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SABRAO Journal
of Breeding and Genetics
48 (4) 518-527, 2016
School for Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Chatha,
Jammu-180009Jammu & Kashmir, India
2
Division of Plant Breeding and Genetics, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir,
Shalimar, Srinagar, Jammu & Kashmir-190025, India
3
Division of Plant Breeding and Genetics, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu,
Jammu-180009, India
*Corresponding authors email: [email protected]
Email addresses of co-authors: [email protected], [email protected], [email protected],
[email protected]
SUMMARY
In India maize is emerging as third most important crop that contributes 2.5 billion dollar to Indian agriculture GDP.
The maize productivity figures are low primarily because of the cultivation of landraces and composite varieties.
Therefore, efforts are needed to develop hybrids for exploiting maximum heterosis for increased yield and quality
traits. In this regard, 20 maize inbred lines suited to high altitude and plain areas of Kashmir Valley are
comparatively evaluated for diversity analysis using both agro-morphological and SSR markers. Analysis of
variance showed that all the characters except ear girth were significantly different (P < 0.01) among the genotypes.
The first four principal components (PCs) of the PCA analysis contributed 97.9% of the variability. The dendrogram
obtained through agro-morphological and SSR analysis separated the genotypes into three (I, II and III) and four (I,
II, III and IV) major clusters, respectively. Out of 25 SSR markers tested only 10 primer pairs were found
polymorphic and detected a total of 31 alleles with an average of 3.1 alleles per locus. The maximum and minimum
polymorphic information content (PIC) values were found to be 0.78 and 0.29 for the primers Phi022 and
Phi109188, respectively. The Mantel test revealed a non-significant low correlation (r = 0.12, P < 0.148) between
the agro-morphological and SSR matrices. Both methods result in diverse clustering of genotypes suggesting
considerable diversity among the studied genotypes. The diverse maize inbred lines identified can be used as parents
in exploiting heterosis as well as to identify transgressive segregants for yield and quality traits of maize. Hence,
both methods proved effective for the diversity analysis of maize inbreds, and their combined study provides useful
information.
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INTRODUCTION
Maize (Zea mays L.) also known as corn, is the
only cereal crop of American origin that is
cultivated in tropical and subtropical regions
throughout the world. Maize is currently
produced on nearly 100 million hectares in 125
developing countries and is among the three
most widely grown crops in 75 countries (FAO
STAT, 2010). In India, maize is emerging as
third most important crop after rice and wheat,
and contributes 2.5 billion dollar to Indian
agriculture GDP (Kumar et al., 2013). India
occupies fifth place in average under maize in
the world after US, Brazil, China and Mexico.
As regards, Jammu & Kashmir it plays an
important role in the livelihood of the people of
this hilly and sub-mountainous state and
occupies highest area in the state, but
productivity figures are very low primarily
because of the cultivation of landraces and
composite varieties. Therefore, efforts are
required to develop hybrids for exploiting
maximum heterosis in order to increase
production and productivity of maize.
The choice of parents is the initial step
in plant breeding and directly benefit
transgressive segregation and heterosis, which is
considered to be high by the parents that are
distantly related (Joshi et al., 2004). The diverse
parents are observed to give progeny with higher
heterosis (Joshi and Dhawan, 1966; Anand and
Murrty, 1968). Thus, genetic diversity
estimation of crop species determines its
potential for improved efficiency and its use for
breeding, which inevitably prompted increased
food production. The genetic diversity among
individuals/populations can be determined using
different markers systems viz., morphological,
biochemical and molecular.
Morphological traits have been already
used to assess genetic diversity of maize
genotypes by number of earlier studies (Kashiani
et al., 2014; Azad et al., 2012; Syafii et al.,
2015; Kumar et al, 2015). Various types of
molecular markers (RFLP, RAPD, AFLP, ISSR
and SSR etc.) are available for varietal
identification and genetic characterization of
crop germplasm, among them SSR are the
marker of choice being co-dominant, multiple
allelic, simple, reproducible and reliable in
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Morphological characterization
The data on ten agro-morphological traits are
recorded from five randomly selected
representative plants in all the genotypes in each
replication. The standard method of DUS test
(Distinctiveness, Uniformity and Stability, Govt.
of India) was used for recording observation for
each of the character which includes plant
height, ear height, days to 50% pollen shed, days
to 50% silking, ear length, ear girth, 100 grain
weight, grain yield per plant, grain yield and
shelling
%
(Biodiversity
protocols:
www.bioversity.org). The mean values of the
data obtained were used for the various
statistical analyses.
Table 1. List of the maize (Zea mays L.) genotypes used for morpho-molecular characterization with their
name, source population, altitude and place of collection.
Line
KDM-361A
KDM-343A
KDM-332A
KDM-914A
KDM-895A
KDM-340A
KDM-362A
KDM-916A
KDM-500A
CM-502
W5
462
30
53
401
W3
YI-1
114-2
460
39
Source population
F-7012
Seed Tech 3435
AAMH 204
AH-1139
C-170
PRO-349
DMR-6520
DMR-00RIBK114
CM-128
CM-502
CML-354
CML-349
-
Altitude
Low and mid
Low and mid
Low and mid
Low and mid
Low and mid
Low and mid
Low and mid
Low and mid
Low and mid
Low and mid
High
High
High
High
High
High
High
High
High
High
Place of collection
Dryland (Karewa) Agriculture Research Station, Budgam
Dryland (Karewa) Agriculture Research Station, Budgam
Dryland (Karewa) Agriculture Research Station, Budgam
Dryland (Karewa) Agriculture Research Station, Budgam
Dryland (Karewa) Agriculture Research Station, Budgam
Dryland (Karewa) Agriculture Research Station, Budgam
Dryland (Karewa) Agriculture Research Station, Budgam
Dryland (Karewa) Agriculture Research Station, Budgam
Dryland (Karewa) Agriculture Research Station, Budgam
Dryland (Karewa) Agriculture Research Station, Budgam
High Altitude Maize Research, Sub-Station, Sagam, Anantnag
High Altitude Maize Research, Sub-Station, Sagam, Anantnag
High Altitude Maize Research, Sub-Station, Sagam, Anantnag
High Altitude Maize Research, Sub-Station, Sagam, Anantnag
High Altitude Maize Research, Sub-Station, Sagam, Anantnag
High Altitude Maize Research, Sub-Station, Sagam, Anantnag
High Altitude Maize Research, Sub-Station, Sagam, Anantnag
High Altitude Maize Research, Sub-Station, Sagam, Anantnag
High Altitude Maize Research, Sub-Station, Sagam, Anantnag
High Altitude Maize Research, Sub-Station, Sagam, Anantnag
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RESULTS
Data analysis
Agro-morphological analysis
Analysis of variance was performed for all agromorphological traits in order to test the
significance of variation among the genotypes
using SPSS 16.0 software. Cluster analysis was
done to yield a dendrogram depicting the
morphological relatedness of the inbred lines.
Principal component analysis (PCA) was also
used to detect underlying sources of
morphological variability, and to investigate
patterns of genetic diversity (Mohammadi and
Prasanna, 2003). Bray-Curtis distances and
UPGMA (Unweighted pair group method with
arithmetic mean) was the clustering method and
all these analyses were done using the PAST
software (Hammer et al., 2001).
For SSR data, the presence or absence of
the band was scored as 1 or 0, respectively. In
order to determine the utility of the SSR
markers, Number of alleles per marker,
Polymorphic Information Content (PIC),
Effective multiplex ratio (EMR) and Marker
Index (MI) were calculated. The Polymorphism
Information Content (PIC) values of individual
primers were calculated based on the formula
PIC= 1- ni=1 P2ij (Anderson et al., 1997).
Marker Index, a product of information content,
as measured by PIC, and Effective Multiplex
Ratio (EMR), was calculated following (Powell
et al., 1996). The Jaccards similarity index was
calculated using NTSYS-pc version 2.02e
(Applied Bio-Statistics, Inc., Setauket, NY,
USA) package to compute pair wise Jaccards
similarity coefficients (Jaccard, 1980) and this
similarity matrix was used in cluster analysis
using an unweighted pair-group method with
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Table 2. Analysis of variance for yield and yield component traits in maize (Zea mays L.).
Mean squares
Source
of variation
Replication
Treatment
Error
d.
f.
Plant
height
(cm)
Days to
50%
pollen
shed
Ear
girth
(cm)
Ear
length
(cm)
100
Grain
weight
(g)
119.75**
38.57**
41.75**
46.51**
0.38*
4.57**
0.01NS
19
93.34**
222.59**
311.25**
318.66**
0.32NS
15.26**
19
0.63
3.18
0.34
0.35
0.07
0.11
Days to
50%
silking
Ear
height
(cm)
Grain
yield
(q ha1
)
Shellin
g %age
39.64**
8.44**
27.22**
23.77**
105.04**
69.37**
150.75**
0.02
0.14
0.49
0.96
Grain
yield
plant-1
Table 3. Eigenvectors, Eigen values, total and cumulative variability (%) for 20 maize genotypes based
on ten agro-morphological traits.
Principal component (axes)
Eigen value
Variability (%)
Cumulative (%)
Traits
Plant height (cm)
Ear height (cm)
Days to 50% pollen shed
Days to 50% silking
Ear length (cm)
Ear girth (cm)
100 Grain weight (g)
Grain yield per plant (g)
Grain yield (q ha-1)
Shelling %
PC1
8.336
83.364
83.364
0.322
0.334
0.3233
0.342
0.332
0.169
0.283
0.341
0.339
0.336
PC2
0.827
8.276
91.64
PC3
0.376
3.762
95.402
Eigenvectors
0.008
0.091
-0.117
0.075
0.118
-0.347
-0.049
-0.081
-0.093
-0.228
0.949
0.216
-0.233
0.848
-0.056
-0.143
-0.049
-0.072
-0.035
-0.125
PC4
0.253
2.527
97.929
-0.699
0.303
0.478
0.176
-0.322
-0.004
0.169
-0.054
-0.127
0.092
Figure 1. Dendrogram based on agro-morphological traits showing three clusters (I, II and III) of 20
maize genotypes using UPGAMA method and Bray-Curtis distance.
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Figure 2. Gel picture showing banding pattern of 20 maize genotypes with phi022 marker.
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Table 4. List of markers used, chromosome number, number of alleles, PIC value, effective multiplex
ratio (EMR) and marker index (MI).
Markers
Phi034
Phi022
Phi015
Phi006
Zcaa391
Phi101049
Phi109188
Phi063
Phi064
Phi053
Average
Chromosome
Number
7
3
4
4
9
10
5
10
1
3
Number of
alleles
2
3
4
4
4
3
2
3
3
3
3.1
PIC
0.48
0.78
0.58
0.71
0.56
0.62
0.29
0.43
0.77
0.59
0.58
Marker index
(MI)
0.97
1.19
1.07
1.10
1.01
1.19
0.01
0.85
1.09
1.11
1.00
Figure 3. UPGMA dendrogram based on SSR data showing four clusters (I, II, III and IV) of 20 maize
genotypes.
DISCUSSION
The analysis of genetic diversity and relationship
among the elite breeding materials can
significantly aid in crop improvement (Hallauer
et al., 1988). In maize, this information is useful
in planning for hybrid and line development,
assigning lines to heterotic groups and in plant
variety protection (Yuan et al., 2002). There
exists an urgent need to promote maize breeding
to meet the increasing demands for maize grain
and its products. In this context, maize hybrid
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525
ACKNOWLEDGEMENTS
We thank the Vice Chancellor and Centre for Plant
Biotechnology of SKUAST-K for providing the lab
facilities and financial assistance for carrying this work.
Conflict of Interest: The authors declare that they have no
conflict of interest.
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