**ORIGINAL ARTICLES**

**Variance components and genetic parameters for milk
production of Holstein cattle in Antioquia (Colombia) using
random regression models ^{¤}**

**Componentes de varianza y parámetros genéticos para producción de leche en ganado Holstein de
Antioquia (Colombia), utilizando modelos de regresión aleatoria**

**Componentes de variância e parâmetros genéticos para produção de leite em gado Holandês da
Antioquia, (Colombia) utilizando modelos de regressão aleatória**

**Ana C Herrera ^{*}, Zoot, MS; Oscar D Múnera, Zoot, MS student; Mario F Cerón-Muñoz, Zoot, MS, Dr.**

* Corresponding author: Ana Cristina Herrera Rios. Grupo de investigación GaMMA, Facultad de Ciencias Agrarias, Universidad de Antioquia. Carrera 75 No. 65-87, Bloque 47-233. Ciudadela de Robledo. AA 1226, Medellìn, Colombia. Tel (574) 2199140. e-mail: anacristinah@gmail.com

Grupo de Genética, Mejoramiento y Modelación Animal,(GaMMA),Facultad de Ciencias Agrarias e Instituto de Biología, Universidad de Antioquia, Medellín Colombia.

(Received: September 9, 2012; accepted: December 18, 2012)

**Summary**

**Background:** genetic parameters of lactation curve in dairy cattle can be analyzed as longitudinal data
using random regression models (RRM). **Objective:** the goal of the present study was to estimate variance
components and genetic parameters for milk production in Holstein cattle located in Antioquia province using
RRM. **Methods:** a total of 3,158 monthly controls corresponding to 741 first lactations of Holstein cows
were evaluated. The RRM included several Legendre polynomials to estimate the population fixed-curve
coefficients and to predict the direct additive genetic and the permanent environment effects. Additionally,
heterogeneous residual variances were considered by grouping the days in milk into 5 and 10 classes. Eleven
models with first to fourth order polynomials were used to describe the direct additive genetic and the
permanent environment effects. The residue was modeled by considering five variance classes. Models were
compared using Schwartz Bayesian and Akaike's information criteria. **Results:** the best model was obtained
by fourth order Legendre polynomials to estimate the fixed curve of the population, genetic and permanent
environment effects. In addition, 5 kinds of days were used to model the residual variances. The variance for
the animal genetic, phenotypic, permanent environment, and residual effects decreased as days increased.
Milk production heritability in early lactation was 0.36, increasing until 95 days (0.41), with subsequent
decrease, reaching 0.10 at 245 days. The permanent environment variance values decreased to 125 days (0.13)
and then increased to 215 days (0.21), to finish at the last stage of lactation with values of 0.05. The genetic
and phenotypic correlations between milk yields at different days of lactation decreased as days intervals increased. **Conclusion:** the findings of this study suggest that in the first 150 days of lactation animals better
express their genetic potential and that after 180 days there is greater environmental effect.

**Key words:** dairy cattle, genetic evaluation, heritability.

**Resumen**

**Antecedentes:** los parámetros genéticos de la curva de lactancia en ganado de leche pueden ser analizados
como datos longitudinales usando modelos de regresión aleatoria (RRM). **Objetivo:** el objetivo de este
estudio fue estimar componentes de varianza y parámetros genéticos para la producción de leche en vacas
Holstein en el departamento de Antioquia, utilizando RRM. **Métodos:** se utilizaron 3.158 controles mensuales
de 741 primeras lactancias. Se usaron RRM con diferentes grados de polinomios de Legendre para estimar
los coeficientes de la curva fija de la población y la predicción de los efectos genético aditivo directo y de
ambiente permanente y se consideraron 5 y 10 clases de varianzas residuales heterogéneas. Se emplearon
once modelos con polinomios de primer a cuarto orden, para describir los efectos genético aditivo directo
y ambiente permanente. Los modelos fueron comparados mediante los criterios de información bayesiano
de Schwartz y de Akaike. **Resultados:** el mejor modelo presentó polinomios de cuarto orden 4, 4 y 4 de la
curva fija, del efecto genético aditivo y de ambiente permanente, respectivamente, y con 5 clases de varianzas
heterogéneas (444.het5). La varianzas para los efectos genético animal, fenotípico, de ambiente permanente
y residual disminuyeron con el aumento de los días. La heredabilidad de la producción de leche al inicio de
la lactancia fue de 0,36 y fue aumentando hasta los 95 días (0,41), con posterior disminución, llegando a 0,10
a los 245 días. Para la trayectoria de la proporción de ambiente permanente los valores descendieron hasta
los 125 días (con 0,13), luego aumentaron hasta los 215 días (con 0,21), para finalizar en la última etapa de
la lactancia con valores de 0,05. Las correlaciones genéticas y fenotípicas entre producciones de leche en los
diferentes días de lactancia disminuyeron con el aumento del intervalo de los días. **Conclusión:** los resultados
encontrados en este estudio sugieren que en los primeros 150 días de lactancia los animales expresan mejor
su potencial, y que despues de 180 días hay mayor impacto ambiental.

**Palabras clave:** evaluaciones genéticas, ganado de leche, heredabilidad.

**Resumo**

**Antecedentes:** os parâmetros genéticos da curva de lactação em gado leiteiro podem ser analisados
como dados longitudinais usando modelos de regressão aleatória (RRM). **Objetivo:** o objetivo deste
estudo foi estimar os componentes de variância e os parâmetros genéticos para produção de leite de vacas
holandesas em Antioquia, utilizando um modelo de regressão aleatória (RRM). Métodos: foram utilizados
3.158 controles mensais de 741 primeiras lactações. Usaram-se RRM com diferentes graus de polinômio
ortogonal de Legendre para estimar os coeficientes da curva fixa da população e a predição dos efeitos
genéticos aditivos diretos e de ambiente permanente. Consideraram-se 5 e 10 classes de variâncias residuais
heterogêneas. Foram empregados 11 modelos com polinômios de primeira ate quarta ordem para descrever
os efeitos genéticos aditivos diretos e de ambiente permanente. Os modelos foram comparados mediante os
critérios de informação bayesiano de Schwartz e de Akaike. **Resultados:** o melhor modelo foi o de quarto
ordem (4, 4 e 4) da curva fixa, do efeito genético aditivo e de ambiente permanente, respectivamente, e com
cinco classes de variâncias heterogéneas (444.het5). A variância para os efeitos genético animal, fenotípico,
de ambiente permanente e residual diminuiu com o aumento dos dias. A herdabilidade da produção de leite ao
inicio da lactação foi de 0.36 e foi aumentando até os 95 dias (0.41), com posterior diminuição, chegando até
0.10 aos 245 dias. Para a trajetória da proporção de ambiente permanente os valores descenderam até os 125
dias (com 0.13), com posterior aumento até os 215 dias (com 0.21), para finalizar na última etapa da lactação
com valores de 0.05. As correlaciones genéticas e fenotípicas entre produções de leite nos diferentes dias de
lactação diminuíram com o aumento do intervalo dos dias. **Conclusão:** os resultados encontrados sugerem
que nos primeiros 150 dias da lactação os animais expressaram melhor seu potencial genético.

**Palavras chave:** avaliações genéticas, gado de leite, herdabilidade.

**Introduction
**

Genetic evaluations in dairy cattle require
estimating the variance components and genetic
parameters of populations. To accomplish this
objective, several methods taking total, partial,
and daily milk yield (DMY) records into account
have been used. The simplest model uses milk
production adjusted to 305 days. Some models
include a more sophisticated level of complexity
(Mark, 2004). Among these is the Test-Day model,
which uses measurements spanning a period of time
of complete lactation to describe milk production
and milk constituents at any given point on the
curve (Rodriguez-Zas *et al.*, 2000). The DMY can
be analyzed using repeated measures throughout the
lactation length using random regression models
(RRM), which describe the covariance structure
over time in a continuous manner to estimate the
genetic parameters on any lactation day for an
animal by using polynomials and other functions
of days in milk as a covariate (Henderson, 1982;
Schaeffer and Drekkers, 1994; Jamrozik *et al.*,
1997; Kistemaker *et al.*, 1997; Meyer, 2004).

The RRM also allow us to model deviations of
phenotypic trajectories, which may have different
shapes and can be more easily described by
Legendre polynomials (Kirkpatrick *et al.*, 1990)
facilitating the prediction of missing records and
improving convergence (Meyer, 2004). In addition,
it is necessary to consider heterogeneous residual
variances to improve the total variance partition,
despite the increase in the number of parameters
to be estimated for the maximization process of
the likelihood function (Meyer, 1999; Olori *et al.*,
1999a; Muir *et al.*, 2007).

According to some literature reports, researchers
have used RRM with differing degrees of Legendre
polynomials and several heterogeneous variance
classes with high heritability values throughout the
milk production curve (Van der Werf, 2001; Strabel
and Misztal, 1999; Veerkamp and Thompson, 1999,
Liu et al, 2000; Albuquerqe and Meyer, 2001).
In addition, such studies have proposed the use
of heterogeneous residual variances by grouping
classes with similar variations (Meyer, 1999; Olori
*et al.* 1999a). Consequently, the purpose of this
study was to estimate variance components and
genetic parameters for milk production of Holstein
cows in Antioquia using a random regression model.

**Materials and methods
**

A total of 3,158 monthly controls from 741 first lactation Holstein cows were used. Lactations occurred between November 2007 and October 2011 in 32 dairy herds in northern and eastern Antioquia. The herds are subscribed to the Milk Control Program of Antioquia Holstein Corporation and the University of Antioquia. The program included individual milk measurements collected using A4 methodology (ICAR, 2002) with monthly visits and two milking controls (morning and afternoon). Lactations with more than 4 monthly records were considered in the analysis; the pedigree file included 8,032 animals.

Controlled herds are located in a very humid
premontane forest (bmh-PM), with an average
temperature of 16 °C, an altitude between 2,000
and 3,000 m above sea level, and annual rainfall
between 2,000 and 4,000 mm which falls onto a
flat and undulating topography. Animals grazed
mostly on kikuyu grass (*Pennisetum clandestinum*)
and some ryegrass associations. Animals were
supplemented with commercial concentrate feed
according to production stage and herd management
criteria.

Varying degrees of the Legendre polynomial were used in the RRM to estimate population fixed curve coefficients and to predict direct genetic and permanent environment effects, considering 5 and 10 classes of heterogeneous residual variances. Days in milk intervals of 5-90, 91-120, 121-190, 191-250, 251-305 d were used for the 5 variance classes, while 1-30, 31-64, 65-92, 93-121, 122- 155, 156-188, 189-211, 212-255, 256-290, 291- 323 d intervals were considered for the 10 variance classes. The fixed effect of contemporary group (farm, season and year of birth) was also included. Calving seasons were defined as: 1 (December to February), 2 (March to May), 3 (June to August), and 4 (September to November).

The random regression model used was as follows:

Where:

*y _{ij}* = Milk production at the j

*control of the ith animal;*

^{th}*F _{ij}* = Contemporary group fixed effect of the j

*control of the i*

^{th}*animal;*

^{th}*b _{m}* = m

*fixed regression coefficient for kb regressors;*

^{th}*Φ _{m}t*

_{(ij)}= m

*Legendre polynomial evaluated at the j*

^{th}*control day of the i*

^{th}*animal;*

^{th}α* _{im}* = m

*random regression coefficients for the additive genetic effect of the ith animal;*

^{th}γ* _{im}* = m

*random regression coefficients for the permanent environment effect of the ith animal;*

^{th}*kb*-1, *ka*–1, and *kap*-1= Legendre polynomials
order to describe the mean curve and the additive
genetic and permanent environment effects,
respectively;

ε* _{ij}* = Random error associated to the j

^{th}control the i

*animal.*

^{th}The (co) variance components and genetic parameters were obtained with the restricted maximum likelihood method using the WOMBAT statistical program (Meyer, 2007). The random regression models were compared using Akaike information criterion (AIC; Akaike, 1974) and Bayesian information criterion (BIC; Schwarz, 1978), which allow comparing non-nested models and penalize models having a high number of parameters, BIC being the most rigorous (Nunez- Anton and Zimmerman, 2000). Low AIC and BIC values correspond to a better model fit.

**Results
**

The AIC and BIC results for each model tested are shown in table 1. The lowest AIC value corresponded to the polynomial-degree model 4, 4, and 4 of the fixed curve, additive genetic, and permanent environment effect, respectively, and 10 heterogeneous variance classes (444.het10). The lowest BIC value was for the model with the same polynomial degree above, but with 5 heterogeneous classes (444.het5). In this study, (co) variance components and genetic parameters were estimated using model 444.het5, since it showed the lowest BIC value, was more parsimonious and displayed faster convergence.

The first eigenvalue (λ) accounted for 83.89% of the total additive genetic covariance matrix, and the first three eigenvalues explained it by 99.99%. For the permanent environmental effect, the first eigenvalue accounted for 80.33% of the total permanent environmental variance and the first three values explained it by 99.99% (Table 2).

Variance trajectories are shown in figure 3.
The direct genetic variance increased until d70
(12.44 kg^{2}) with subsequent decrease until d239
(1.75 kg^{2}). The permanent environment interaction
was higher at the beginning of lactation (12.67
kg^{2}), with subsequent reduction to d59 (4.11 kg^{2}),
followed by an increase to d224 (11.8 kg^{2}). The
residual variance showed a downward trend from d5
(7.5 kg^{2}) to d305 (2.8 kg^{2}). The highest phenotypic
variance occurred at the beginning of lactation
(29.3 kg^{2}), decreasing to d305 (15.8 kg^{2}).

Milk yield heritability in early lactation was 0.36. It increased up to d95 (0.41), with a subsequent decrease, reaching 0.10 at d245, with low standard errors fluctuating between 0.013 and 0.021. Heritabilities increased during the last lactation phase (up to 0.34), but had high standard errors (0.14 to 0.21). The permanent environment trajectory values decreased to d125 (0.13), then increased to d215 (0.21), finishing at 0.05 during the final lactation stage (Figure 2).

Genetic and phenotypic correlations between milk yields at different lactation days are presented in figures 3 and 4, respectively. In general, genetic correlations decreased as day intervals increased, with positive values between 0.04 and 0.99. These results were higher than those obtained for phenotypic correlations, but followed the same path with values between 0.004 and 0.66.

**Discussion**

The AIC and BIC values decreased as the number
of parameters increased for each model evaluated.
The best models were 444.het10 (for AIC) and 444.
het5 (for BIC). Several researchers have tested
different orders of Legendre polynomials for milk
production. Assuming homogeneous residuals
variance, Cobuci *et al.* (2006) and Cobuci *et al.* (2011) reported that model 555 with homogeneous
residual variances was best (for both AIC and
BIC). Albuquerque *et al.* (2011) also found models
with polynomial orders 2 through 5 to be better for
the same effects using 5 heterogeneous residual
variances. Olori *et al.* (1999) tested RA models with
3 to 5 polynomial orders for different effects, using
10 classes of heterogeneous residual variances. The
best models found were those of higher order (i.e.,
the fourth order, having more number of classes of
heterogeneous residual variances).

It can be considered that higher adjustment orders for Legendre polynomials increase the flexibility of RA models. Furthermore, due to the mathematical properties of orthogonal Legendre polynomials, they are considered the most appropriate for daily milk production analysis (Schaeffer, 2004; Strabel and Jamrozik, 2006). However, biological interpretation of these coefficients is more difficult compared to other parametric functions, such as the Wilmink function and the Ali and Schaeffer polynomial functions. Some researchers, such as Cobuci (2005) and Bignardi (2011), tested these functions, obtaining the best results with models that used Legendre polynomials with orders from 4 to 7.

The decline is very pronounced after 150 days
and up to 275 for the additive variance. Similarly,
Gonzalez-Pena *et al.* (2007), using heterogeneous
residual variances, reported the highest value for
the additive variance (σ^{2}a) on d5 and the lowest
on d302. A similar trend was estimated by Strabel
and Jamrozik (2006) using fourth order Legendre
polynomials for the additive effect of the animal.

Different results were reported by Fujii (2006), who found the lowest animal variance at the beginning of lactation, and the highest at its conclusion. This was similar to results for Holstein cows in Brazil, where 3, 4 and 5 orders Legendre polynomials were used for fixed effects, animal genetic, and permanent environment, respectively (Vieira, 2006). Similarly, permanent environment variance was found to sharply decrease for the first 30 days, remaining relatively constant for the majority of lactation, and increasing at the end of it (Fujii, 2006). Other studies have reported that permanent environment variance decreased from the start of lactation to 250 days, approximately, and increased at the end of it above the initial values (Strabel and Jamrozik, 2006).

Heritabilities found at the beginning and up to
150 days were greater than 0.30, indicating that
considerable genetic variability exists in the studied
population. Similar values were reported by Strabel
and Jamrozik (2006) who found that the heritability
curve increases as lactation proceeds to 150 days or
so, decreasing slightly afterwards, and increasing at the
end of the curve. Herrera *et al.* (2011), using ordinary
test-day models for Holstein cows in Antioquia, found
milk production heritability values of 0.31 for the first
months of lactation, declining thereafter.

According to the present study, in the first five months of lactation animals express better their genetic potential (higher genetic variances and heritabilities), and after six months there are environmental effects which have a greater influence than the genetic factors. Although heritabilities were high during late lactation, standard errors were also high, mainly due to the reduction in the number of lactating animals and the exclusion of females reaching advanced pregnancy. The heritability curve for milk production in the evaluated population suggested that it is possible to achieve a greater efficiency in animal selection up to the first five months of lactation.

Gonzalez-Pena *et al.* (2007) and Olori *et al.* (1999)
reported heritabilities greater than 0.50 for some
stages of the lactation curve. These oscillations during
lactation have no clear biological explanation. It is
assumed that they can result from using higher-order
functions to explain the random effects in the model.
On the other hand, Albuquerque (2011), DeGroot
*et al.* (2007), and Muir *et al.* (2007) reported lower
heritabilities than those observed in this study, with
values ranging between 0.10 and 0.16.

Genetic correlations for milk production between
lactation days prior to day 215 were greater than
0.60. Similar results were found by Takma *et al.*
(2007) and Olori *et al.* (1999) in Holstein cows at
first calving where genetic correlations were high
for consecutive days, decreasing as the interval
between them increased.

Phenotypic correlations between start and end
days of lactation (e.g., day 35 with 305, and 65 with
305) were close to zero and negative. These results
are usually obtained with Legendre polynomials
(Brotherstone *et al.*, 2000; Cobuci, 2005; Gonzales-
Herrera *et al.*, 2008), because the parametric
functions do not model the association between
production at the beginning and at the end of the
lactation curve. Small numbers of observations for
the extreme ages, distance of the average and over
parameterized models are reported as possible
causes of these problems (de Sousa, *et al.*, 2011).

It can be concluded that there is a high genetic variability for milk production of first-calving Holstein cows in Antioquia.

**Notes**

^{¤} To cite this article: Herrera AC, Múnera OD, Cerón- Muñoz MF. Variance components and genetic parameters for milk production of Holstein cattle in Antioquia
(Colombia) using random regression models. Rev Colomb Cienc Pecu 2013; 26:90-97.

**Acknowledgements
**

Financial support to this study was provided by Colciencias (Evaluación genético-económica de bovinos Holstein en sistemas de producción de leche en Antioquia).

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