Published March 20, 2015
Research
Eberhart and Russel’s Bayesian Method
in the Selection of Popcorn Cultivars
Mauricio Farias Couto, Moysés Nascimento, Antônio Teixeira do Amaral, Jr.,*
Fabyano Fonseca e Silva, Alexandre Pio Viana, and Marcelo Vivas
Abstract
The goal of this work was to estimate stability
and adaptability parameters using a Bayesian
approach to Eberhart and Russel’s method and
to assess the efficiency of using an a priori dis-
tribution. The information from assessing the
popping expansion and grain yield of 16 pop-
corn genotypes was used in randomized block
experiments implemented in five environments
in the North and Northeast regions of the State
of Rio de Janeiro, Brazil. The Bayesian method-
ology was implemented using the free software
package R with the MCMCregress function of
the MCMCpack package. Eberhart and Rus-
sel’s method using a Bayesian technique was
found to be efficient in recommending cultivars
to more or less favorable environments. The
incorporation of a priori information provided
greater accuracy in estimating the stability and
adaptability parameters. In the comparison of
a priori distributions, the BayesFactor function
indicated the informative a priori as the most
effective for obtaining reliable estimates.
crop science, vol. 55, march– april 2015  www.crops.org
M.F. Couto, A.T. do Amaral, Jr., A.P. Viana, and M. Vivas, Laboratório
de Melhoramento Genético Vegetal, Universidade Estadual do Norte
Fluminense Darcy Ribeiro, Av. Alberto Lamego, 2000, 28013-602,
Campos dos Goytacazes, Rio de Janeiro, Brazil; M. Nascimento and F.F.
e Silva, Departamento de Estatística, Universidade Federal de Viçosa,
Avenida P.H. Rolfs, s/n, CEP 36571-000 Viçosa, Minas Gerais, Brazil.
Received 16 July 2014. *Corresponding author (amaraljr@uenf.br).
Abbreviations: GE, genotype and the environment; GY, grain yield;
NID, normally and independently distributed; PE, popping expansion.
I n plant genetic improvement programs, the goal is to obtain
cultivars that achieve high yields in the environments intended
for cultivation. To select better cultivars, it is necessary to con-
sider the interaction between the genotype and the environment
(GE) (Fehr, 1987; Falconer and MacKay, 1996; Bach et al., 2012),
which is defined as the differential response of genotypes in the
face of environmental variation (Crossa, 2012; Bach et al., 2013).
To reduce the effects of GE interaction, it is convenient for plant
breeders to know their magnitude as well as to identify more stable
genotypes and cultivars adapted to specific environments (Crossa,
1990; Ransul et al., 2012). Methods that predict the performance
of genotypes can greatly increase the efficiency of genetic improve-
ment programs for commercial corn (Bernardo, 1992; Vieira et al.,
2012). In this context, several methods to study adaptability and sta-
bility have been described, predominantly based on linear regression
models (Finlay and Wilkinson, 1963; Tai, 1971; Eberhart and Russel,
1966), bisegmented regression (Verma et al., 1978; Cruz et al., 1989),
non-parametric analysis (Lin and Binns, 1988; Nascimento et al.,
2009) and multivariate analysis, such as additive main effects and
multiplicative interaction analysis (AMMI) (Gauch, 2006).
Published in Crop Sci. 55:571–577 (2015).
doi: 10.2135/cropsci2014.07.0498
© Crop Science Society of America | 5585 Guilford Rd., Madison, WI 53711 USA
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has been obtained by the publisher.
571
 Traditional methods that predict cultivars’ perfor-
mances in multiple environments are based on a “classic”
(or frequentist) approach to statistics, which estimates one
or more parameters from a set of observations. The variables
are used to make statements about a statistical model, which
is characterized in terms of parameters with a “true” value.
Uncertainty is described through distributions that attri-
bute probabilities to the values of all random variables in
the statistical model. In general, the values of these distribu-
tions’ parameters are unknown and must be inferred from
the available information (Sorensen and Gianola, 2002).
An alternative to classical statistical inference is the
Bayesian approach, which is based on the principles of
likelihood and the incorporation of a priori information.
It is a robust statistical procedure with many possible appli-
cations (Geweke, 1992; Kass ande Raftery, 1995; Meuwis-
sen et al., 2001; Silva et al., 2013b). Variance heterogene-
ity, uneven data distribution and the relaxation of normal-
ity assumptions, all of which are constraining conditions
for many methodologies, are not limiting factors for the
application of the Bayesian approach (Cotes et al., 2006).
The use of the Bayesian approach in plant genetic
improvement is still limited. Silva et al. (2009) showed that
calculating genotypic probabilities increased the precision
of additive effect estimates and decreased the error estimate
associated with the Bayesian model. Mora et al. (2009)
used Bayesian analysis to predict the inheritability values
for forest species and concluded that the Bayesian method
makes it possible to obtain low standard deviation values
associated with inheritability, which makes it an important
tool for the genetic assessment and inference of perennial
species. Balestre et al. (2012) conducted a Bayesian survey
of multiple corn (Zea mays L.) characteristics, in which
they highlighted the importance of pleiotropic effects in
the study of the inheritance of quantitative characteristics.
Silva et al. (2013a) used the Bayesian methodology in the
selection of sugarcane (Saccharum officinarum L.) families
and concluded that the informative prioris influence not
only genotypic effects but also variance and inheritability.
Bayes’ paradigm has also met with very limited use in
GE modeling. The Bayesian approach is usually more labo-
rious and very difficult to obtain analytically, which makes
it harder to use (Gianola, 1996). Molina et al. (2011) used
the Bayesian methodology to evaluate rice (Oryza sativa L.)
genotypes in regional tests, to estimate genotype means,
phenotypic Shukla stability variance and also in the form
of the Bayesian Yield-Stability index (BYS). Cotes et al.
(2006) proposed a Bayesian approach to the phenotypic
Shukla stability method in potato (Solanum tuberosum L.),
wheat (Triticum aestivum L.) and corn genotypes in mul-
tiple environments. Nascimento et al. (2011) formulated
a Bayesian approach for Eberhart and Russel’s method of
selecting alfalfa (Medicago sativa L.) genotypes. These authors
observed that, in applying the Bayesian methodology, the
572 www.crops.org
selection of genotypes in different environments is more
accurate when a priori information is used. The application
of a priori information allows improvement programs to
select the best genotypes both for specific environments and
for general and unconstrained environments.
In light of the above points, the goal of this work was
to use the Bayesian Eberhart and Russel method to ana-
lyze the phenotypic adaptability and stability of popcorn
cultivars–an economically relevant crop–and to evaluate
the efficiency of using informative and minimally infor-
mative a priori distributions in the selection of cultivars.
Materials and Methods
The experiments took place in the agricultural years of 2009/2010
in the municipalities of Campos dos Goytacazes and Cambuci
and later in 2010/2011 in the municipalities of Campos dos
Goytacazes, Cambuci, and Itaocara, totaling five environments
representative of the North and Northeast regions of the State
of Rio de Janeiro, Brazil. For those places we have: Campos dos
Goytacazes (21°4532 S, 41°2032 W), with altitude varying
in the city between 20 and 30 m, classified as tropical rainy,
with an average annual rainfall of 1023 mm and average annual
temperature of 23°C. Itaocara (21°3912 S, 42° 04 36 W), at
a 60 m altitude, with an average annual temperature of 22.5°C
and average annual rainfall of 1041 mm. Cambuci (21°3431 S,
41° 5440  W), at an altitude of 35 m, hot and humid climate,
with an average annual temperature of 25°C and average annual
rainfall in around 1170 mm. Campos dos Goytacazes is located
80 km from Cambuci and 110 km from Itaocara. The distance
between Cambuci and Itaocara is 23 km.
In total, 16 genotypes of popcorn were evaluated: eight
varieties–BRS Angela, UFVM2-Barão de Viçosa, Viçosa, Beija
Flor, SAM, UNB2U-C3, UNB2U-C4, and UNB2U-C5–and
eight hybrids–Zélia, Jade, IAC 112, P1 ´ P3, P1 ´ P7, P2 ´ P4,
P2 ´ P9, P3 ´ P7 (Table 1). The experimental design was of
randomized blocks with three repetitions. The plot contained
two 12 m lines with 0.90 m space between them, and the plants
were spaced 0.20 m apart along each line, for a total of 120
plants per plot. Three seeds were used in each hole at a depth
of 0.05 m, and the stalks were pruned 21 d after sprouting.
Coverage fertilization and other culture specific treatment was
performed as recommended for this crop (Paula et al., 2010).
The two main economically relevant characteristics of this
crop were assessed, namely, the popping expansion (PE) in mL
kg–1 and the grain yield (GY) in kg ha–1. The GY was calculated
from the plot’s mean by weighing the grains. The PE was deter-
mined in a laboratory as follows: 0.03 kg of seeds were placed
in a plastic container and put into a microwave oven at 1000 W
for 2 min and 20 s, with three repetitions per treatment. The
expanded volume was measured in a 2000-mL graduated cyl-
inder, and the PE was calculated as the ratio between the final
expanded volume (mL) and the initial weight of the grains (0.03
kg) (Silva et al., 2011).
The data thus obtained underwent variance analysis for
each environment, and the residual variance homogene-
ity (MSRs) was later verified using Hartley’s test. The model
adopted for conjoint analysis was Yijk = µ + R/Ek( j) + G i +
Ej + GEij + ijk , in which Yijk is the plot’s mean phenotypical
crop science, vol. 55, march– april 2015
Table 1. Characterization of the genotypes evaluated in five The estimates for Ij indicate the environmental quality, in
environments in Northern and Northwestern State of Rio which negative values identify unfavorable environments, and
de Janeiro. positive values identify favorable environments. The adaptability
Means
parameters are given by b0 j = Yi and b1i =
YI
j ij j
, and the
å
Grain Popping
Genotypes Type Origin yield expansion
Ij 2j å
BRS Ângela Open-pollinated Embrapa† 2192.11 34.52 MSDi - MSR
stability parameter is given by ˆ di =
2
variety , in which
r
UF VM2- Barão Open-pollinated UFV 2314.5 33.31 MSDi is the mean square of the regression deviation for each
de Viçosa variety
Viçosa Open-pollinated UFV 2863.55 24.41
genotype, and MSR is the mean square of the residual obtained
variety in the variance analysis (Eberhart and Russel, 1966).
Beija-Flor Open-pollinated UFV 2212.18 27.47 In the generally employed frequentist approach, the hypoth-
variety eses of interest H0:1i = 1 vs. H1:1i  1 and H0 : 1di = 0 vs.
SAM Open-pollinated unknown 1790.56 27.59 H1 : di2 > 0 are assessed by the t and F statistics, respectively.
variety
In the Bayesian approach, based on the Bayes theorem–
UNB2U-C3 Open-pollinated UENF 2225.14 29.77
variety
posteriori m similarity ´ priori-all information regarding the
UNB2U-C4 Open-pollinated UENF 2986.93 31.38 parameters to be estimated is contained in the a posteriori dis-
variety tribution, which consists of the prior information about the
UNB2U-C5 Open-pollinated UENF 3047.58 35.69 parameters, represented by the a priori distributions, and the
variety information contained in the data to be analyzed, represented
Zélia Three-way hybrid Pionner 2509.81 33.36 by the likelihood function.
Jade Three-way hybrid Pionner 2423.52 33.53 Considering the statistical model Yij = b0i  b1i I j  ij  ij
IAC 112 Modified one-way IAC 2724.4 37.87 and assuming that each observation Yij has a distribution
hybrid
Yij ~ N b0i  b1i I j : i2  , the likelihood function for each geno-
P1 ´ P3 One-way hybrid UEM/UENF 3037.78 29.11
type i is given by
P1 ´ P7 One-way hybrid UEM/UENF 2875.46 36.82
P2 ´ P4 One-way hybrid UEM/UENF 3262.13 20.93
a
1 ìï 1 2ü
ï
Li b0i , b1i , i2 ,Yij  = Õ exp ïí- 2 éêYij - b0i  b1i I j ùú ïý
P2 ´ P9 One-way hybrid UEM/UENF 3485.71 29.54 2p 2 ï 2 ë û ïþï
j =1 i îï i
P3 ´ P7 One-way hybrid UEM/UENF 3144.9 28.2
†
Embrapa, Empresa Brasileira de Pesquisa Agropecuária; UFV, Universidade
Federal de Viçosa (Federal University of Viçosa); UENF, Universidade Estadual 1 ìï 1 a
2 ü ï
do Norte Fluminense Darcy Ribeiro (State University of North Fluminense Darcy = exp íï- 2 å ëêéY - b
ij 0i  b1i I j  úùýï , " i
ûï
  ïï 2i
a
Ribeiro); IAC, Instituto Agronômico de Campinas (Campinas Agronomic Institute) 2pi2 î j =1 þï
UEM, Universidade Estadual de Maringá (State University of Maringa).

To estimate the adaptability and stability parameters,

value; µ is the general constant; R/Ek( j) is the effect of the kth one must first establish the parameters’ a priori distributions.
repetition in the jth environment; G i is the fixed effect of the The following distributions were considered for b 0i, b1i and
ith genotype; Ej is the effect of the jth environment normally 2i : b0i ~ N m 0i , 02i  , b1i ~ N m1i , 12i  , i2 ~ GammaInv a i , bi  .
and independently distributed (NID) 0, 2E  ; GEij is the effect This last distribution is an inverse  with mean and variance
of the interaction of the ith genotype in the jth environment b bi2
equal to i and , respectively.
NID 0, GE 2
 ; and ijk is the experimental error NID (0, 2). 2
ai a i - 1 a i - 2
For the Bayesian analysis incorporating a priori information,
only those genotypes evaluated in at least two of the following Assuming the parameters of these distributions to be inde-
studies were taken into consideration: Nunes et al. (2002); Von pendent of one another, the conjoint a priori for each genotype
Pinho et al. (2003); Faria et al. (2010) and Scapim et al. (2010). can be written as follows:
The method proposed by Eberhart and Russel (1966) is é ù
1 1 1
Pi b0 , b1i , i2  = exp êê- úx
2
based on simple linear regression analysis, which measures the 2
 b 0 i , m 0 i  ú
response of each genotype to environmental variation. For an
2
2p0i êë 2p0i úû 2p12i
experiment with g genotypes, a environments, and r repetitions,
the following statistical model is defined: Yij = b0 i b1i I j  ij  ij
ïì 1 2ï ü 1 æ 1 öa 1 ïì 1 ïü
i

, in which: Yij is the response of genotype i in environment exp íï- 2 b1i , m1i  ýï´ a ççç 2 ÷÷÷ exp íï- 2 ýï
j; 0i is the response of genotype i;1i is the regression coefficient îïï 21i ïþï bi G a i  è i ø÷i ïîï bi i ïþï
that measures the response of the ith genotype to the environ-
mental variation; and Ij is the coded environmental index. By ìï 1 2üï 1 ìï 1 2üï
æ ö
çå Yj å å Yj ÷
 exp ïí- 2 b0i , m 0i  ïý´ exp ïí- 2 b1i , m1i  ïý
this analysis, I j = çççç j - i j ÷÷÷÷ , in which  ij refers to the ïîï 2i ïþï 2
2p1i ï
ïî 21i
ïþï
è g ga ø
regression’s deviation, and ij NID 0, 2  represents the average
experimental error. æ 1 öa 1i
ìï 1 üï
´çç 2 ÷÷÷ exp ïí- 2 ïý
èç i ø÷ ïîï bi i ïþï

crop science, vol. 55, march– april 2015  www.crops.org 573

 1
To make inferences about the parameters of interest,
å L Y|q , M i 
Q

it is necessary to obtain their a posteriori marginal distribu- Pˆ Y|M i  Q q =1

FBij = =
tions. Denoting the parameter vector for each genotype i by Pˆ Y|M j  1
 
å
Q
L Y|q , M j
 pi =b1i , b2i , i2  , in which p = 1, 2, 3, the a posteriori marginal Q q =1

distribution for parameter q pi was obtained by the following

integral: P(  pi | x) = ò P(  pi | x)d pi , which is the integral rela- The term  (q) represents the values generated for the
tive to all parameters in the vector except the pth component. parameters at the qth iteration (q = 1, 2,..., Q) for each of the
In most cases, these integrals are complex and do not have models being compared. Therefore, L Y|q , M p  corresponds
exact solutions. To work around this problem, another method- to the values for the likelihood function obtained by substitu-
ology was used. A sample of the conjoint a posteriori distribu- tion of the current parameter values. Using the similarity func-
tion was obtained using Markov chains and the Monte Carlo tion adopted in this study yields the following estimate for the
method, which gave the marginal distributions’ moments of marginal likelihood of a model p:
interest (Cassela and George, 1992).
Q æ n- p ö÷
1
å  
- mççç ÷÷
This methodology was implemented in the program R Pˆ Y|M q  Y Fq , e2q|Y p e2q
è 2 ø÷

(R Development Core Team, 2013) and the conjoint distribu- Q q =1

tion sample was obtained using the MCMCregress function of

the MCMC package. To evaluate the influence of the a priori
information in estimating the stability and adaptability param-
eters, two different models were used.
In Model 1, informative a priori distributions were used.
These distributions contained information from previous stud-
ies, namely: Nunes et al. (2002), Von Pinho et al. (2003), Faria et
al. (2010), and Scapim et al. (2010). The information was incor-
porated into the analysis by means of the values assumed for the
parameters in the a priori distributions, called hyperparameters.
These values were obtained from the mean and variance of
the sample composed by the parameter estimates obtained from
the cited references, which resulted in the following distribu-
tions: b 0i ~ N éëêm 0i = b0i , 02i = Var  b0i ùûú , b1i ~ N éêm1i = b1i , 12i = Var  b1i ùú
ë û
and i2 ~ GammaInv(a i b i), in which b0i = mean of the b 0i esti-
mates; b1i = mean of the b1i estimates; Var  b0i  = variance of
the b 0i mean values; Var  b1i  = variance of the b1i mean values;
and a i and b i are values obtained from the system equation:
bi
i2 =
ai - 1
bi2
Var i2  = 2
, and
a i - 1  a i - 2
3
i2 
2
i2 
ai = 2´ 2 , bi = 2 ´ 1
V i2  V i2 
In Model 2, minimally informative a priori distributions
were used instead, representing probability distributions with
large variances. The following distributions were adopted:
b0i ~ N m 0i = 0, 02i = 1,000,000 , b1i ~ N m1i = 0, 12i = 1,000,000
and i2 ~ GammaInv a i = 0.0001; bi = 5,000 .
Models 1 and 2, that is, models with informative and mini-
mally informative a priori distributions, were compared based
on the Bayes Factor (BF) (Kass and Raftery, 1995; Nascimento
et al., 2011), which uses values generated by the MCMC meth-
ods to obtain estimates for the normalization factor P(Y|Mp),
also known as Marginal Likelihood, which composes the fol-
lowing expression for the Bayes Factor:
ì
ï 1 é q  ù é ü
q  ù ï
exp ï
í- 2q  ëY1 - X F û ' ëY1 - X F û ï ý
ï ï
ï 2e
î ï
þ
The Bayes Factor was calculated using the BayesFactor
function of the MCMCpack package. According to Jeffreys
(1961), the Bayes Factor can be interpreted as follows: FBij < 1
is evidence in favor of model j; 1  FBij < 3 is moderate evi-
dence in favor of model i; 3  FBij < 10 is substantial evidence
in favor of model i; 10  FBij < 30 is strong evidence in favor
of model i; 30  FBij < 100 is very strong evidence in favor of
model i; and FBij  100 is decisive evidence in favor of model i.
Regarding the stability parameter di2  , its marginal dis-
tribution samples were obtained indirectly, as this parameter is a
function of 2i . As values for 2i are indirectly obtained at each
iteration, the values for 2di are given by the following expres-
 
sion: ˆ di2 = ˆ i2 - MSR , in which MSR is the mean square
r
of the residual obtained in the variance analysis, and r is the
number of repetitions in the experiment.
The hypotheses of interest were tested by calculating confi-
dence intervals for the parameters. These intervals were obtained
directly from the parameters’ a posteriori marginal distribution.
Because the Gibbs sampler is an iterative algorithm, it is
necessary to verify its convergence. In this work, its conver-
gence was verified through Raftery and Lewis’ (1992) and
Geweke’s (1992) criteria, both implemented in the Bayesian
Output Analysis (BOA) package of program R (R Develop-
ment Core Team, 2013).
In the Bayesian adaptability and stability analysis, for each
parameter in the adopted regression model, 250,000 iterations
of the Gibbs sampler algorithm were considered, with a “burn-
in” period of 10,000 iterations. To obtain an uncorrelated
sample, a spacing (“thinning”) of five iterations between the
sampled points was adopted, which resulted in a posteriori mar-
ginal distributions for each parameter, from which the param-
eter values were inferred.

574 www.crops.org crop science, vol. 55, march– april 2015

Table 2. Mean square estimates for the two characteristics
assessed over five environments and 16 popcorn genotypes.
Sources of Mean square
variation df Grain yield Popping expansion
Replication/ 10 1188258.06
Environment
Genotype (G) 15 3308784.39**
Environment (E) 4 1714511.75**
GE 60 775175.81**
Error 150 333652.88
MSR > /MSR < – 4.11
** Significant at 0.01 probability levels by F test.
†
ns, not significant.
Results and Discussion
The variance analysis of GY and PE showed that the
variation due to GE was significant, and therefore that
there was variation among the tested genotypes and envi-
ronments (Table 2). The results showed that there is a
significant effect of the interaction between GE only in
relation to GY, which indicates the existence of differenti-
ated performance for these cultivars in the environments
evaluated. Regarding the PE variable, there were no sig-
nificant differences for the GE interaction. These results
stand in contrast to the results found by some other authors
(Faria et al., 2010; Scapim et al., 2010). Although PE may
be a quantitative characteristic, its expression is controlled
by fewer genes than GY. Li et al. (2008), while studying
the genetic relationship between PE and two performance
components for popcorn using conditional and uncondi-
tional quantitative trait loci (QTL) analysis, identified five
QTLs related to the PE of linkage groups 1, 6, and 8,
explaining 45% of the trait’s phenotypic variation. The
fact that there are few genes related to PE variation may
indicate that it is also subject to less environmental influ-
ence, which would explain the lack of significant GE
interaction. Because of these variations, it was necessary
to study the behavior of these genotypes in greater detail
by means of stability and adaptability analysis.
Of the 16 genotypes considered in the experiment,
only four were evaluated in at least two of the studies used
as reference for the priori specification. For this reason,
only the four genotypes presented in Table 3 were consid-
ered in the Bayesian analysis Viçosa, Beija Flor, Zélia, and
IAC 112, respectively show 2863.55, 2212.18, 2509.81
and 2724.4 112 kg ha–1 of GY (Table 1).
The stability and adaptability parameters were
obtained by calculating the a posteriori mean, whose esti-
mates are shown in Table 3, along with their respective
confidence intervals. In Model 1, in which informative
prioris were used, only Beija Flor, of the four genotypes
evaluated using Bayesian methodology, was considered to
have general adaptability (1i = 1) because its 1i value fell
within the limits of the 95% confidence interval (CI). The
crop science, vol. 55, march– april 2015  www.crops.org
Viçosa genotype was classified as having specific adapt-
ability to unfavorable environments (1i < 1), with its 1i
estimate also falling within the limits of the 95% con-
fidence interval (CI). The Zélia and IAC112 genotypes
12.50 were characterized as having specific adaptability to favor-
able environments (1i > 1), with their respective 1i values
316.44**
54.52**
contained in the 95% CI.
7.66ns†
According to the stability parameter 2di , only the
6.18 IAC112 genotype had 2di equal to zero, which also
2.12 belonged to the 95% CI and was therefore classified as
having high stability. The remaining genotypes displayed
low predictability in the analyzed environments, as the 2di
estimates within the 95% CI limits were greater than zero.
In Model 2, the prioris are minimally informative. The
genotype analysis showed that all displayed specific adapt-
ability to favorable environments (1i > 1) and low stability,
as the 2di values were greater than zero and within the limits
of the 95% CI. The genotypes were classified according to
the same criteria considered for Model 1, that is, the CI.
Incorporating a priori information into Model 1 led
to smaller limits for the CIs in comparison to Model 2,
which led to greater accuracy in estimating the parameters
and, consequently, in the reliable selection of genotypes.
A comparative analysis of the parameters obtained
by the two models reveals that the 1i estimates were
equivalent for Zélia and IAC112, as in both models these
genotypes were classified as having specific adaptability
to favorable environments. There was disagreement only
regarding the Beija Flor genotype, which in Model 1 was
considered to have general adaptability and in Model
2 was classified as having specific adaptability to favor-
able environments. The Viçosa genotype was classified
in Model 1 as having specific adaptability to unfavorable
environments and in Model 2 as having specific adaptabil-
ity to favorable environments.
It can be observed, therefore, that using the frequen-
tist model, in which a priori information is not taken into
account, tends to allocate genotypes as having specific
adaptability to favorable environments, disfavoring the
reliable indication of genotypes.
Regarding stability, there was agreement regarding
most genotypes in both models. The only divergence
occurred for the IAC112 genotype, which in the model
with a priori information was classified as having high sta-
bility and in the model with minimal a priori information
was classified as having low stability because its 2di value
was greater than zero (Table 4).
As the Bayes Factor (Table 5) is a method of comparing
the two models, it was necessary to employ it to determine
which of the two models provided a better quality-of-fit.
Regarding the classification limits of the Bayes Factor, it
can be observed that Model 1, with a priori information,
has strong evidence supporting it, as it conforms to the
interval 10  FBij < 30.
575
Table 3. Adaptability and stability estimates obtained through Eberhard and Russel’s method (1966) based on the studies by
Nunes et al. (2002), Von Pinho et al. (2003), Scapim et al. (2010), and Faria et al. (2010).
Grain yield, at kg ha –1
Nunes et al. (2002) Von Pinho et al. (2003) Scapim et al. (2010) Faria et al. (2010)
Genotypes 2† 0 1 2 0 1 2 0 1 2 0 1
Viçosa 32,325 2781 1.05 – – – – – – 0 2051 0.86
– – – – – – – – – 0 2157 0.84
– – – – – – – – – 0 2188 0.81
Beija Flor 15,290 2771 0.58 – – – – – – 81,159 2034 0.83
– – – – – – – – – 0 1982 1.02
– – – – – – – – – 0 2051 0.91
Zélia 119,256 2413 0.71 335,922 2710 1.53 273,068.2 3805 1.25 39,200 2282 1.31
IAC 112 53,136 3045 0.49 69,235 2728 1.47 – – – 82,315 2189 1.05
†
Negative  2 values were considered to be equal to zero; dashes indicate estimates that were not found in the literature consulted.

Table 4. Estimates for the a posteriori mean and confidence intervals (95%) for the stability and adaptability parameters,
considering informative and non-informative prioris.
Genotypes b0 LI b0 LSb0 b1 LI b1 LSb1 i2 di2 LIdi2 LSdi2
Informative prioris
Viçosa 2297 2261 2333 0.8 0.2 1.4 4.29E+06 317782.4 27182.37 1113782
Beija Flor 2209 2172 2247 1 0.2 1.8 2.20E+08 53173.56 –94396.44 455274
Zélia 2883 2883 28883 1.4 –1 3.9 1.78E+08 67182.37 –54080.4 399782
IAC112 2652 2612 2692 1.3 0.2 2.3 91421.53 0 –49957.63 242824
Non-informative prioris
Viçosa 2832 2110.19 3467 1.38 –2.62 5.41 6.28E+05 516582.4 –37187.62 3.00E+06
Beija Flor 2174 1266.68 2977 1.83 –3.25 6.96 1.01E+06 893782.4 9937.26 4.86E+06
Zélia 3033 2573.69 3453 1.83 –0.76 4.43 2.64E+05 152782.4 –80821.24 1.18E+06
IAC112 2667 1638.29 3542 1.57 –4.08 7.24 1.25E+06 1135782 –183919.1 6.07E+06

Table 5. Values obtained for the Bayes Factor, used to com-
pare the models with informative (i) and minimally informative
(ii) prioris for the genotypes being studied.
Genotypes FBij
Viçosa 13.9
Beija Flor 18.3
Zélia 21.2
IAC112 18.4
As a result, there was greater accuracy in estimating
the parameters for all genotypes when Model 1 was used,
even if the stability estimates ( b1i ) agreed for the Zélia and
IAC112 cultivars. Therefore, the Bayes Factor provides
evidence of the superiority of using informative prioris in
constructing the model, to obtain more accurate results.
Returning to the base-studies that allowed these a
priori inferences, the divergences in results can now be
better elucidated by the Bayesian approach. Specifically,
Nunes et al. (2002) considered the Viçosa genotype to be
of specific adaptability to favorable environments (1 > 1),
whereas Faria et al. (2010) classified this same genotype as
having specific adaptability to unfavorable environments
(1 < 1), which is in agreement with the results of the
Bayesian inference. The Beija Flor genotype was classi-
fied by Nunes et al. (2002) as having specific adaptability
to unfavorable environments (1 < 1), while Faria et al.
(2010) classified this same genotype as having specific
adaptability to favorable environments (1 > 1) and spe-
cific adaptability to unfavorable environments (1 > 1).
When the Bayesian approach was used, this genotype was
classified as having general adaptability. Moreover, the
Zélia genotype was considered by Nunes et al. (2002) to
have specific adaptability to unfavorable environments,
in Coimbra, Minas Gerais State, Brazil, whereas the
remaining base-authors made a priori information pos-
sible (Von Pinho et al., 2003; Scapim et al., 2010; Faria
et al., 2010) by classifying Zélia as having specific adapt-
ability to favorable environments, which agreed with the
results obtained with the Bayesian procedure. The IAC
112 genotype was considered to have specific adaptability
to favorable environments by Von Pinho et al. (2003) and
Faria et al. (2010), which agrees with the Bayesian meth-
odology incorporating a priori information: however,
Nunes et al. (2002) classified it as having specific adapt-
ability to unfavorable environments.
The accuracy logic of the Bayes Factor therefore
becomes evidence that the frequentist model can produce
unreliable results for the identification of genotypes with
broad or specific adaptability, with ensuing economic
losses for producers.

576 www.crops.org crop science, vol. 55, march– april 2015

References
Bach, S., R.Y. Yada, B. Bizimungu, M. Fan, and J.A. Sullivan. 2013. Gen-
otype by environment effects on Starch content and digestibility in
potato (Solanum tuberosum L.). J. Agric. Food Chem. 61:3941–3948.
doi:10.1021/jf3030216
Bach, S., R.Y. Yada, B. Bizimungu, and J.A. Sullivan. 2012. Genotype by
environment effects on fibre components in potato (Solanum tuberosum
L.). Euphytica 187:77–86. doi:10.1007/s10681-012-0734-9
Balestre, M., R.G.V. Pinho, C.L. Souza Junior, and J.S.S. Bueno Filho.
2012. Bayesian mapping of multiple traits in maize: The importance
of pleiotropic effects in studying the inheritance of quantitative traits.
Theor. Appl. Genet. 125:479–493. doi:10.1007/s00122-012-1847-1
Bernardo, R. 1992. Best linear unbiased prediction of maize single-cross
performance. Crop Sci. 36:50–56. doi:10.2135/cropsci1996.0011183X
003600010009x
Cassela, G., and E.I. George. 1992. Explaining the Gibbs sampler. Am. Stat.
46:167–174 10.1080/00031305.1992.10475878.
Cotes, J.M., J. Crossa, A. Sanches, and P.L. Cornelius. 2006. A Bayesian
approach for assessing the stability of genotypes. Crop Sci. 46:2654–
2665. doi:10.2135/cropsci2006.04.0227
Crossa, J. 1990. Statistical analysis of multilocation trials. Adv. Agron.
44:55–85. doi:10.1016/S0065-2113(08)60818-4
Crossa, J. 2012. From genotype x environment interaction to
gene x environment interaction. Curr. Genet. 13:225–244.
doi:10.2174/138920212800543066
Cruz, C.D., R.A.A. Torres, and R. Vencovsky. 1989. An alternative
approach to the stability analysis proposed by Silva and Barreto. Braz.
J. Genet. 12:567–580.
Eberhart, S.A., and W.A. Russel. 1966. Stability parameters for comparing
varieties. Crop Sci. 6:36–40. doi:10.2135/cropsci1966.0011183X00060
0010011x
Falconer, D.S., and T.F.C. Mackay. 1996. Introduction to quantitative
genetics. Logman Group Limited, Edinburgh.
Faria, V.R., J.M.S. Viana, G.B. Mundim, A.C. Silva, and T.M.M. Câmara.
2010. Adaptabilidade e estabilidade de populações de milho pipoca
relacionadas por ciclo de seleção. Pesqi. Agropecu. Bras. 45:1396–1403
10.1590/S0100–204X2010001200009.
Fehr, W.R. 1987 Principle of cultivar development. Macmillan, New York.
Finlay, K.W., and G.N. Wilkinson. 1963. The analysis of adaptation
in a plant breeding programme. Aust. J. Agric. Res. 14:742–754.
doi:10.1071/AR9630742
Gauch, H.G. 2006. Statistical analysis of yield trials by AMMI and GGE.
Crop Sci. 46:1488–1500. doi:10.2135/cropsci2005.07-0193
Geweke, J. 1992. Evaluating the accuracy of sampling based approaches to
the calculation of posterior moments. In: J.M. Bernardo, J.O. Berger,
A.P. David, and A.F.M. Smith, editors, Bayesian statistics. Oxford
Univ., New York. p. 625–631.
Gianola, D. 1996. Bayesian analyses with applications to genetics e biology.
Class notes of a course tough at the department of genetics. Medical
School, São Paulo, Brazil.
Jeffreys, H. 1961. Theory of probability. Oxford. Claredon 1961:459.
Kass, R.E., and A.E. Raftery. 1995. Bayes factors. J. Am. Stat. Assoc.
90:773–795. doi:10.1080/01621459.1995.10476572
Li, Y.L., Y.B. Dong, D.Q. Cui, Y.Y. Wang, M.G. Wel, and X.H. Li. 2008.
The genetic relationship between popping expansion volume and two
yield components in popcorn using unconditional and conditional
QTL analysis. Euphytica 162:345–351. doi:10.1007/s10681-007-9513-4
Lin, C.S., and M.R. Binns. 1988. A superiority measure of cultivar per-
formance for cultivar x location data. Can. J. Plant Sci. 68:193–198.
doi:10.4141/cjps88-018
Meuwissen, T.H.E., B.J. Hayes, and M.E. Goddard. 2001. Prediction of
total genetic value using genome-wide dense marker maps. Genetics
157:1819–1829.
Molina, L.M.R., A. Sanches, and J.M.C. Torres. 2011. Inferência bayesiana
na análise de testes regionais de arroz em dois sistemas de cultivo. Rev.
Fac. Nal. Agr. Medellín. 64:5883–5891.
crop science, vol. 55, march– april 2015  www.crops.org
Mora, F., C.A. Scapim, and R.J.B. Pinto. 2009. El análisis bayesiano y la
precisión de los valores de la heredabilidad en especies perenes Ci Fl
19: 343–349.
Nascimento, M., A. Ferreira, A.C.M. Campana, C.C. Salgado, and C.D.
Cruz. 2009. Multiple centroid methodology to analyze genotype
adaptability. Crop Breed Appl. Biotechnol. 9:8–16. doi:10.12702/1984-
7033.v09n01a02
Nascimento, M., F.F. Silva, T. Sáfadi, A.C.C. Nascimento, R.P. Ferreira,
and C.D. Cruz. 2011. Abordagem bayesiana para avaliação da adapt-
abilidade e estabilidade de genotipos de alfafa. Pesqi. Agropecu. Bras.
46:26–32. doi:10.1590/S0100-204X2011000100004
Nunes, H.V., G.V. Miranda, J.C.C. Galvão, L.V. Souza, and L.J.M. Gui-
marães. 2002. Adaptabilidade e estabilidade de cultivares de milho
pipoca por meio de dois métodos de classificação. Revista Brasileira de
Milho e Sorgo. 1:78–88.
Paula, T.O.M., A.T. Amaral, Jr., L.S.A. Gonçalves, C.A. Scapim, L.A.
Peternelli, and V.Q.R. Silva. 2010. Pi statistics underlying the evalua-
tion of stability, adaptability and relation between the genetic structure
and homeostasis in popcorn. Acta Sci. Agron. 32:269–277 10.4025/
actasciagron.v32i2.7312.
R Development Core Team. 2013. R: A language and environment for sta-
tistical computing, reference index version 2.13.0. R Foundation for
Statistical Computing, Vienna, Austria. www.R-project.org (accessed
10 July 2013).
Raftery, A.L., and S.M. Lewis. 1992. Comment: One long run with diag-
nostics: Implementation strategies for Markov chain Monte Carlo.
Stat. Sci. 7:493–497. doi:10.1214/ss/1177011143
Ransul, G., G.D. Humphereys, J. Wu, A. Brûlé-Babel, B. Fofana, and K.D.
Glover. 2012. Evaluation of preharvest spouting traits in a collection of
spring wheat germplasm using genotype and genotype x environment
interaction model. Plant Breed. 131:244–251. doi:10.1111/j.1439-
0523.2011.01931.x
Scapim, C.A., C.A.P. Pacheco, A.T. Amaral, Jr., A.R. Vieira, R.J.B. Pinto,
and T.V. Conrado. 2010. Correlations between the stability and
adaptability statistics of popcorn cultivars. Euphytica 174:209–218.
doi:10.1007/s10681-010-0118-y
Silva, V.Q.R., A.T. Amaral, Jr., L.S.A. Gonçalves, S.P. Freitas, Jr., and
R.M. Ribeiro. 2011. Heterotic parametrizations of crosses between
tropical and temperate lines of popcorn. Acta Sci Agron 33:243–249.
doi:10.4025/actasciagron.v33i2.9607
Silva, M.I.S., E. Bearzoti, and J.S.F. Bueno. 2009. Análise bayesiana do
modelo de herança monogênica no melhoramento vegetal: Um exem-
plo com abobrinha. Ciên agrotec 33:1463–1468. doi: 10.1590/S1413-
70542009000600002.
Silva, M.A.G., L.A. Peternelli, M. Nascimento, and F.L. Silva. 2013a.
Modelos mistos na seleção de famílias de cana de açúcar aparentados
sob o enfoque clássico e bayesiano. Rev. Bras. Biol. 31:1–12.
Silva, F.F., J.M.S. Viana, V.R. Faria, and M.D.V. Resende. 2013b. Bayesian
inference of mixed models in quantitative genetics of crop species.
Theor. Appl. Genet. 126:1749–1761. doi:10.1007/s00122-013-2089-6
Sorensen, D., and D. Gianola. 2002. Likelihood, Bayesian and MCMC
methods in quantitative genetics. Springer, Amsterdam.
Tai, G.C.C. 1971. Genotypic stability analysis and its application to potato
regional trials. Crop Sci. 11:184–190. doi:10.2135/cropsci1971.001118
3X001100020006x
Verma, M.M., G.S. Chahal, and B.R. Murty. 1978. Limitations of con-
ventional regression analysis a proposed modification. Theor. Appl.
Genet. 53:89–91. doi:10.1007/BF00817837
Vieira, R.A., C.A. Scapim, L.M. Moterle, D.J. Tessmann, A.A. Teixeira,
and L.S.A. Gonçalves. 2012. The breeding possibilities and genetic
parameters of maize resistence to foliar diseases. Euphytica 185:325–
336. doi:10.1007/s10681-011-0454-6
Von Pinho, R.G., A. Brugnera, C.A.P. Pacheco, and M.S. Gomes. 2003.
Estabilidade e adaptabilidade de milho pipoca em diferentes ambien-
tes, no estado de Minas Gerais. Revista Brasileira de Milho e Sorgo
2:53–61.
577