivalent to each other, similar to the case of estimates of other variance components for BWT.
Table 3
shows estimates of covariances between direct genetic and maternal genetic effects for BWT, WWT, and YWT. For covariance components within the same trait, estimates were all negative and generally less negative for SFM than for MTM. Because the fraction of progeny of first-parity cows was large, and the proportion of missing data was very high for YWT, estimates of direct-maternal genetic covariances between different traits had relatively large estimated sampling variances, resulting in estimates not significantly different from zero for most trait combinations in both MTM and SFM. The only exception was the estimated covariance between the maternal genetic effect for WWT and the direct genetic effect for YWT. These estimates were 133.7 ± 40.7 and 74.6 ± 39.8 for SFM and MTM, respectively.
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estimates decreased for WWT and then increased for YWT with both models. A lower estimate of
for WWT relative to BWT and YWT was in agreement with previous findings obtained using animal models (Meyer, 1992
estimates (0.28 and 0.48) for WWT and YWT obtained with SFM were approximately 20% lower than the corresponding MTM estimates (0.36 and 0.59). Maternal heritability (h2m) estimates for BWT, WWT, and YWT ranged from 0.08 to 0.13 with MTM and from 0.06 to 0.11 with SFM, and they were substantially lower than those for
. Reviewing reported estimates, Mohiuddin (1993)
were around 0.10 for the three traits, whereas the averages for
were higher. For WWT, depending on various factors such as breed and population structure, some previous estimates of
were similar to, or larger than, those of
(Meyer, 1992
with SFM than with MTM, although differences between the estimates from the two models were small. Estimates of the fraction of maternal permanent environmental variance (c2) ranged from 0.09 to 0.12 for MTM and from 0.07 to 0.14 for SFM, and they were almost of the same magnitude as
ratios. However, the c2 estimate for WWT was higher than those for BWT and YWT, which was more evident in the estimates with SFM.
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Genetic correlations among three growth points for direct genetic and maternal genetic effects are listed in Table 5
. As expected, correlations for direct effects were moderately positive with both models (Table 5
). Estimates of correlations between maternal genetic effects for BWT and WWT were negative with both models, indicating that prenatal and postnatal maternal effects would be genetically antagonistic. Genetic correlations of YWT with other traits were close to zero with MTM when taking into account their posterior standard deviations. With SFM, the genetic correlation between BWT and YWT was negative, and the correlation between YWT and WWT was not significantly different from zero.
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For longitudinal weight data from birth to 630 d of age in Nellore beef cattle, assuming that direct-maternal correlation was unimportant, Albuquerque and Meyer (2001)
estimated direct and maternal genetic covariance functions employing RRM with cubic Legendre polynomials and found that RRM modeled the pattern of (co)variances in the data well, with estimates similar to those obtained with the corresponding univariate analysis. Nonetheless, some estimation artifacts were observed for parameters estimated using RRM, particularly those at later ages. Moreover, using RRM with cubic Legendre polynomials, Nobre et al. (2003a)
analyzed similar weight data from Nellore cattle, creating two data sets sampled from all herds and sampled from herds with no missing traits. They observed that parameter estimates with RRM were generally similar to those with MTM; however, estimates of variances were shown to contain more estimation artifacts for data with missing traits. It was found that EPD based on RRM using parameters estimated from the data were inaccurate relative to MTM (Nobre et al., 2003b
). Therefore, RRM with Legendre polynomials would be susceptible to estimation artifacts due to the nature of polynomials to be poorly fit at extremes where small amounts of data are available. Following these findings, one alternative to fitting Legendre polynomials could be the use of certain functions, such as fractional polynomials (Robert-Granie et al., 2002
), that are less susceptible to these artifacts. Another alternative is the use of spline-fitting (Verbyla et al., 1999
; White et al., 1999
; Huisman et al., 2002
) that might possibly provide a better fit in the setting of a limited number of growth points that are separated enough in time to be considered different traits.
Age of calf effect in MTM was modeled by fitting an overall linear regression of WWT and YWT on age of calf at recording, and other fixed effects were included in the usual discrete fashion. Fixed effects in SFM were fitted as fixed regressions with linear splines. Results here suggest that the corresponding estimates of variances and covariances from SFM and MTM would be similar even with missing records, when there are few traits measured and the age range for each trait is narrow (90 d in the current study for WWT and YWT). Furthermore, it was found that the two models were in very close agreement for parameters associated with BWT that had no missing records and age range variation. In all cases, with the exception of the total residual variance, the (co)variance, heritability, and genetic correlation estimates provided via SFM were slightly lower and had smaller estimated sampling variances than those estimated via MTM.
Of interest was the decrease in the absolute values of the negative estimates for direct and maternal covariances and correlations from SFM compared with MTM when direct and maternal effects within the same trait were considered. Direct-maternal genetic correlations estimated with the conventional reduced-Willham model (Koerhuis and Thompson, 1997
) may be overestimated, assuming no environmental covariance between dams and offspring (Meyer, 1997
; Quintanilla et al., 1999
) or not considering the effect of sire x herd-year interaction (Robinson, 1996b
; Dodenhoff, 1999
). In a sense, the less extreme estimate of the genetic correlation obtained with SFM compared with MTM might be more realistic, due to a smooth fit of the linear spline function to the data.
Conducting a simulation with some realistic generated data sets, Meyer (2004)
suggested that some improvement in the accuracy of genetic evaluation of beef cattle for growth could be expected by replacing MTM with RRM for the analysis of BWT, and 200-, 400-, and 600-d weights. In the current setting of three early growth points from birth to yearling, it may generally be anticipated that the SFM analysis could be essentially equivalent to RRM with polynomials. However, the linear splines used here are computationally easier and faster to implement than polynomials. In contrast to polynomials, the behavior of splines in different intervals are not related (Wold, 1974
). For the type of data represented in the current study, estimates of direct and maternal genetic parameters with SFM may be superior to those from MTM due to better modeling of differences due to age in both fixed and random effects, particularly for growth at yearling. A simulation study that considers various realistic data sets of early growth would be helpful to clarify the potential benefits of the SFM analysis.
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| Footnotes |
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2 On leave from Dept. of Agro-biology, Niigata Univ. ![]()
3 Correspondencephone: 706-583-0017; fax: 706-583-0274; e-mail: shogo{at}uga.edu.
Received for publication September 13, 2004. Accepted for publication December 28, 2004.
| Literature Cited |
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This article has been cited by other articles:
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J. P. Sanchez, I. Misztal, I. Aguilar, and J. K. Bertrand Genetic evaluation of growth in a multibreed beef cattle population using random regression-linear spline models J Anim Sci, February 1, 2008; 86(2): 267 - 277. [Abstract] [Full Text] [PDF] |
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F. Kohn, A. R. Sharifi, S. Malovrh, and H. Simianer Estimation of genetic parameters for body weight of the Goettingen minipig with random regression models J Anim Sci, October 1, 2007; 85(10): 2423 - 2428. [Abstract] [Full Text] [PDF] |
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R. J. C. Cantet, A. N. Birchmeier, A. W. C. Cayo, and C. Fioretti Semiparametric animal models via penalized splines as alternatives to models with contemporary groups J Anim Sci, November 1, 2005; 83(11): 2482 - 2494. [Abstract] [Full Text] [PDF] |
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