International Journal of Chemical Studies 2017; 5(4): 975-983
P-ISSN: 23498528
E-ISSN: 23214902
IJCS 2017; 5(4): 975-983
2017 IJCS
Received: 15-05-2017
Accepted: 16-06-2017
Lokesh Gour
Department of Plant Breeding &
Genetics Jawaharlal Nehru Krishi
Vishwavidhyalay Krishi Nagar,
Madhya Pradesh, India
Maurya SB
Department of Food science and
Technology, Jawaharlal
Neharu Krishi Vishwavidhyalay
Krishi Nagar, Madhya Pradesh,
India
Koutu GK
Department of Plant Breeding &
Genetics Jawaharlal Nehru
Krishi Nagar Adhartal,
Jabalpur, Madhya Pradesh,
India
Singh SK
Department of Plant Breeding &
Genetics Jawaharlal Nehru Krishi
Vishwavidhyalay Krishi Nagar,
Madhya Pradesh, India
Shukla SS
Department of Food science and
Technology, Jawaharlal
Neharu krishi vishwavidhyalay k
rishi nagar, Madhya Pradesh,
India
DK Mishra
Department of Plant Breeding &
Genetics Jawaharlal Nehru Krishi
Vishwavidhyalay Krishi Nagar,
Madhya Pradesh, India
Correspondence
Lokesh Gour
Department of Plant Breeding &
Genetics Jawaharlal Nehru Krishi
Vishwavidhyalay Krishi Nagar,
Madhya Pradesh, India
Characterization of rice (Oryza sativa L.)
genotypes using principal component analysis
including scree plot & rotated component matrix
Lokesh Gour, SB Maurya, GK Koutu, SK Singh, SS Shukla and DK
Mishra
Abstract
Total 83 rice genotypes comprising traditional landraces and released varieties from JNKVV was
evaluated for 33 quantitative and quality traits by principal component analysis for determining the
pattern of variation, relationship among individuals and their characteristics. Principal component
analysis was utilized to examine the variation and to estimate the relative contribution of various traits for
total variability. The PC1 showed 18.683%, while, PC2, PC3, PC4, and PC5 exhibited 15.404%,
13.401%, 9.433%, 8.037%, and 5.232% variability. Rotated component matrix revealed that PC3
accounts for yield & yield attributing traits. PC1 was also dominated by yield related traits. The PC2,
PC4 & PC5 was dominated by quality traits.It can be observed that scoring germplasm R 304,
Mahamaya, R-710, R-435, IR 64, Lakna, ShriRam, Rani Kajar, Surajone and Safari-17 comes in
different principal component which has relation with yield and quality attributing trait both. Sugandha-2
comes in PC2, PC4 & PC5 which all related quality aspect. Thus the results of principal component
analysis used in the study have revealed the traits contributing for the variation were identified. Resulting
germplasm of that study will be greater beneficial to identify the parents for improving various yield and
quality attributes with early maturity variety development.
Keywords: Rotated component matrix, Screed plot, germplasm, Principal component
Introduction
Rice is one of the three most important food grain crops in the world and forms the staple diet
of more than 2.7 billion people. Except Antarctica, it is grown in all the continents, occupying
165 million hectare area and producing 720 million tonnes (Anon. 2012) [4]. In India, it
accounts for more than 43% of food grain production. It is grown in 44.8 million hectare under
4 major ecosystems: irrigated, rainfed lowland, rainfed upland and flood-prone with average
annual production of 100 million tonnes (Song et al. 2007 [17] & Sohgaura et al. 2015) [16].
Presently, high yielding varieties are most lacking the quality characteristics like basmati so
market price fetched poor (Yumnam et al. 2011) [18]. But the incorporation of basmati quality
in the high yielding background has been the most challenging one. It might be due to its
complex nature with respect to its constitution and inheritance pattern of component indices
(Yumnam et al. 2015) [19]. In favour of this reason, greater genetic variation with greater
diversity contained in rice gene pool is necessary for utilization in breeding programmes
(Sivaranjani et al. 2010) [15]. Genetic diversity represents the heritable variation within and
between populations. Information on the genetic diversity and distance among the breeding
lines and the correlation between genetic distances are important for determining breeding
strategies, classifying the parental lines, defining heterotic groups, and predicting future hybrid
performance (Acquaah G. 2012) [1]. Genetic distance estimates for population grouping can be
estimated by different methods as it is crucial to understand the usable variability existing in
the population panel (Nachimuthu et al. 2014) [11]. One of the approaches is to apply
multivariate analysis. Multivariate statistical tools include Principal Component Analysis
(PCA), Cluster analysis and discriminate analysis (Oyelola. 2004) [12]. Principal Component
Analysis (PCA) may be used to reveal patterns and eliminate redundancy in data sets as
variations routinely occur in crop species for yield and grain quality (Maji et al. 2012) [9].
Principal components are generally estimated either from correlation matrix or covariance
matrix.
~ 975 ~
International Journal of Chemical Studies

When the variables are measured in different units, scale
effects can influence the composition of derived components.
In such situations it becomes desirable to standardize the
variables. In the present investigation correlation matrix was
used to extract the principal components. It accomplishes this
reduction by identifying directions (positive & negative),
called principal components, along which the variation in the
data is maximal (Singh & Narayanan 1993) [17]. Thus the
primary benefit of PCA arises from quantifying the
importance of each dimension for describing the variability of
a data set. Considering the importance of PCA, an
investigation was carried out on rice germplasm with an
objective to dissecting yield and quality related inter-
componential traits. To identify and classify maximum
variability into total variability for grouping the accessions by
taking into account several characteristics and relationship
between them.
Material and methods
Source Material and experimental site: Eighty three (O.
sativa L) lines including germplasm & released varieties were
used for characterization and evaluation (table 1). The
experiment was carried out at Seed Breeding Farm,
Department of and Plant Breeding and Genetics, College of
Agriculture, J.N.K.V.V., Jabalpur (M.P.). The experimental
scheme was randomized block design with three replications.

Table 1: List of contributing rice germplasm in this study

S. No. Name of Germplasm S. No. Name of Germplasm
1. IR-36 43. OR 1045-1-6
2. IR-64 44. Poornnima
3. Kranti 45. OR 1045-1-2
4. Mahamaya 46. JR-3-45
5. R-650 47. JR-503
6. R-548 48. SPS-71
7. R-704 (Tall) 49. Kathra
8. R-704 (Dwarf) 50. SuluxPonni
9. Abhya 51. Sugandha-2
10. R-321 52. Sugandha-3
11. R-652 53. Tulsi
12. ShriRam 54. Govinda
13. R-296 55. JR 82-1-10
14. R-712 56. Vanprabha
15. R-435 57. JR-305-7
16. R-671 58. P-677
17. R-710 59. P-364
18. R-820 60. Masuri
19. R-304 61. Karnal Basmati
20. Shymla 62. Safad Luchai-1
21. Ruchi 63. Safad Luchai-2
22. R-714 64. Pili Luchai-1
23. TRC-87 65. Pili Luchai-2
24. Pusa-150 66. BadiLuchai
25. H.M.T. 67. BalaghatLuchai
26. B.G.-380 68. Nungi
27. IR-54896 69. Suraniat
28. IR-42221 70. Sulehdas
29. IR-42342 71. Baspatri
30. IR-54742 72. Kakeria
31. Madhuri 73. Kardhana
32. Pusa Basmati-1 74. Amachur
33. Tarrori Basmati 75. Sorna
34. Safari-17 76. Surajone
35. Chhatrya 77. Rani Kajar
36. Luchi 78. Ram Ker -1
37. JR-353 79. Ram Ker -2
38. JR-75 80. Chipdu
39. JR-201 81. Lakna
40. JR-199 82. Dugsuchia
41. JR-82 83. Jeera Shankar
42. R 302-111

Assessment of Characteristics: Thirty three following and estimate genetic diversity of local rice germplasm and
quantitative & quality characters were used to characterize released varieties as per DUS guideline of rice. (Table: 2).

~ 976 ~
International Journal of Chemical Studies

Table 2: List of yield and quality contributing traits of rice

S. No. Quantitative traits S. No. Quality traits
1. Days to heading (DTH) 1. Grain length (GL)
2. Days to 50 % flowering (DFF) 2. Grain width (GW)
3. Days to maturity (DTM) 3. Length breadth ratio (LBR)
4. Thousand grain weight (TGW) 4. Hulling percent (H%)
5. Filled grain per plant (FGPP) 5. Milling percent (M%)
6. Unfilled grain per plant (UFGPP) 6. Head rice recovery (HRR%)
7. Total number of tillers (TNOT) 7. Milling density (MD),
8. Effective tiller per plant (ETPP) 8. Decorticated grain length (DGL)
9. Flag leaf length (FLL) 9. Decorticated grain width (DGW)
10. Flag leaf width (FLW) 10. Decorticated grain length breadth ratio (DLBR)
11. Culm length (CL) 11. Cooked grain length (CGL)
12. Panicle length per plant (PaL) 12. Grain elongation ratio (GER)
13. Panicle weight per plant (PaW) 13. Amylose content (AC%)
14. Culm thickness (CT)
15. Harvest index (HI%)
16. Panicle index (PI%)
17. Total number of spikelet (TNOS)
18. Spikelet fertility (SF%)
19. Spikelet density (SD%)
20. Grain yield per plant (GYPP)

2.2 Statistical Analysis: In order to identify the patterns of
variation, Principal component Analysis was conducted.
Those PCs with Eigen values greater than one were selected
as proposed by Jeffers (1967) [6]. Correlations between the
original traits and the respective PCs were calculated. Data
were processed using statistical program (Statistical analysis
System). The principal component analysis was computed
using the following equation:
Where; PC = Principal component, a1j = Linear coefficient
Eigen vectors
Results & discussion
Principal Component Analysis (PCA) is a powerful tool in
modern data analysis because this is a well-known
multivariate statistical technique which is used to identify the
minimum number of components, which can explain
maximum variability out of the total variability (Anderson,
1972 [3] and Morrison, 1978 [10]) and also to rank genotypes
on the basis of PC scores. Principal components are generally
estimated either from correlation matrix or covariance matrix.
When the variables are measured in different units, scale
effects can influence the composition of derived components.
In such situations it becomes desirable to standardize the
variables.
Variability: Principal components analysis was performed
using phenological, yield and quality components on rice
germplasm. Out of thirty three (table. 3), only fourteen
principal components (PCs) exhibited more than 0.5 eigen
values and showed about 92.753% total variability among the
characters were studied (here only five is considered having
most variability in the proposed characters) whereas Sohgaura
et al. 2015[16] found only twelve PCs more than 0.5 eigen
values and 93.878% total variability. So, these fourteen PCs
were given due to importance for further explanation. The
PC1 showed 18.683% which is far from findings of kiani G.
2012 [7] who got 28.99%, while, PC2, PC3, PC4, and PC5
exhibited 15.404%, 13.401%, 9.433%, 8.037%, and 5.232%
variability, respectively among the germplasm for the traits
under study (table 2). But Ashfaq et al. 2012[5] resulted PC1
with 33%, PC2 14.3%, PC3 11.4% and PC4 showed 9%
variability which is far different.

Table 3: Eigen values, % variance and cumulative eigen values of rice germplasm
Traits Principal component Eigen values % of Variance Cumulative %
DTH PC1 6.165 18.683 18.683
DFF PC 2 5.083 15.404 34.087
DTM PC 3 4.422 13.401 47.488
TGW PC 4 3.113 9.433 56.921
FGPP PC 5 2.652 8.037 64.957
UFGPP PC 6 1.727 5.232 70.190
TNOT PC 7 1.525 4.622 74.812
ETPP PC 8 1.117 3.386 78.198
FLL PC 9 1.054 3.194 81.392
FLW PC 10 0.908 2.753 84.145
CL PC 11 0.853 2.586 86.731
PaL PC 12 0.772 2.338 89.069
PaW PC 13 0.654 1.983 91.052
CT PC 14 0.561 1.701 92.753
HI% PC 15 0.478 1.449 94.202
PI% PC 16 0.416 1.260 95.463
~ 977 ~
International Journal of Chemical Studies

TNOS PC 17 0.384 1.163 96.626

SF % PC 18 0.264 0.801 97.426
SD % PC 19 0.236 0.714 98.141
GL PC 20 0.167 0.507 98.648
GW PC 21 0.150 0.455 99.102
LBR PC 22 0.117 0.354 99.456
H% PC 23 0.068 0.205 99.661
M% PC 24 0.062 0.188 99.849
HRR % PC 25 0.016 0.049 99.898
MD PC 26 0.015 0.046 99.944
DGL PC 27 0.008 0.024 99.968
DGW PC 28 0.006 0.017 99.986
DLBR PC 29 0.003 0.008 99.994
CGL PC 30 0.002 0.005 99.999
GER PC 31 0.000 0.001 99.999
AC % PC 32 0.000 0.001 100.000
GYPP PC 33 1.686E-13 5.109E-13 100.000

Scree Plot: Scree plot explained the percentage of variance flowering, and days to maturity, days to heading, unfilled
associated with each principal component obtained by grain per panicle, flag leaf width, total number of spikelets
drawing a graph between eigen values and principal (FIG: 2). Also PC3 has the characters allowed for developing
component numbers. PC1 showed 18.683 % variability with early and late maturity varieties and regarded as earliness
eigen value 6.165 which then declined gradually herewith factor but Nachimuthu et al. 2014 [11] was not in agreement
Nachimuthu et al. 2014 [11] also got highest variability in PC1 with this result. Lateness and earliness are important
with eigen value more than 1.0. Semi curve line is obtained characteristics for developing biotic and abiotic stress
after fourteen PC tended to become straight with little resistance.
variance observed in each PC. From the graph, it is clear that
the maximum variation was observed in PC1 in comparison to
other 33 PCs. So, selection of lines from this PC will be
useful (Fig. 1). Those principal components having more than
one eigen value that showed more variation among the rice
genotypes for the selection of the diverse parents.

Fig 2: Graphical representation of rotated component matrix for

different traits in PC 3
PC1 was also dominated by yield related traits i.e. total
spikelet per panicle, spikelet density, grain yield per plant,
harvest index %, panicle index, panicle weight per plant,
effective tillers per plant and number of tillers per plants
(FIG: 3), this was similar findings to Kumar et al. 2014 [8]. In
the study of Sanni et al. 2012 [13] & Nachimuthu et al. 2014
[11]
, PC1 regarded as earliness factor and a yield related trait in
single PC which is some of different then our result.
Fig. 1: Scree plot of principal component analysis of rice germplasm
between eigen value and principal components.

Rotated Component Matrix

The rice germplasm included in this investigation for PCA
analysis on the 33 yield and quality traits, all the characters
were estimated on the basis of principal component scores
(PC scores) and presented in (table 4 and table 5). These
scores can be utilized to propose precise selection indices
whose intensity can be decided by variability explained by
each of the principal component. High PC score for a
particular germplasm in a particular component denotes high
values for the variables in that particular germplasm. Rotated Fig 3: Graphical representation of rotated component matrix for
component matrix revealed that PC3 accounts for yield & different traits in PC 1
yield attributing traits like culm thickness, days to 50%
~ 978 ~
International Journal of Chemical Studies

Thus PC1 and PC3 can be regarded as yield factor and an
intensive selection procedures can be designed to bring about
rapid improvement of dependent traits i.e., grain yield by
selecting the lines from PC1 and PC3. The PC2, PC4 & PC5
was dominated by quality traits (Table: 4 & 5). PC2 included
grain length, length breadth ratio, decorticated grain length,
decorticated length breadth ratio, cooked grain length it has
totally quality aspect traits (FIG: 4) here Sohgaura et al. 2015
[16]
also concluded similar result.

Fig 4: Graphical representation of rotated component matrix for different traits in PC 2

PC4 included thousand grain weight, panicle length, grain
weight, decorticated grain length (FIG: 5). This result helps in
starch filling capacity of germplasm in grains comes under
PC4. Adebisi et al. 2013 [2] found similar result as 1000 grain
weight included in PC4 but Sohgaura et al. 2015 [16]
concluded PC4 in yield related trait which is vary from our
result. Panicle length & thousand grain weight are
characteristics which show negative direction to each other
but both characteristics comes under PC4 simultaneously.
This will be very useful when selection for germplasm comes
under PC4.

Fig 5: Graphical representation of rotated component matrix for different traits in PC 4

PC5 included hulling%, milling%, head rice recovery %, al. 2014 [8] & Sohgaura et al. 2015 [16]
because she found
milling density (FIG: 6) which is totally beneficial for yield earliness factor in PC5.
loss recovery. This result is not in agreement with Kumar et

Fig 6: Graphical representation of rotated component matrix for different traits in PC 5

~ 979 ~
International Journal of Chemical Studies

Table 4: Rotated component matrix* for 33 variables of rice germplasm.

Component
Traits
PC1 PC2 PC3 PC4 PC5
DTH -0.220 0.166 0.776 -0.332 0.009
DFF -0.223 0.093 0.829 -0.326 -0.047
DTM -0.223 0.095 0.830 -0.321 -0.038
TGW 0.037 -0.028 -0.055 0.806 0.256
FGPP 0.471 -0.061 0.355 -0.528 -0.093
UFGPP 0.446 0.003 0.653 0.069 -0.175
TNOT 0.678 0.062 -0.142 -0.032 0.058
ETPP 0.700 0.143 -0.078 -0.102 0.017
FLL -0.294 -0.430 0.146 0.108 -0.017
FLW -0.076 -0.297 0.556 0.230 0.195
CL -0.514 -0.491 0.258 0.113 0.021
PaL -0.134 0.014 0.023 0.542 -0.201
PaW 0.856 0.019 0.035 0.006 0.155
CT -0.176 -0.176 0.691 0.207 0.252
HI% 0.634 0.162 -0.153 -0.023 0.074
PI% 0.707 0.058 0.035 0.021 0.177
TNOS 0.550 -0.051 0.519 -0.427 -0.137
SF % -0.284 -0.068 -0.519 -0.307 0.114
SD % 0.503 -0.048 0.444 -0.611 -0.036
GL 0.150 0.758 -0.019 0.464 0.028
GW -0.002 -0.681 -0.056 0.561 -0.025
LBR 0.051 0.889 0.015 -0.120 0.036
H% 0.219 -0.191 0.239 0.246 0.553
M% 0.191 0.002 0.054 0.031 0.939
HRR % 0.090 0.014 -0.047 0.016 0.897
MD 0.080 0.139 -0.108 -0.142 0.777
DGL 0.124 0.750 -0.002 0.504 -0.139
DGW -0.003 -0.766 -0.082 0.397 0.013
DLBR 0.039 0.923 0.068 -0.001 -0.091
CGL -0.063 0.717 -0.012 0.315 0.188
GER -0.149 -0.331 0.004 -0.330 0.327
AC % -0.209 0.081 -0.010 -0.150 0.124
GYPP 0.898 0.033 0.021 0.010 0.174
Extraction Method: Principal Component Analysis.
Rotation Method: Varimax with Kaiser Normalization.
*Rotation converged in 9 iterations.

Table 5: Interpretation of rotated component matrix for the traits having values >0.5 in each PCs.
PC1 PC2 PC3 PC4 PC5
TNOT GL DTH TGW H%
ETPP LBR DFF PaL M%
PaW DGL DTM GW HRR %
HI% DLBR UFGPP DGL MD
Traits
PI% CGL FLW
TNOS CT
SD % TNOS
GYPP
An asterisks (*) represents more related traits in each principal component

Table 6: Scoring Germplasm in Different PCs

S. No. Germplasm lines PC1 PC2 PC3 PC4 PC5
1. IR-36 1.300 0.786 -1.492 -1.109 0.997
2. IR-64 1.466 1.041 -1.125 -0.729 0.376
3. Kranti 1.568 -0.979 0.068 -0.353 0.264
4. Mahamaya 1.777 -0.314 0.499 1.112 0.874
5. R-650 0.431 -0.089 1.191 -0.044 -0.097
6. R-548 -0.021 -0.528 0.086 0.096 -0.118
7. R-704 (Tall) 1.030 -0.266 0.110 0.962 -0.284
8. R-704 (Dwarf) 2.255 -0.855 0.400 -0.121 0.734
9. Abhya 1.251 0.759 0.209 0.540 -1.219
10. R-321 1.880 0.607 0.447 0.224 0.003
11. R-652 -0.676 1.372 0.386 0.660 0.572
12. ShriRam -0.399 0.817 1.767 1.565 0.267
13. R-296 1.150 -0.283 0.668 0.001 0.083
14. R-712 0.071 -1.214 -1.265 0.608 0.177

~ 980 ~
International Journal of Chemical Studies

15. R-435 1.573 1.040 0.078 -0.838 0.943

16. R-671 -0.550 0.758 0.498 1.057 0.431
17. R-710 1.601 -0.094 0.163 1.645 0.855
18. R-820 0.518 0.387 0.136 -0.068 0.470
19. R-304 1.838 0.176 1.002 -0.043 -0.269
20. Shymla -0.019 0.946 0.296 0.905 0.533
21. Ruchi 0.498 -0.117 0.085 -0.264 2.243
22. R-714 -0.240 0.241 0.064 1.120 0.094
23. TRC-87 0.761 -2.990 0.103 -0.875 0.900
24. Pusa-150 0.801 -0.027 -0.641 0.483 -1.932
25. H.M.T. 0.171 -0.009 0.598 -2.878 0.039
26. B.G.-380 1.393 -0.178 0.545 0.427 -2.048
27. IR-54896 0.088 0.889 -0.994 -0.027 -1.279
28. IR-42221 0.085 0.222 -0.374 -0.251 -0.754
29. IR-42342 -0.107 1.534 -0.386 -0.210 -0.960
30. IR-54742 1.165 0.445 0.861 0.411 -1.252
31. Madhuri -0.037 1.206 0.832 -1.055 0.110
32. Pusa Basmati-1 -0.555 1.191 -0.274 -0.972 -0.553
33. Tarrori Basmati -0.637 1.196 0.131 0.435 -1.346
34. Safari-17 -1.126 0.652 1.081 -0.998 1.931
35. Chhatry -1.985 -0.249 -0.364 -0.593 -2.324
36. Luchi -0.656 0.039 0.368 -0.325 0.571
37. JR-353 -0.170 0.807 0.828 0.476 -1.130
38. JR-75 1.980 -0.284 -1.676 -1.212 0.071
39. JR-201 0.628 0.145 -2.319 0.548 -0.264
40. JR-199 0.696 0.589 -1.986 -0.547 0.064
41. JR-82 0.661 0.866 -0.778 -0.422 -0.394
42. R 302-111 -0.598 0.516 -2.691 -0.208 -0.571
43. OR 1045-1-6 0.043 0.070 -1.976 -0.019 1.298
44. Poornnima -0.729 0.880 -0.502 -0.088 -0.355
45. OR 1045-1-2 0.553 -0.133 -0.425 1.093 -1.800
46. JR-3-45 -1.292 -0.781 -2.487 -0.080 -0.475
47. JR-503 -0.249 0.425 -0.210 -1.481 0.365
48. SPS-71 -0.255 0.968 2.115 -0.147 -2.721
49. Kathra 0.080 -0.062 1.096 -3.820 -0.210
50. Sulux Ponni 0.404 0.028 -0.173 -0.892 -1.293
51. Sugandha-2 -1.123 2.705 -0.381 1.454 1.669
52. Sugandha-3 -1.149 2.224 -0.486 0.791 0.485
53. Tulsi 0.927 -0.129 0.465 0.890 -0.144
54. Govinda -0.225 0.403 0.846 -0.463 2.020
55. JR 82-1-10 -0.836 -0.373 -1.594 0.030 0.996
56. Vanprabha -0.395 0.762 -0.465 0.176 -0.632
57. JR-305-7 0.983 -0.579 -0.109 -0.807 0.889
58. P-677 0.686 -0.291 -0.670 -0.167 0.557
59. P-364 0.259 0.508 -0.629 1.122 0.495
60. Masuri -1.066 0.063 1.071 -1.328 -1.093
61. Karnal Basmati -1.917 2.053 -0.547 0.402 -0.087
62. Safad Luchai-1 -1.232 -0.364 0.014 -1.482 0.806
63. safad Luchai-2 -0.995 -0.917 -0.285 -1.233 0.857
64. Pili Luchai-1 -0.843 -1.571 0.131 -0.945 -0.120
65. Pili Luchai-2 -0.337 -1.473 1.303 -0.235 0.028
66. Badi Luchai -0.465 -0.724 1.413 0.269 -0.224
67. Balaghat Luchai -0.848 -0.765 2.016 0.070 -0.841
68. Nungi -1.247 -1.414 0.804 -1.022 -0.155
69. Suraniat -0.131 -1.837 -0.340 0.275 -0.618
70. Sulehdas -2.031 -0.771 -0.951 1.248 0.044
71. Baspatri -0.508 -1.748 0.039 1.359 -1.347
72. Kakeria -0.974 -1.115 -0.593 0.724 -0.838
73. Kardhana -0.193 -1.855 -0.466 0.898 -1.279
74. Amachur -1.496 -0.183 0.036 -1.448 -0.434
75. Sorna 0.666 -1.365 -0.553 1.627 -0.623
76. Surajone -0.951 -0.907 1.083 1.511 1.024
77. Rani Kajar -1.400 -0.399 1.163 1.542 1.146
78. Ram Ker -1 -1.030 -1.855 -0.625 0.728 1.331
79. Ram Ker -2 -0.976 -1.557 -0.781 0.604 1.338
80. Chipdu -0.886 0.155 0.226 -1.847 -0.088
81. Lakna 0.136 1.056 1.237 0.349 0.731
82. Dugsuchia 0.465 -0.173 2.196 0.403 0.631
83. Jeera Shankar -0.276 0.290 0.859 0.807 1.856
Figure in coloured represent top values in each PC

~ 981 ~
International Journal of Chemical Studies

PC scores of the germplasm selected on the basis of >1.0
each PCs
The PC scores of the each component (PC 1, PC 2, PC3, PC4
and PC5) contain positive values (table 6 & 7). In PC1 the
positive scores ranged from 1.030 [R-704 (Tall)] to 2.255 [R-
704 (Dwarf)]. In PC 2 the positive value of the component
ranged from 0.016 (R-435) to 1.687 (Sugandha 2.) In PC 3 the
positive value of the components ranged from 0.013 (R 304)
to 3.329 (Dugsuchia). In PC 4 the positive value of the
components ranged from 1.057 (R 671) to 1.645 (R 710). In
PC 5 the positive value of the components ranged from 1.024
(Surajone) to 2.243 (Ruchi).
It can be observed that germplasm R 304 comes in PC1 &
PC3 both which has relation with yield and yield attributing
trait both. Sugandha-2 comes in PC2, PC4 & PC5 and
exhibited better performance for quality traits. Mahamaya &
R-710 comes in PC1 & PC4 same as R-435 & IR 64 comes in
PC1 & PC2 has relation with yield and quality trait both.
ShriRam comes in PC3 & PC4 similarly Safari-17 comes in
PC3 & PC5 showing their relation with yield and quality. But
both of germplasm has early and lateness factors. Rani Kajar
& Surajone comes in PC3, PC4 & PC5 showing earliness
factor, yield and quality traits all. So such germplasm were
the best for both yield and quality traits can be recommended
directly for cultivation programme.
Dugsuchia, SPS-71, Balaghat Luchai, ShriRam(Mandla),
Badi Luchai, Pili Luchai-2, Lakna, Rani Kajar, Kathra,
Surajone, Safari-17, Masuri, R-304 exhibited high score in
PC3 (Table 6). But Nachimuthu et al. 2014 [11] was not in
agreement with this result. So, selection of germplasms with
high score in PC3 will be desirable for developing late
maturity varieties with high yield potential whereas
germplasm having low PC score will be desirable for
developing early maturity varieties.

Table 7: Germplasm are selected on the basis of PC score in each component having positive values & more than >1.0 in each PCs
PC1 PC2 PC3 PC4 PC5
R-704 (Dwarf) (2.255) Sugandha-2 (2.705) Dugsuchia (2.195) R-710 (1.645) Ruchi (2.243)
JR-75 (1.980) Sugandha-3 (2.224) SPS-71 (2.115) Sorna (1.627) Govinda (2.020)
R-321 (1.880) Karnal Basmati (2.053) Balaghat Luchai (2.016) ShriRam (Mandla) (1.565) Safari-17 (1.931)
R-304 (1.838) IR-42342 (1.534) ShriRam(Mandla) (1.767) Rani Kajar (1.542) Jeera Shankar (1.85575)
Mahamaya (1.777) R-652 (1.372) Badi Luchai (1.413) Surajone (1.511) Sugandha-2 (1.669)
R-710 (1.601) Madhuri (1.206) Pili Luchai-2 (1.303) Sugandha-2 (1.454) Ram Ker -2 (1.338)
R-435 (1.573) Tarrori Basmati (1.196) Lakna (1.237) Baspatri (1.359) Ram Ker -1 (1.331)
Kranti (1.568) Pusa Basmati-1 (1.191) R-650 (1.191) Sulehdas (1.248) OR 1045-1-6 (1.298)
IR-64 (1.466) Lakna (1.056) Rani Kajar (1.163) P-364 (1.122) Rani Kajar (1.156)
B.G.-380 (1.393) IR-64 (1.041) Kathra (1.096) R-714 (1.120) Surajone (1.024)
IR-36 (1.300) R-435 (1.040) Surajone (1.083) Mahamaya (1.112)
Abhya (1.251) Safari-17 (1.081) OR 1045-1-2 (1.093)
IR-54742 (1.165) Masuri (1.071) R-671 (1.057)
R-296 (1.150) R-304 (1.002)
R-704 (Tall) (1.030)

Conclusion Safari-17 comes in different principal component which has

Principal component analysis was utilized to examine the
variation and to estimate the relative contribution of various
traits for total variability. The PC1 showed 18.683%, while,
PC2, PC3, PC4, and PC5 exhibited 15.404%, 13.401%,
9.433%, 8.037%, and 5.232% variability. It can be concluded
that principal component analysis highlights the characters
with maximum variability.
Rotated component matrix revealed that PC1 & PC3 accounts
for yield & yield attributing traits. The PC2, PC4 & PC5 was
dominated by quality traits i.e. grain length, grain L/B ratio,
decorticated grain length, decorticated grain L/B ratio, cooked
grain length, 1000 grain weight, panicle length per plant,
grain width, decorticated grain length, hulling %, milling %,
head rice recovery and milling degree. Panicle length &
thousand grain weight are characteristics which show
negative direction to each other. But germplasm comes under
PC4 caring both traits simultaneously and very useful for
further yield enhancement. So, intensive selection procedures
can be designed to bring about rapid improvement of yield
and quality traits with.
Dugsuchia, SPS-71, Balaghat Luchai, ShriRam(Mandla),
Badi Luchai, Pili Luchai-2, Lakna, Rani Kajar, Kathra,
Surajone, Safari-17, Masuri, R-304 exhibited high score in
PC3 (Table 6). So, selection of germplasms with high score in
PC3 will be desirable for developing late maturity varieties
with high yield potential whereas germplasm having low PC
score will be desirable for developing early maturity varieties.
It can be observed that germplasm R 304, Mahamaya, R-710,
R-435, IR 64, Lakna, ShriRam, Rani Kajar, Surajone and
~ 982 ~
relation with yield and quality attributing trait both. So those
can be recommended directly for cultivation programme.
Sugandha-2 comes in PC2, PC4 & PC5 which all related
quality aspect. However, this germplasm might be utilised for
crossing programme to develop superior hybrids governing
high quality traits. Hence the result of that study will be
greater beneficial to identify the parents for improving various
yield and quality attributes with early maturity variety
developm
References
1. Acquaah G. Principles of plant genetics and breeding.
Second edition. Wiley-blackwell publications. 2012; 127-
129.
2. Adebisi MA, Okelola FS, Ajala MO, Kehinde TO, Daniel
IO, Ajani OO. Evaluation of Variations in Seed Vigour
Characters of West African Rice (Oryza sativa L.)
Genotypes Using Multivariate Technique. American
Journal of Plant Sciences. 2013; (4):356-363.
3. Anderson TW. An Introduction to Multivariate Analysis.
Wiley Eastem Pvt. Ltd. New Delhi. 1972.
4. Anonymous. FAO, Rice Market Monitor. 2012; 14(2):1-
36.
5. Ashfaq M, Khan AS, Khan SHU, Ahmad R. Association
of various morphological traits with yield and genetic
divergence in rice (Oryza Sativa L.). Int. J. Agric. Biol.
2012; 14:55-62.
International Journal of Chemical Studies

6. Jeffers JNR. Two case studies in the application of

principal component analysis. Appl. Stat. 1967; 16:225-
236.
7. Kiani G. Diversity assessment among some restorer lines
using agronomic traits in rice (Oryza sativa L.). Biharean
biologist. 2012; 6(1):1-4
8. Kumar V, Koutu GK, Singh SK, Mishra DK, Singh PK,
Sohgaura N. Genetic analysis of inter sub-specific
derived mapping population (RILS) for various yield and
quality attributing traits in rice. International science
journal (Peer-Rewied). 2014; 1(3).
9. Maji AT, Shaibu AA. Application of principal
component analysis for rice germplasm characterization
and evaluation. Journal of Plant Breeding and Crop
Science. 2012; 4(6):87-93;30.
10. Morrison DE. Multivariate Statistical Methods (2nd ed.
4th Print, McGraw Hill Kogakusta Ltd. 1978.
11. Nachimuthu VV, Robin S, Sudhakar D, Raveendran M,
Rajeswari S, Manonmani S. Evaluation of Rice Genetic
Diversity and Variability in a Population Panel by
Principal Component Analysis. Indian Journal of Science
and Technology. 2014; 7(10):1555-1562.
12. Oyelola BA. The Nigerian Statistical Association
preconference workshop, University of Ibadan, 2012, 20-
21.
13. Sanni KA, Fawole I, Ogunbayo A, Tia D, Somado,
Futakuchi EA, Guei RG. Multivariate analysis of diver-
sity of landrace rice germplasm. Crop Science. 2012;
(52):494-504.
14. Singh P, Narayanan SS. Biometrical techniques in plant
breeding. Fifth revised edition. 2013, 24-30.
15. Sivaranjani AKP, Pandey MK, Sudharshan I, Kumar GR,
Madhav MS and Sundaram RM. Assessment of genetic
diversity among basmati and non-basmati aromatic rices
of India using SSR markers. Curr. Sci. 2010; 99:221-226.
16. Sohgaura N, Mishra DK, Koutu GK, Singh SK, Kumar
V, Singh P. Evaluation of high yielding and better quality
rice varieties using principal component analysis. Eco.
Env. & Cons. 2015; (21):187-195.
17. Song XJ, Huang W, Shi M, Zhu MZ, Lin HX. A QTL for
rice grain width and weight encodes a previously
unknown RING- type E3 Ubiquitin ligase. Nat. Genet.
2007; 39:623-630.
18. Yumnam S, Nandeshwar BC, Adhikari B, Senapati BK.
Variability and charchter association in recombinant lines
(F6) of basmati derivative. Curr. Advan. Agril. Sci. 2011;
3(1):24-28.
19. Yumnam S, Sawarkar A, Patil SG, Senapati BK.
Multivariate analysis of recombinant inbred lines (F6) of
basmati derivative. The Ecoscan. 2015; 9(1-2):289-294.

~ 983 ~