Evaluation of seed storage proteins in common bean by some biplot analysis

101 Marzooghian et al.
Int. J. Biosci. 2013
RESEARCH PAPER OPEN ACCESS
Evaluation of seed storage proteins in common bean by some
biplot analysis
Akbar Marzooghian1*
, Mostafa Valizadeh1
, Mohammad Moghaddam1
, Mohammad
Hasan Kooshki2
1
Department of Plant Breeding and Biotechnology, University of Tabriz, Tabriz, Iran
2
Agricultural and Natural Resources Research Center of Lorestan Province, Broujerd, Iran
Key words: Cluster analysis, GGE biplot, factor analysis, Phaseolus vulgaris L., seed storage proteins.
doi: http://dx.doi.org/10.12692/ijb/3.5.101-107 Article published on May 20, 2013
Abstract
In order to study of seed storage proteins, proteins samples of common bean genotypes were prepared by 0.2 M
NaCl of extracting soluble. Genotypes were located in two groups by cluster analysis using Wilks’ lambda
statistic. Two groups were different for yield components (number of pods per plant, number of seeds per plant
and seed weight). Factor analysis showed that two factors described 61% of total proteins variation. Correlated
bands with yield components characters had the highest coefficients for the first factor. This factor was named
“yield components proteins”. Protein bands via RM 58 and 64 had relationship with days to flowering.
Therefore, the second factor was named “phenologic proteins”. Genotypes were located in four groups by these
factors. Length, angle and presence of protein bands were important characteristics to explain graphical
information in GGE biplot compared to factor analysis.
* Corresponding Author: Akbar Marzooghian  marzooghian@tabrizu.ac.ir
International Journal of Biosciences | IJB |
ISSN: 2220-6655 (Print) 2222-5234 (Online)
http://www.innspub.net
Vol. 3, No. 5, p. 101-107, 2013

Introduction
The results of SDS-PAGE have been used correctly to
evaluation of between genus genetic diversity
(Ocompo and Toro, 2008; 2004; Garvin and
Weeden, 1994) and species (Duran et al., 2005). The
banding patterns produced by seed protein
electrophoresis have been used to effectively
characterize cultivars of pasture grasses and legumes
(Sheidai et al., 2000). Multiple domestication
centers have been suggested through the seed
storage protein electrophoresis analysis from
different wild and cultivated accessions of common
bean (Gepts et al., 1986). Seed storage protein
electrophoresis has been also used to estimate
diversity among accessions in genetic resources
collection (Gardiner et al., 1992). Generally, proteins
bands such as seed storage proteins have been used
as markers in the following four main applications:
analysis of genetic diversity within and among
populations (Marzooghian et al., 2011; Gepts,
1990b), plant domestication in relation to genetic
resources conservation and breeding, genome
relationships, and as a tool in plant breeding (Gepts,
1990b). Diversity in the types of phaseolin, the major
seed storage protein in common bean, has been
especially useful for classifying beans into Andean
and Mesoamerican gene pools since most of the
cultivars from one center of domestication possess a
certain set of phaseolin types which are not found in
cultivars or wild types from the other center of
domestication (Gepts, 1990a).
Common bean (Phaseolus vulgaris L.) is the most
important edible food legume in the world,
representing 50% of the grain legumes for direct
human consumption (McClean et al., 2004). China,
Iran, Turkey, and Japan are the most important
countries that produce common bean in Asia.
Common bean has the highest yield than other food
legumes in Iran (FAO, 2003). Three types of white,
red and pinto bean are produced in Iran.
Some appropriate methods such as cluster analysis,
PCA, factor analysis and GGE biplot are used for
genetic diversity evaluation, parental selection, study
interaction between the genotypes and environments
and applications to other types of two-way data
(Aharizad et al., 2012; Eivazi et al., 2008;
Mohammadi and prasanna, 2003; Bhatt, 1970)
When a large number of variables had relationship,
factor analysis transforms these variables to smaller
number of unobservable factors. A method widely
used for determining a first set of loadings is the
principal component method. This method seeks
values of the loadings that bring the estimate of the
total communality as close as possible to the total of
the observed variation (Walton, 1971). Yan (2001)
provided to the agricultural research community an
excellent scientific method of visual analysis, called
GGE biplot analysis.
Plants’ choice is the first step in plant breeding
program to hybridization. In order to benefit
transgressive segregation, genetic distance between
parents is necessary (Joshi et al., 2004). Also,
Recombination and selection methods depend
mainly upon the genetic distance among parents,
breeding objectives and available resources.
Maintenance and availability of germplasm as a
source of genetic variation is especially important to
fulfill the increasing needs of breeders. The objective
of the study was to use seed storage proteins to study
variety inter-relationships and the role of these
proteins to selection among genotypes of P. vulgaris
by formal statistical and graphical analysis.
Materials and methods
Seventy common bean genotypes randomly selected
from collection genotypes exist in Iran (data not
shown) were evaluated it this study. The common
bean genotypes were obtained from National Bean
Research Station of Khomeyn, Iran.
Protein patterns were studied by SDS-PAGE. The
method of Krochko and Bewley was used for the
extraction of soluble seed storage proteins in salt
(Krochko and Bewley, 2000). Low salt (0.2 M NaCl)
solution was used in this research. After seed coat
separation, seeds were ground and the resulting flour
was filtered by a sieve (40 mesh). Forty mg of floured

seed was poured in a micro tube. Then extraction
solution was added in each micro tube and soluble
protein samples in low salt were prepared.
Polyacrylamide gels and buffers were prepared by
Hames and Richwood method (Hames and
Richwood, 1990). The Laemmli method was used for
protein electrophoresis (Laemmli, 1970).
Electrophoresis was performed using vertical gels
(10%) with 20 μl loading (Table 1). After staining,
protein bands were evaluated qualitatively. Each
band was named according to its relative mobility
(RM). A zero-one coding was used for the presence
or absence of proteins in a special location.
Furthermore, the genotypes under study were
evaluated for several agronomic characters such as
number of days to flowering, number of days to
maturity, plant height, pod number per plant, seed
number per plant and 100 seed weight in National
Bean Research Station of Khomeyn, Iran. Seed
length, width and thickness were also measured for
three grains of each genotype. Relationship between
agronomic characters and protein bans was
calculated by t-test statistic. UPGMA base on simple
maching coefficient was used for genotypes
clustering. Discriminate analysis based on Wilks’
lambda (Wilks’ lambda = SS within groups/SS total) was
used to identify cutting point in cluster tree. Factor
and GGE biplot analysis was also carried out to
explain the variation.
Statistical analyses were performed by SPSS,
STATISTITA and GGE biplot software.
Results
Cluster analysis
Electropherogram of several common bean
genotypes in terms of soluble proteins based on the
method of extraction are shown (Fig. 1). Cluster tree
was cut via discriminate analysis using Wilks’
lambda statistics (Table 2) and consequently,
genotypes were located in two groups (Fig. 2).
Genotypes that located in group1 had higher number
pod per plant, number seed per plant and seed
weight than genotypes in other group (Table 2).
Table 1. Consumed materials for the preparation of storage protein sample and loading of sample in common
bean.
Extracted soluble
protein (μl)
Reload buffer
(μl)
2–mercaptoethanol
(μl)
Loaded sample
in wells (μl)
Sample
type
1572.520S1
S1 = Soluble proteins in low salt.
Table 2. Group means difference of studied common bean genotypes by T-test in cluster analysis.
Characteristics
Groups Pod number per plant Seed number per plant Seed weight
Mean 1 12.95 45.37 44.17**
2 19.89** 76.42** 32.38
Wilks'
Lambda
0.036**
* * Significant at the 1% level of probability
Biplot analysis
Factor analysis transformed electrophoresis bands
into two factors (Table 3). These factors explained
61% of total for proteins variation. First factor
described 48% of the variation. Proteins via RM 17,
18, 30, 32, 38, 40 and 54 had the highest coefficients
for first factor. Genotypes located in two groups for
this factor (Fig.3). Comparing two groups it was
revealed that one of groups had lower 100 seed
weight and higher pod number per plant and seed
number per plant than the other group (Table 4).
Therefore, this factor was named “yield components

proteins”. Furthermore, the genotypes were
separated into two groups for the second factor.
These groups were also different for days to
flowering. Thus, this factor was named “phenologic
proteins”. Considering the independence of factors
for “yield components proteins” and “phenologic
proteins”, it seems these proteins bands could be
used to select genotypes simultaneously for the
above agronomic and phenologic characters.
Fig. 1. Gel samples of several common bean
genotypes for the extraction method of soluble
proteins in low salt.
Fig. 2. UPGMA dendrogram based on simple
matching coefficient showing relationship among 70
studied common bean based on electrophoresis
bands.
Fig. 3. Features of studied common bean genotypes
based on their factor scores.
Correlations between genotypes and protein bands
have been shown in figure 4 by GGE biplot analysis.
Genotypes classification in biplot figures (Figs. 3 and
4) was similar, because of principle components
method (PC) was used in both GGE biplot and factor
analysis.
Table 3. Factor analysis based on principal
component analysis of protein bands in studied
common bean genotypes.
Components
Proteins via RM Factor 1 Factor 2 Communality
3 0.644 -0.154 0.486
5 0.312 0.075 0.836
7 -0.632 -0.243 0.461
11 0.385 -0.198 0.710
13 -0.171 0.307 0.678
17 -0.920 -0.092 0.856
18 0.920 0.092 0.856
30 0.945 0.150 0.943
32 0.945 0.150 0.943
38 -0.945 -0.150 0.943
40 -.0945 -0.150 0.943
48 -0.748 0.023 0.591
54 0.869 -0.022 0.765
58 -0.250 0.882 0.940
60 0.301 -0.545 0.516
64 -0.322 0.866 0.938
70 0.614 0.023 0.436
Variance 48.835% 12.681%
Cumulative variance
(%)
48.835% 61.516%
Factor 1 = Yield components proteins; Factor 2 =
Phenologic proteins
Discussion
The amount of graphical information in GGE biplot
was more than the factor analysis because of
presence, length and angle of vectors of proteins
bands. Effective protein bands can be identified with
vector length. Proteins bands 17, 18, 30, 32, 38, 40,
54 for principle component 1(PC1) and proteins
bands 58 and 64 for PC2 were located between two
groups for each principle component. A protein

bands located near the biplot origin has little effect
on genotypes grouping.
Fig. 4. Features of studied common bean genotypes
based on their PC scores in GGE biplot analysis.
Amount of bands correlation can be identified by
their angle. If the angle is 90˚, the bands are
independent and can be concluded loci for these
bands are probably different. It seems that bands via
RM 58 and 64 had no relationship with mentioned
proteins bands in PC1. In the other hand, bands had
180˚ angle they had different control for correlated
trait. Protein bands with this angle more probably
are alleles with each other, for example Protein
bands 17 and 18.
Table 4. T-test analysis for groups in yield components proteins and phenologic proteins factors.
yield components proteins Phenologic proteins
Characteristics Groups Mean Sig. Groups Mean Sig.
Seed thickness 1 0.6104 0.166 1 0.5907 0.617
2 0.2822 2 0.6010
Seed length 1 1.2762 0.398 1 1.2715 0.173
2 1.3097 2 1.3256
Seed width 1 0.8052 0.997 1 0.8045 0.943
2 0.8051 2 0.8061
Days to flowering 1 47.28 0.405 1 45.22 0.008
2 46.17 2 48.69
Days to maturity 1 98.00 0.635 1 96.44 0.551
2 96.55 2 98.26
Plant height 1 63.03 0.103 1 54.29 0.193
2 52.50 2 62.90
Pod number per plant 1 20.17 0.010 1 17.17 0.335
2 12.95 2 14.38
Seed number per plant 1 78.76 0.004 1 65.04 0.265
2 45.37 2 51.17
Seed weight 1 32.28 0.000 1 39.41 0.690
2 44.47 2 38.34
One application of evaluation for diversity is to
choose genotypes from two ends of the phenotypic
distribute on. Graphical information obtained from
biplot analysis was more than the Cluster analysis.
For instance, bands 58 and 64 had no effect to group
separation, while these bands had main role to
genotypes classification in biplot analysis. Crossing
of the genotypes in the opposite locations in the
distribution allows the breeders to increase the
probability of heterosis and transgressive

segregation. Significant heterosis has also been
found for number of days to flowering (Barelli et al.,
2000; Mitranov, 1983), plant height (Gonçalves-
Vidigal et al., 2008), number of pods per plant,
number of seeds per plant, seed weight (Gonçalves-
Vidigal et al., 2008; Barelli et al., 2000; Nienhuis
and Singh, 1988) seed thickness, seed length and
seed width (Corte et al., 2010) in beans. The results
of analysis pointed above can be used to breeding
programs.
Conclusion
Common bean genotypes were located in different
groups based on seed storage proteins. Selection of
genotypes in these groups can help breeders to
indirect selection for some traits, accumulate
favorable alleles and broaden the genetic base.
Genotypes can be selected based on factor scores or
PC scores and improvement for several traits,
simultaneously. GGE biplot was better graphical tool
than factor analysis because of present, angel and
length of protein bands. Graphical analysis and
formal statistical analysis are complementary to
maximize understanding of the data.
Acknowledgements
Authors thank to Hamid Reza Dorri for assistance in
evaluating genotypes in field experiments. This
research was supported by University of Tabriz.
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