Cereal Research Communications 37(1), pp.

139-148 (2009)
DOI: 10.1556/CRC.37.2009.1.16

Appraisal of Environmental Interaction on Quality Traits of

Rice by Additive Main Effects and
Multiplicative Interaction Analysis
A. ANANDAN*, T. SABESAN, R. ESWARAN, G. RAJIV, N. MUTHALAGAN and
R. SURESH

Department of Agricultural Botany, Faculty of Agriculture, Annamalai University,

Chidambaram - 608 002, Tamil Nadu, India

(Received 26 March 2008; accepted 10 September 2008)

Superior grain quality is the main goal of rice breeders because of its high commercial
value. Progress in selection for grain quality with yield in harsh environments is markedly af-
fected by environmental variation. The genotype by environmental (G x E) interaction influ-
ence on grain quality was analyzed in this study, comprised of 17 rice hybrids grown in six lo-
cation-year environments. The objective of this study was to examine the influence of G x E
interaction for grain quality in hybrid rice by using AMMI model. Results of the trial revealed
that grain quality was highly influenced by environmental factors and brings out the suitability
of specific genotype to specific location/season through the biplot. On the other hand, external
environmental variables can be regressed on the environmental scores to lead to a useful bio-
logical interpretation of the interaction effects, which is not possible in additive effect models.
The implications of these results for rice hybrids on grain quality in varied environmental loca-
tion are discussed.

Keywords: AMMI, G x E interaction, Oryza sativa, quality traits

Introduction
Breeding for quality rice has received importance in recent years. Defining grain
quality in rice is very difficult, as quality expectations vary from country to country. The
preference varies according to the rice preparation. Rice grain qualities are also highly in-
fluenced by environmental factors. Each variety performs best with respect to quality
traits, in its own native area of cultivation. Breeders are trying to release high yielding va-
rieties less effect on its yield by assessing their wide adaptability, however, varieties will

* Corresponding author; E-mail: anandanau@yahoo.com

0133-3720/$20.00 © 2009 Akadémiai Kiadó, Budapest

140 ANANDAN et al.: Appraisal of Quality Traits in Rice by AMMI

vary respect to quality traits from region to region. Although a little information is avail-
able on stability of quality in rice, it is believed that the quality varies depending upon the
location, soil type and soil fertility (Rohilla et al. 2000). A comprehensive account of ge-
notype x environment (G x E) over grain quality requires more sophisticated statistical
tool. Additive main effects and multiplicative interaction (AMMI) model (Gauch 1988) is
efficient in eliminating noise from the data pattern and to reveal the structure in the data.
The objectives of the current study are to evaluate the presence of G x E for physico-
chemical, cooking and milling traits in data collected from three locations in two seasons
and to determine the value of testing environments and seasons. Information gained from
this investigation will facilitate in understanding the influence of G x E interaction and as-
sist in identifying the environmental factors responsible for variation in quality traits, be-
sides aiding in selection of superior genotypes for target growing environments.

Materials and Methods

The data used in the present study pertain to 2006-2007 in six location-year environ-
ments. The genotypes included in the trial were 17 hybrids viz., APHR2 (A), CORH2 (B),
DRRH1 (C), DRRH2 (D), KRH2 (E), ADTRH1 (F), PHB71 (G), NSD2 (H), PA6201 (I),
PUSA RH10 (J), PSD1 (K), CORH1 (L), Sahyadri (M), CRHR5 (Rajalaxmi) (N), CRHR7
(Ajay) (O), AU-003-101 (P), and AU-003-117 (Q) which were evaluated in six environ-
ments. Hereafter, genotypes will be discussed by their code mentioned above in the paren-
thesis. The two locations representing rice growing areas in Cauvery delta zone of Tamil
Nadu include, Annamalai Nagar (E2 & E5) (11° 24' N latitude, 79° 43' E longitude, 6 ft al-
titude) and Bhuvanagri (E3 & E6) (11° 28' N latitude, 79° 43' E longitude, 36 ft altitude),
and third location Attur (E1 & E4) (1 1o35' N latitude, 78° 37' E longitude, 695 ft altitude)
represents North west zone of Tamil Nadu for the two successive seasons of 2006-2007
(Table 1). First season represents dry season of 2006 (April-September) comprising E1,
E2 and E3 environments and second season represents wet season of 2006-2007
(September-February) comprising E4, E5 and E6 environments. The experiment was
conducted in randomized complete block design with three replicates in each trial. Each
entry was grown in six rows in 2 sq.m plot with spacing of 20 x 15 cm. Plots were man-
aged conventionally following the established normal practices. Each plot was harvested

Table 1. Temperature, status of rainfall, relative humidity, soil properties and code for each environment
is given

Environments 2006 (Dry season) 2006-07 (Wet season)

Environmental factors E1 E2 E3 E4 E5 E6
Temp (max.) 34.47 33.97 33.97 31.19 30.10 30.10
Temp (min.) 21.32 22.56 22.56 21.32 20.85 20.85
Relative humidity 91.16 76.44 76.44 92.89 88.94 88.94
Rainfall (mm) 1.66 6.86 6.86 2.75 55.49 55.49
Soil texture Loamy soil Clayey loam Clayey loam Loamy soil Clayey loam Clayey loam
Soil pH 7.05 7.35 8.90 7.02 7.26 8.51

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 ANANDAN et al.: Appraisal of Quality Traits in Rice by AMMI 141

and threshed manually. Random sample of 1000 gm of grain was collected to evaluate the
quality parameters. The seeds obtained were evaluated for three milling traits (hulling per-
cent, milling percent and head rice percent) (Asish et al. 2006), five physiochemical and
cooking properties (kernel length, kernel breadth, kernel length after cooking (IRRI
1996), alkali spreading value (Little et al. 1958) and amylose content (Juliano 1971)) in
rice. All the eight traits were measured in duplicate rice samples for each replication.
Analysis was carried out at Indian Institute of Crop Processing Technology (IICPT),
Tanjore, Tamil Nadu, India.
The AMMI analysis was used to evaluate similarities among test environments based
on environmental main effects and G x E interaction effects. AMMI model is a combina-
tion of two simpler models, ANOVA and principal component analysis (PCA) (Gauch
1988). AMMI first calculates genotype and environment additive (main) effects using
ANOVA and then analyzes the residual from this model (interaction) using PCA. The
AMMI model equation is:
Yge = μ + αg + βe + Σnλnγgn δen + ρge + ∈ger
where, Yge is the trait of genotype g in environment e; µ is the grand mean, αg is the geno-
type deviation from grand mean and the environment deviation βe. λn is the eigen value of
PCA axis n; γgn and δen are the genotype and environment PCA scores for PCA axis n; ρge is
the residual of AMMI model and ∈ger is the random error. The additive part (ANOVA) of
the AMMI model leaves a non-additive residual, the interaction and the multiplicative
part of the AMMI model uses PCA to decompose this interaction into PCA axes 1 to N and
a residual remains if all axes are not used. If most of the G x E interaction sum of squares
(SS) can be captured in the first N PCA axes, a reduced AMMI model, incorporating only
the first N axes, can be used. Interpretation of AMMI analyses follows plotting the IPCA
(interaction principal components analysis axis) of G x E in biplot. An AMMI biplot with
the main effects plotted against the IPCA 1 scores of both the genotypes and the environ-
ments can usually explain >90% of the total SS of a two-way table. The percentage of the
treatment SS captured by an AMMI biplot is a useful statistic for assessing the overall
goodness of fit. It is calculated by percentage addition of sum of square (Genotype + Envi-
ronment + IPCA 1) divide treatment SS. In addition, root mean square (RMS) residual is a
useful summary statistic regarding model fit. It equals the square root of the residual SS di-
vided by the number of the observations. To avoid specious interpretation of statistical re-
sult, the relevant portion of G x E was calculated for each trait. Factoring the errors from
uncontrolled variation ("noise") out of the total G x E SS is important because most of the
noise appears in the interaction, since the interaction contains a majority of the treatment
degrees of freedom. "Noise" SS, "real structure" SS and target relevant variation percent-
age were calculated as described by Gauch and Zobel (1997).

Correlation between IPCA axes and external factors

Correlation with external factors helps to study the measurable changes in the envi-
ronments or genotypes, which are related to the interaction in the data (McLaren and

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142 ANANDAN et al.: Appraisal of Quality Traits in Rice by AMMI

Chaudhary 1998). Correlation between environment IPCA scores of a trait and some fac-
tor represents the particular environmental factor's influence on the trait.

Results and Discussion

Bartlett's test of homogeneity of variance tests indicated homogeneous error variance
for each trait in the six environments and allowed for pooled analysis of the data across en-
vironments. ANOVA across environment indicated variances due to genotypes, environ-
ments and G x E interaction are highly significant (P < 0.01) for all the traits observed ex-
cept kernel breadth and alkali spreading value for G x E interaction (data not shown). This
indicates the presence of substantial variation in the mean performance of the 17 geno-
types over environments. The significant G x E variation for six of the traits allowed us to
proceed further for estimating G x E using AMMI analysis.
The AMMI analysis of variance indicated highly significant variation for genotypes,
environments and G x E interaction for all the traits (data not shown). The G x E was
highly significant and was further partitioned into three PCA axes (IPCA) for kernel
length, two IPCA axes for kernel length after cooking (KLAC) and amylose content and
one IPCA axis for remaining traits. The IPCA components of all traits were highly signifi-
cant and first IPCA component explained 54.63% to 88.44% of G x E interaction. The sec-
ond IPCA component explained between 17.6% (AC) and 28.3% (KLAC) of G x E inter-
action. The third IPCA components explained 15.6% of G x E interaction for kernel
length. The residual SS of AMMI for all the traits were nonsignificant with minimum re-
sidual mean sum of square, demonstrate a greater accuracy of the model. The first IPCA
has a high contribution to the interaction SS, while the other principal components are
small. This indicates that one primary factor affects G x E interaction; this could be either
genotypic or environmental in nature. For the traits, hulling percent, milling percent and
head rice percent, the G x E interaction was partitioned into IPCA 1 and residual variation.
This situation seems to arise due to the presence of high level of uncontrolled varia-
tions-the noise- but not due to the real G x E interaction (Shanmuganathan and Ibrahim
2005). The error due to uncontrolled variation ("noise") from the total G x E SS was calcu-
lated using the method described by Gauch and Zobel (1997). For hulling percent, the in-
teraction contained 55.5% noise and 44.4% real structure (pattern) with the relevant varia-
tion being 84.9% of the treatment SS. The noise SS, pattern and relevant variation for
other traits are also presented in Table 2. Treatment SS variation explained real and rele-
vant patterns in the data and capturing more than the target percentages would be noise
and irrelevant features in the data. The first IPCA component of hulling percent explained
87% of the treatment SS, which was very close to the target percentage SS explained
(85%). Similarly, first IPCA component of other traits also explained that treatment SS
was very close to the target percentage (Table 2). The root mean square (RMS) residual of
the AMMI 1 model for hulling percent is 1.5% of the grand mean. Similarly the RMS
residual of the AMMI 1 model for other traits ranged between 0.55% (kernel length) and
2.7% (head rice percent) of the grand mean, explaining the fitness of the model.

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 ANANDAN et al.: Appraisal of Quality Traits in Rice by AMMI 143

Table 2. The errors from uncontrolled variation and percent G x E interaction explained by each statistically
significant IPCA
Hulling % Milling % HR% KL KLAC AC

Errors from Noise SS 55.54 49.94 63.05 25.75 37.06 25.54

uncontrolled Real structure (pattern) 44.46 50.06 36.95 74.25 62.94 74.46
variation Relevant variation (target) 84.95 59.89 94.67 56.18 89.12 92.85
Percent % G x E o f IPCA l 85.31 88.44 69.29 54.63 55.35 73.67
GxE % G x E o f IPCA 2 - - - 25.19 28.39 17.60
interaction % G x E o f IPCA 3 - - - 15.76 - -

Hulling percent: The Figure 1 a of biplot presents AMMI results. The main effects are
shown along the abscissa and the ordinate represents the first IPCA. The interpretation of a
biplot assay is that if main effects have IPCA score close to zero, it indicates negligible in-
teraction effects and when a genotype and an environment have the same sign on the IPCA
axis, their interaction is positive; if different, their interaction is negative. The AMMI 1
model for the hulling percent captures 99.26% of the treatment SS. Among all the loca-
tion-year testing environments, environments E1, E2, E4 and E5 displayed similar inter-
action effect, as they exhibited negative IPCA with average and above average hulling
percent. However, environments E3 and E6, the same environment in two different years,
displayed higher positive interaction than others with below average hulling percent. The
separation of E3 and E6 from the other four locations might probably be due to salinity
stress. The environment E5 shared same sign on the IPCA with seven genotypes. On the
other hand genotypes B and E shared same sign with environments E1, E2, E4 and E5 with
above average hulling percent.
Milling percent: The AMMI biplot with the main effects plotted against the IPCA 1
scores explained 98.9% of the treatment SS. In location-year environments, E1, E2, E4
and E5 were grouped together with negative IPCA1 score (Figure 1b). Environments E1
and E4 differed in main effects alone, wherein E1 recorded high main effect than E4. The
difference in main effect between E1 and E4 might be because of differences in tempera-
ture and rainfall. The effect of change in month of planting on milling percent in Basmati
varieties was reported by Rao et al. (1996). The separation of the location E3 and E6 from
other environments might be due to salinity stress. Furthermore, the environments E1, E2
and E3 displayed higher main effect than their corresponding environments E4, E5 and E6
respectively which, can be explained by differences in temperature and precipitation.
Three locations E1, E2 and E4 with negative IPCA1 scores recorded positive specific in-
teraction with genotypes O, H, D, N, E, B and P. Genotypes A, G, M, L and J with positive
values of IPCA1 had positive interaction with E3 and E6, the saline stress environments.
Head rice percent: The AMMI biplot model for the head rice percent captured 99.5%
of the treatment SS. The environment E2 scores near zero had a little interaction across ge-
notypes and low discrimination among genotypes (Figure 1c). The separation of E2 from
the other environments was probably due to its favourable soil texture nature, temperature
and precipitation. Hou et al. (1988) also reported that head rice percent was highly influ-
enced by soil texture in two different Taiwanese cultivars under greenhouse conditions. In

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144 ANANDAN et al.: Appraisal of Quality Traits in Rice by AMMI

location-year environment, E1 and E4 had small negative values for IPCA1 with high
main effect, while E5 had a low negative value for IPCA1 with low main effect. Further-
more, E3 and E6 were tightly grouped and separated from others. The separation of these
two environments was probably due to soil salinity. The year-location 2006 dry season,
comprised of E1, E2 and E3 exhibited lower interaction effects than their corresponding
environments E4, E5 and E6 respectively. This might have been due to high temperature
and low precipitation favouring location-year environment 2006 dry season for E1, E2
and E3. High head rice yielding genotypes with low IPCA score are G and A and with high
positive values for first IPCA score are D and I. Furthermore, the genotype J had high pos-
itive first IPCA. Four genotypes E, N, O and Q with negative values for the first IPCA,
shared the same sign with environments E1 and E4 with high main effect, showed positive
specific interactions.
Kernel length: The biplot of AMMI 1 (Figure 1d) captured 96.1% of the treatment
SS. When considering the environments, E3 showed low interaction across genotypes.
However, the same climatic factors prevailed in E2. This exposed that, low interaction of
E3 might be because of saline soil that had not supplied nutrient to the crop invariably to
all the genotypes. In remaining environments, soil and other climatic factors might have
interacted well with the crop exhibiting high interaction effect. In the same way, Singh et
al. (1998) reported that, length of kernels were influenced by the field in which crop was
grown. The environments E4, E5 and E6 (31 °C and 21 °C maximum and minimum tem-
perature respectively) grouped tightly belong to same season (short photoperiod) had fa-
voured conditions for kernel length. The genotypes G, H, Q and I differ in their main ef-
fects considerably but not in interaction. Six genotypes (D, K, M, F, J, and C) with positive
values for the first IPCA comprised of kernels lengthier than population mean. The geno-
types L and E exhibited positive interaction with two environments E1 and E2 with posi-
tive IPCA. The biplot of two IPCA axes, together accounted for 98.2% of treatment SS
and 79.8% of interaction SS. The IPCA 1 versus IPCA 2 biplot, explain the magnitude of
interaction of each genotype and environment. The genotypes and environments that are
farthest from the origin being more responsive, fit the worst. Genotypes and environments
that fall into the same sector interact positively; negatively if they fall into opposite sec-
tors. In AMMI 2 biplot, except E3, other environments are the most discriminating loca-
tions, while D, E, C, O, N, B, P and A are farther from the origin and exhibited their high
responsiveness. The genotypes N, O and B are particularly stable for E4 and E6 (same sec-
tor) and to some extent E5 since they fall in adjacent sector.
Kernel length after cooking (KLAC): The AMMI 1 model for KLAC, captured 99%
of the treatment SS. Among all the location-year testing environments, E4, E5 and E6 dis-
played negative IPCA1 score with above average KLAC. On the other hand, E1, E2 and
E3 displayed differences in interaction effect but not in main effect. E1 exhibited more
variability for interaction effect than others with above average main effect. The geno-
types G, C and I exhibited low interaction effect with high main effect, whereas, the geno-
types H, O, N, J and E displayed similar main effect with different interaction effect. Ali et
al. (1992) observed that cultivation practices had its influence on cooked kernel length.
Figure 2a represents the AMMI 2 biplot accounting for 99.6% of treatment SS and 83.7%

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 ANANDAN et al.: Appraisal of Quality Traits in Rice by AMMI 145

2.0
1.5 E6
J J
1.5
1.0 E3
E6E3
1.0
L

IPCA 1
A
IPCA 1

0.5 M
0.5 Q F
L G
H
G I
K 0.0 GM O
0.0
D QA CI GM
K67 DH
N
E B 79 65 66 68 69 70
73 75 O M 77
P E2 81 E5
E5 -0.5 E2
-0.5 N F E
E1 C B E4 E1 P
E4
-1.0 -1.0
MEAN MEAN

Figure 1a. Hulling percent Figure 1b. Milling percent

1.5 E1
J 0.7
1.3
E3E6 E
1.0 0.5
0.8
0.5 0.3 D
IPCA 1
IPCA 1

F D I F
0.3 C A E2 K
0.1 L M J
H P GM C
0.0 E5
K G E3 GMG H
-0.3 45 L 50 M Q
E255 E 60 65 -0.1 5.5 I
6.0 6.5
-0.5 Q N O A
E5 E4 O
-0.8 B E4 -0.3 N
P
-1.0 E1 B E6
-1.3 -0.5
MEAN MEAN

Figure 1c. Head rice percent Figure 1d. Kernel length

Figures 1a to 1d. AMMI – 1 biplot for qualitative traits of hybrid rice, showing both main and interaction
effects for both genotypes and environments.

0.8 1.5
E2
C E5
1
0.4 I
H
E E3 ON 0.5
IPCA 2
IPCA 2

E5 I H
D F0 0.00 E2
Q DN
G B
KJ Q P KC0 G 0.00 P J
-1 -0.5 ML 0 0.5 1 O
E6 A0 E4
E1 -2 -1 L M 1E1 2
-0.4E4 E6 F E
A -0.5
E3 B
-0.8 -1
IPCA 1 IPCA 1

Figure 2a. Kernel length after cooking Figure 2b. Amylose content
Figures 2a and 2b. Projection of genotypes on the first two principal components of
G x E interaction effect.

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146 ANANDAN et al.: Appraisal of Quality Traits in Rice by AMMI

of interaction SS. Environment E3 alone displayed low interaction with small scores
closer to the center of the axes. Genotypes I, Q, L, M, J, G, K and F were close together to
the center of the axes, they tend to have similar yields in all environments. Genotypes A,
E, D, H, O, N, B and P were the most responsive genotypes, while E1, E2, E4, E5 and E6
were the most differentiating locations.
Amylose content: The biplot of AMMI 1 captured 98.9% of the treatment SS. Envi-
ronments E1 and E4 showed more variability for interaction effects with high positive
IPCA 1 score. However, environments E2, E3, E5 and E6 also showed variability for in-
teraction effect with negative IPCA 1 score with varying main effects among them. The
differences in positive and negative IPCA 1 score between environments may be ex-
plained by temperature, rainfall, altitude and soil texture. Genotypes O, F and N differ in
their main effect considerably with low interaction effect. The genotypes B, P, E and J dis-
played high positive interaction effect with E1 and E4. Whereas, G, Q, C, H and K, exhib-
ited high negative IPCA 1 score and positive interaction with E2 and E3. The AMMI 2
biplot (Figure 2b) captured 99.6% of treatment SS and 91.2% of the interaction SS. In Fig-
ure 2b, H, D, N, O, A, F, G, M and Q are close to the origin and exhibited low interaction
effect. Among the six environments, E2 alone exhibited interaction considerably lower
than others. However, the three locations E1, E2 and E3 were grouped with their corre-
sponding locations E4, E5 and E6 respectively in the same sector. This exhibited that
amylose content varied significantly among locations.
Correlation between environmental IPCA scores of a trait and environmental factors
give a useful insight about the interaction effects. The correlation between environmental
IPCA scores and environmental factors varied in relationship from moderate to high (Ta-
ble 3). All traits of environmental IPCA axes were correlated with environmental factors
like latitude, altitude, soil pH, minimum and maximum temperature, with moderate to
high interaction effect on grain quality in positive or negative direction. On the other hand
longitude, relative humidity and rainfall had exhibited low influence on quality traits in
rice. IPCA axis of hulling percent, milling percent and head rice percent was favoured by

Table 3. Correlation between IPCA axes and environmental factors for the AMMI analysis of eight quality
traits of rice

IPCA Temperature Relative

Characters Latitude Longitude Altitude Soil pH Rain fall
axes Max. Min. humidity
Hulling % IPCA 1 -0.347** 0.569** -0.604** 0.963** -0.113** 0.146** -0.408** 0.368**
Milling % IPCA 1 -0.317** 0.542** -0.577** 0. 963** -0.211** 0.043 -0.312** 0.436**
HR% IPCA1 -0.515** 0.711** -0.740** 0.968** -0.066 0.246** -0.547** 0.385**
KL IPCA1 0.387** -0.455** 0.463** -0.411** 0.840** 0.311** -0.084 -0.642**
IPCA -0.783** 0.742** -0.731** 0.394** 0.380** 0.775** -0.935** -0.100**
IPCA 3 0.146** 0.028 -0.057** 0.637** 0.278** 0.328** -0.298** -0.215**
KLAC IPCA 1 0.446** -0.541** 0.554** -0.551** 0.771** 0.219** 0.036 -0.636**
IPCA -0.805** 0.727** -0.710** 0.254* 0.360** 0.693** -0.864** -0.052
AC IPCA1 0.811** -0.923** 0.936** -0.815** 0.148** -0.190** 0.594** -0.572**
IPCA 2 -0.507** 0.306** -0.270** -0.481** -0.407** -0.339** 0.158** 0.473**
*P<0.05and**P<0.01

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 ANANDAN et al.: Appraisal of Quality Traits in Rice by AMMI 147

environmental factors like reduced photoperiod, good soil pH, minimum temperature, re-
duced relative humidity and less rain fall. While other traits kernel length, KLAC and
amylose content was highly favoured by more photoperiod, reduced mean sea level, mod-
erate temperature, good soil pH, reduced relative humidity and less rainfall might possibly
improve these traits. Correlating the external environmental factors with the environmen-
tal IPCA scores will help to identify the particular factor responsible for the interaction
effects. Such hidden information in the data would not be gleaned from the traditional
statistical methods.

Conclusion
In the present study, AMMI analysis identified the interactive and stable genotype
groups and further identified the driving forces for G x E interactions. Furthermore, the
correlation studies revealed that latitude, soil pH, minimum temperature, relative humid-
ity and rain fall had highly interacted and markedly influenced the hulling percent, milling
percent and head rice percent. Environmental factors like latitude, altitude, temperature,
soil pH, reduced relative humidity and minimum rainfall seemed to have affected the traits
kernel length, KLAC and amylose content. The AMMI model would be helpful to breed-
ers to select few efficient genotypes, which performs well. This model explains the inter-
actions in detail and identifies regions of adaptation for different varieties through the
biplot graph. In addition, percentage of noise can be calculated from G x E SS and RMS
residual calculated to study the model fit. AMMI model gives more valuable and brings
out many hidden useful information from the data, giving greater insight into the
magnitude and nature of G x E interaction.

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