500
INTRODUCTION
The beneft of crossbreeding includes improve-
ment in growth and carcass traits (Williams et al.,
2010) and has been studied by many researchers over
the past decade (Roso et al., 2005a,b; Carvalheiro et al.,
2006; Dias et al., 2011). For the purpose of selection
for production, the greatest challenge is the nonbiased
comparison of breeding bulls and dams of different
breed compositions. In crossbred populations, effects
that are assumed to be null in pure populations become
important and must be taken into account. For a fair
comparison, a multibreed genetic evaluation including
crossbred and purebred individuals in the same data set
is required, as proposed by Arnold et al. (1992).
Multibreed analysis requires the inclusion of ef-
fects for direct and maternal breed additive, heterosis
(Cardoso et al., 2008; Williams et al., 2010), epistatic
loss (Dias et al., 2011), and complementarity between
different breeds (Carvalheiro et al., 2006; Cardoso et
al., 2008) effects. However, this model may be dif-
fcult to ft if the data structure does not adequately
sample all the genetic relationships. The additive ge-
netic effect for each breed involved and their combin-
ing ability, general or specifc, should be considered.
The nonadditive genetic effects are usually included as
covariates (Carvalheiro et al., 2006; Dias et al., 2011).
The inclusion of these effects as fxed covariates may
Comparing methodologies to estimate fxed genetic effects
and to predict genetic values for an Angus × Nellore cattle population
C. D. Bertoli,*†
1
J. Braccini,† V. M. Roso‡
*Departamento de Zootecnia, Instituto Federal Catarinense Campus Camboriú
(IFC-Camboriu), Camboriú, SC, Brasil; †Departamento de Zootecnia, Universidade Federal do Rio Grande
do Sul (UFRGS), Porto Alegre, RS, Brazil; and ‡GenSys Consultores Associados, Porto Alegre, RS, Brazil
ABSTRACT: The study assesses the need for and
effectiveness of using ridge regression when estimat-
ing regression coeffcients of covariates representing
genetic effects due to breed proportion in a crossbreed
genetic evaluation. It also compares 2 ways of select-
ing the ridge parameters. A large crossbred Angus ×
Nellore population with 294,045 records for weaning
gain and 148,443 records for postweaning gain was
used. Phenotypic visual scores varying from 1 to 5 for
weaning and postweaning conformation, weaning and
postweaning precocity, weaning and postweaning mus-
cling, and scrotal circumference were analyzed. Three
models were used to assess the need for ridge regres-
sion, having 4, 6, and 8 genetic covariates. All 3 models
included the fxed contemporary group effect and ran-
dom animal, maternal, and permanent environment
effects. Model AH included fxed direct and maternal
breed additive and the direct and maternal heterosis
covariates, model AHE also included direct and mater -
nal epistatic loss covariates, and model AHEC further
included direct and maternal complementarity effects.
The normal approach is to include these covariates as
fxed effects in the model. However, being all derived
from breed proportions, they are highly collinear and,
consequently, may be poorly estimated. Ridge regres-
sion has been proposed as a method of reducing the
collinearity. We found that collinearity was not a prob-
lem for models AH and AHE. We found a high variance
infation factor, >20, associated with some maternal
covariates in the AHEC model refecting instability of
the regression coeffcients and that this instability was
well addressed by using ridge regression using a ridge
parameter calculated from the variance infation factor.
Key words: complementarity, crossbred beef cattle evaluation,
epistatic loss, heterosis, nonadditive genetic effects, ridge regression.
© 2016 American Society of Animal Science. All rights reserved. J. Anim. Sci. 2016.94:500–513
doi:10.2527/jas2015-9344
1
Correspondig author: cdbertoli@gmail.com
Received May 25, 2015.
Accepted November 9, 2015.
Published February 12, 2016