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Livestock Science
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a r t i c l e in f o abstract
Article history: The goals of this study were to estimate genetic parameters and to assess alternative
Received 18 May 2012 models for genetic evaluation of number of inseminations to conception (INS) and
Received in revised form success at first insemination (SF) in Iranian Holstein cows. Two models were considered
21 December 2012
for each trait: linear and probit models for SF, and linear and Poisson models for INS. Data
Accepted 18 January 2013
consisted of 72,124 records of parities 1 to 6 from 27,113 cows having lactation between
1981 and 2007 and distributed over 15 large Holstein herds. Genetic parameters and
Keywords: goodness of fit statistics were estimated using the whole data set and predictive ability
Dairy cows of models was assessed via a 4-fold cross-validation based on mean squared error of
Genetic parameters
prediction (MSEP) and correlation between observed and fitted values. Estimates
Model comparison
of heritability ranged from 0.039 to 0.062 for SF and 0.040 to 0.165 for INS. The
Nonlinear models
Fertility traits performance of linear and probit models was very similar for SF. Predictions of random
effects from these models were highly correlated, and both models exhibited similar
predictive ability. For INS, the linear model performed better than the Poisson model
according to goodness of fit statistics, but these two models showed the same predictive
ability. Overall, nonlinear models did not outperform linear models for genetic evalua-
tions of SF and INS in Iranian Holstein cows.
& 2013 Elsevier B.V. All rights reserved.
1871-1413/$ - see front matter & 2013 Elsevier B.V. All rights reserved.
http://dx.doi.org/10.1016/j.livsci.2013.01.009
R. Abdollahi-Arpanahi et al. / Livestock Science 153 (2013) 20–26 21
fertility traits should be considered in genetic evaluations herds of Iran were used in the analysis. Only artificial
and included in the breeding goals (Gonzalez-Recio and insemination mating records were used. Response vari-
Alenda, 2005). ables studied were number of inseminations to concep-
Number of services to conception (INS) as an indicator tion (INS) and success to first insemination (SF). These 15
of reproductive efficiency has been defined as the number dairy herds are under registration of the Dairy Herd
of services required for a successful conception. The INS is Improvement Program of the Animal Breeding Centre of
directly related to open days, pregnancy rate, non-return Iran. Artificial insemination (AI) technicians record all
rate and the reciprocal of services per conception. In insemination events and are in charge of maintaining an
contrast to open days and days to first service which are accurate dataset. All cows had records for both traits.
interval traits that do not account for elapsed time from Reproductive traits in different parities were treated as
first to last insemination and veterinary costs, the variable repeated measurements. For INS, all the values greater
INS takes partly these important issues into consideration. than 9 were set to 9 in order to reduce possible recording
In this sense, Gonzalez-Recio and Alenda (2005) reported errors. SF was a binary trait defined as 1 if the cow
that by including INS in an index with combination of became pregnant at first insemination and 0 otherwise.
production traits, the profit would be increased by 229 h/
cow. Therefore, INS should be registered and considered 2.2. Statistical Models
in genetic evaluations since it would maximize profit-
ability at balancing economically production and fertility. Preliminary least squares analyses were conducted for
Success at first insemination (SF) is a trait that is similar both traits using the GLM procedure of Statistical Analysis
to pregnancy rate (Bormann, 2006) and which is often System (SAS) (SAS, 2004) to decide which non-genetic
included in dairy female selection indices. SF is an econom- effects had to be included in the final models. The
ically important trait due to the cost of the semen, labors following linear predictor was common to both traits:
involved in heat checking and breeding for multiple AI, and
g ¼ Xb þ Z1 a þ Z2 hys þWpe
the difference in the quality and value between AI calves
and natural calves. Moreover, heifers that became pregnant where g is a function of the expected value of SF or INS; b
at first breeding are going to calve earlier, and hence they is a vector for fixed effects of parity (6 levels), age at
will have a better chance to breed back on the following previous calving (10 levels) and months of first insemina-
year. Heritability estimates for first-service conception tion (12 levels); a is the additive genetic effect; hys is
range from 0.03 to 0.22 (Cammack et al., 2009). herd-year-season effect; pe is permanent environmental
Heritability estimates for fertility traits are typically effect for cows; e is the residual term; and X, Z1, Z2 and W
low, ranging from 1% to 5% when using linear models for are incidence matrices relating data to the corresponding
statistical analysis (e.g. Wall et al., 2003). Nonlinear effects.
models could be better alternatives for more accurate Random effects were assumed to follow the multi-
assessment of genetic parameters and genetic merit of the variate normal distribution,
animals in these traits. Several probability models can 0 1 2 0 13
a As2a 0 0
be used for describing the number of inseminations to B hys C 6 B C7
A N6 B 0 Is2hys 0 C7
conception (INS) and success at first insemination (SF) in @ 40, @ A5
dairy cattle. For categorical or counted variables such as pe 0 0 Is2pe
INS, several alternatives are available, e.g., Poisson, linear
or ordinal threshold models (Peñagaricano et al., 2011; where a, hys and pe are the vectors of additive genetic
Vazquez et al., 2009a, 2009b). In general, analysis of animal, herd-year-season and permanent environmental
counts with models based on the Poisson distribution effects, respectively; s2a , s2hys and s2pe are the additive
tends to be more appropriate than models based on genetic, herd-year-season and permanent environmental
normal distribution. For binary outcomes such as SF, the effects variances, respectively; A is the additive relation-
Bernoulli distribution parameterization using either a ship matrix (with order 32,447 32,447) and I is the
probit or a logit link is a natural approach. Another identity matrix of order 838 for herd-year-season and
alternative, despite the binary nature of the variable, is 27,113 for permanent environmental effects. Animal,
the use of a linear model. herd-year-season and permanent environmental effects
The objectives of the current study were, firstly, to were assumed to be independent of residual effects in the
estimate genetic parameters; and, secondly, to assess models. General structure of the data and the pedigree is
alternative models for genetic analysis of SF (probit and presented in Table 1.
linear) and INS (Poisson and linear). Models were com-
pared based on goodness of fit statistics and their pre- 2.2.1. Probit model for SF
dictive ability in a 4-fold cross-validation analysis. The Probit model (Gianola, 1982) describes the obser-
vable outcome (SF) using an underlying linear model
2. Materials and methods z¼ g þe, where e is independent and identically distrib-
uted standard normal random vector. The scoring rule in
2.1. Data this model is:
(
1 ðsuccessÞ
A total of 72,124 records of parities 1 to 6 from 27,113 SF ¼
0 ðfailureÞ
cows collected from 1981 to 2007 in 15 large Holstein
22 R. Abdollahi-Arpanahi et al. / Livestock Science 153 (2013) 20–26
Table 1
General structure of the data and the pedigree by class of parity in Iranian Holstein cows. The traits under study are success at first insemination (SF) and
number of inseminations to conception (INS).
Data
No. of records 25,519 18,700 12,855 7587 4656 2453
SF (%) 45.96 41.95 41.65 41.65 39.21 37.73
Mean INS 2.05 2.18 2.16 2.17 2.23 2.35
SD INS 1.35 1.42 1.39 1.40 1.41 1.55
Pedigree
No. animals in pedigree 31,447 24,622 18,438 12,473 8116 4745
No. sires 1406 1196 1019 792 603 482
No. dams 15,575 12,211 9114 6081 3901 2149
No. of progeny per sire 18.67 16.75 14.25 12.01 9.91 6.91
No. of animals with both parents known 22,125 16,524 11,705 7372 4457 2315
No. of phenotyped animals with at least one parent unknown 2178 295 93 53 16 15
In linear and Poisson models, heritability (h2) and 3.1. Descriptive statistics
repeatability (r) can be evaluated respectively in the
observable and log scale, using standard formulae: Thirty percent of the animals had one record, 23.47%
2 s2a þ s2pe had two records, 18.66% had three records and the rest
2 s a
h ¼ 2 and r ¼ 2 had more than three records (up to 6 per animal). The
sa þ s2pe þ s2hys þ s2e sa þ s2pe þ s2hys þ s2e
average number of service to conception was 2.14 and the
In the Probit model, h2 and r can be evaluated at the percentage of success at first insemination was 42.96.
liability scale using the above formulae with s2e ¼ 1. Table 1 shows the percentage of success at first insemina-
tion (SF) and mean and standard deviation (SD) of number
2.6. Model comparison of inseminations to conception (INS) for each parity.
The percentage of SF decreased as the parity number
Goodness of fit of each of the models was assessed by increased. Other studies (Chebel et al., 2004) argued that
computing the mean-squared error statistic (MSE), multiparous cows had lower conception rate than primi-
X parous cows. In agreement with Badinga et al. (1985),
MSE ¼ n1 ^ 2,
ðyyÞ who reported that heifers required 1.5 services per con-
where y^ is the conditional expectation function evaluated ception compared with 2.3 for lactating cows, our results
at the posterior mean of model unknowns, y is the also showed that INS increased over parity number.
corresponding vector of values of the response (either SF
or INS) and n is the number of observations. The condi- 3.2. Estimates of variance and genetic parameters
tional expectation functions of the linear, probit and
Poisson models are y^ ¼ g ^ , y^ ¼ Fðg
^ Þ and y^ ¼ expðg
^þ Estimates of the mean and quantiles (0.025 and 0.975) of
ð1=2Þs2e Þ, respectively. In addition, Pearson’s correlation the posterior distribution of variance components, heritabil-
between y^ and y was also obtained. Model comparison ities, and repeatabilities calculated by different models for
also involved assessing Spearman rank correlations SF and INS are presented in Table 2. For all models, the herd-
between predictions of random effects obtained with year-season variance showed the highest value, highlighting
different models. Random effects were predicted using the importance of management and hygiene practices on
the estimated posterior mean of those effects. individual farms (e.g. Pérez-Cabal et al., 2009; Vazquez et al.,
To assess the predictive ability of each model, the 2009b). Importantly, variance components are not directly
dataset was partitioned into four parts, with a restriction comparable between models because they belong to differ-
that imposed that all levels of fixed effects were repre- ent distributions. A more meaningful comparison can be
sented in each partition. Then, solutions for all fixed and based on ratios between variances components, i.e., h2 and r.
random effects of the training set (three folds) were Heritability estimates were low for SF (0.062 and 0.039 for
estimated and used to predict observations in the testing probit and linear models, respectively) and low to moderate
set (retained partition). The mean-squared predictive for INS (0.040 and 0.165 for linear and Poisson models,
error was defined as respectively). Additionally, following Dempster and Lerner
XX f (1950), the heritability estimate for SF obtained with the
MSEP ¼ n1 ðyy^ Þ2 , probit model was scaled back to the observed scale: the
f
estimate was equal to 0.045 and it was smaller than that on
f
where y^ is a conditional expectation function evaluated the liability scale due to the loss of information by grouping
at the posterior mean of model unknowns obtained when into two categories (Dempster and Lerner, 1950).
the data in fold f was excluded from the analysis. Finally, Working with the same population, Ghiasi et al. (2011)
the Pearson correlation between observed and fitted reported lower heritability estimates for both SF (0.029) and
values in the testing set was also estimated. INS (0.046) traits. It is important to remark that these
Table 2
Estimates of mean and quantiles (0.025, 0.975) of the posterior distribution of variance components and genetic parameters by response (success or fail
at first insemination, SF, and number of inseminations to conception, INS) and model (linear, probit and Poisson).
SF INS
s2a 0.010 (0.009, 0.011) 0.084 (0.067, 0.105) 0.075 (0.064, 0.092) 0.011 (0.010, 0.013)
s2pe 0.010 (0.009, 0.011) 0.081(0. 061, 0. 103) 0.078 (0.063, 0.094) 0.010 (0.009, 0.011)
s2hys 0.017 (0.015, 0.020) 0. 183 (0.155, 0.208) 0.136 (0.117, 0.152) 0.033 (0.029, 0.038)
s2e 0.217 (0.215, 0.219) 1 1.656 (1.631, 1.673) 0.017 (0.016, 0.019)
h
2 0.039 (0.036, 0.044) 0. 062 (0.050, 0.077) 0.040 (0.033, 0.047) 0.165 (0.140, 0.179)
r 0.081 (0.075, 0.086) 0. 121 (0.109, 0.140) 0.078 (0.072, 0.088) 0.298 (0.270, 0.321)
s2
a, Additive genetic variance; s 2
pe , permanent environmental variance; s 2
hys , heard-year-season variance; s 2
e, residual variance; h2, heritability;
r, repeatability.
24 R. Abdollahi-Arpanahi et al. / Livestock Science 153 (2013) 20–26
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