Proc. Natl. Acad. Sci., India, Sect. B Biol. Sci.

DOI 10.1007/s40011-017-0847-y

RESEARCH ARTICLE

Understanding genetic relationship and population structure

of Indian soybean varieties using microsatellite markers
Devendra Kumar Chauhan1 Javaid Akhter Bhat1 Ajay Kumar Thakur2

Zakir Hussain3 C. Tara Satyavathi4

Received: 12 May 2016 / Revised: 9 November 2016 / Accepted: 12 January 2017

 The National Academy of Sciences, India 2017

Abstract Thirty-nine simple sequence repeat markers Introduction

have been used to estimate the genetic diversity and pop-
ulation structure of 78 soybean varieties released in India. Soybean (Glycine max L. Merrill; 2n = 40), a miracle
A total of 140 alleles were detected and an average of 3.59 legume native from China, is currently one of the most
alleles per locus was recorded. Polymorphism information important crop worldwide. In India, this is the major con-
content values for all the polymorphic markers across 78 tributor of edible oil after groundnut, with a cultivated area
soybean varieties ranged from 0.073 (Satt415) to 0.931 of 10 million ha and 10.44 million ton production [1].
(Satt084), with an average value of 0.59. Mean similarity However, the average productivity of this crop is one ton/
coefficient was recorded as 0.41 for all the genotypes. ha, which is very low to meet the ever increasing demand
Marker index values ranged from 0.051 (Satt498) to 5.556 of edible oil in India. Development of improved and new
(SOYSHP176) with an average value of 2.54. The resolv- varieties is the main aspect for increasing the overall pro-
ing power value ranged from 0.102 (satt498) to 2.086 duction and productivity of this very important oilseed
(GMABABE) with an average value of 1.64. Both the crop. In India, 78 varieties have been developed from
phylogenetic and population structure analysis classified various breeding centres and this figure is increasing every
soybean varieties into five main clusters and five sub- year, but no significant improvement in yield or resis-
populations, respectively. Principal coordinate analysis tance/tolerance to various biotic and abiotic stresses has
results are in agreement with both of these methods, which been achieved so far. After the implementation of Pro-
grouped the varieties on the basis of their origin, pedigree tection of Plant Varieties and Farmers Rights Act-2001,
and releasing centre. varietal identification got much more attention. When
referring to the necessary requirement for the protection of
Keywords Genetic diversity  Soybean  new cultivars, it states that the cultivar should be reliably
Simple sequence repeat markers  Polymorphism New, Distinct, Uniform and Stable. Along with the
development of new varieties, there has been a growing
interest in genetic characterization for protection of vari-
& Devendra Kumar Chauhan eties provided by PPV and FR Act. Also for the breeding
[email protected] and genetic improvement of crop species, a thorough
1
Present Address: Division of Plant Breeding and Genetics,
knowledge of the genetic diversity is necessary to decide
Sher-e-Kashmir University of Agricultural Sciences and the breeding strategies involving the selection of parents to
Technology of Jammu, Chatha, Jammu, J&K 180009, India maximize genetic improvement. More accurate and com-
2
ICAR-Directorate of Rapeseed-Mustard Research, Bharatpur, plete descriptions of existing soybean varieties and patterns
Rajasthan 321303, India of genetic diversity could facilitate introgression of diverse
3
Division of Vegetable Sciences, ICAR-Indian Agricultural germplasm into current commercial soybean genetic base.
Research Institute, Pusa, New Delhi 110012, India Plant breeders have traditionally used morphological
4
Division of Genetics, ICAR-Indian Agricultural Research and biochemical markers for the genetic diversity analysis
Institute, Pusa, New Delhi 110012, India and the registration of varieties under PPV and FR Act.

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 D. K. Chauhan et al.

These are limited in numbers, highly influenced by the pedigree and releasing centres has been shown in Table 1.
environment and are growth stage-specific. These traits Genomic-DNA was extracted from young and tender
create difficulty particularly in closely related cultivars. In leaves of soybean varieties using the cetyl trimethyl
plants with a narrow genetic base in their gene pool such as ammonium bromide (CTAB) method [21] and purified by
soybean, they may not be sufficient for the diversity RNAase treatment. DNA quality and concentration were
analysis and identification of genotypes. So a more reliable evaluated on 0.8% agarose gel electrophoresis stained with
and efficient method is required for characterisation and ethidium bromide in the presence of different concentra-
identification of genotypes. In such cases, molecular tions of undigested k-DNA and a final concentration of
markers can provide additional information about the 50 ng ll-1 was used for PCR.
genetic characterisation, degree of diversity and genetic
relationship of the existing genotypes [2]. Plant protection SSR Genotyping
office of USDA Agriculture Marketing Services now
accepts microsatellite allelic profiles as supporting evi- Simple sequence repeats markers (39 primer pairs), pre-
dence for the uniqueness of a cultivar [3]. viously developed [22], distributed across all the 20 linkage
Among the class of molecular markers, microsatellite groups of soybean genome, with at least 2 markers from
markers/simple sequence repeats (SSRs) are the sequences each linkage group were selected and custom synthesized
of a few repeated and adjacent base pairs, which are very (Table 2). Detailed description of the primers is available
useful for variety of applications in plant genetics and at soybean website USDA-ARS Soybean Genome Data-
breeding. There are a number of advantages of using SSRs base (http://129.186.26.94/SSR.html). Primers were chosen
over various other molecular markers including their co- because of their trinucleotide nature and presented poly-
dominant and multi-allelic nature [4], less expensive PCR- morphism in the previous studies. The PCR reaction
based assay, relative abundance, uniform distribution over (25 ll) contained 1X reaction buffer (20 mM Tris-Cl, pH
the eukaryotic genome [5] and high reproducibility, which 8.4, 50 mM KCl), 10 nM dNTPs, 50 mM MgCl2, 5 pM
are very suitable for accession discrimination and assess- primer, 1.0 Unit of Taq DNA polymerase and 50 ng
ment of genetic variation. SSR markers have been useful genomic DNA. For standardization of annealing tempera-
for integrating the genetic, physical and sequence based tures of SSR primers, gradient PCR was carried out in a
physical maps in plant species and simultaneously have gradient thermal cycler. Initial denaturation at 94 C for
provided breeders and geneticist with an efficient tool to 5 min was followed by 35 cycles at 94 C for 2 min, 47 C
link phenotypic and genotypic variation [6]. Variation in for 1 min and 72 C for 1 min. The final extension was
the number of repeats can be detected by polymerase chain carried out at 72 C for 10 min. The SSR amplified frag-
reaction (PCR) with the development of primers (2030 ments were resolved in 3% metaphore agarose gel in a 1X
base pairs), specifically designed for amplification and TBE buffer. The gels were stained with ethidium bromide
complementary to single sequences flanking the (0.5 lg/ml) and visualized under UV light.
microsatellite. These markers have been used for studying
the genetic relationship in soybean [717] and many other
crops including rice [18], wheat [19], Indian mustard [20], Statistical Analysis
faba bean [6] etc. However, no exhaustive study of genetic
diversity, genetic relationship and population structure of The prominent DNA bands that were amplified by a given
Indian soybean cultivars had been carried out so far using primer, were scored as present (1) or absent (0) for all of
SSR markers. The objective of the present study was to the samples under investigation. To determine the utility of
reveal the genetic relationship and population structure of the SSR markers, number of amplicons per marker, Poly-
Indian soybean varieties released from different soybean morphic Information Content (PIC), Major allelic fre-
breeding centres using SSR markers. quency, Marker Index (MI), Resolving power (Rp) and
Discrimination power (Dp) were calculated for each pair of
primers. The Polymorphism Information Content (PIC)
Material and Methods value of individual primer pair was calculated based on the
following formula [23].
Plant Material and DNA Isolation Xn
PIC 1  P2ij
i1
Seventy-eight soybean varieties developed by different
breeding centres and released by central/state varieties Marker index, a product of information content, as
release committees for different agro climatic regions were measured by PIC, Effective multiplex ratio [5] and
taken up for the present study. Detailed description of Resolving power (Rp) of each primer combination was

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Understanding genetic relationship and population structure of Indian soybean varieties

Table 1 Name of varieties, their pedigree, releasing centre, cluster and sub-population
S. no. Name of the varieties Pedigree Releasing center Cluster Sub-population

1 ADT-1 Selection from Hilly variety TRRI, Aduthurai I C

2 Alankar D63-6094 X D-61-4249 GBPUAT, Pantnagar I C
3 Ankur SPS from composite of 22 crosses GBPUAT, Pantnagar I C
4 Birsa Soya-1 Spontaneous mutant of Sepaya Black I C
5 Bragg Jackson X D 49-2491 GBPUAT, Pantnagar I C
6 CO-1 Selection from EC 398321 TNAU, Coimbatore I C
7 CO Soya-2 UGM21 X JS 335 TNAU, Coimbatore I C
8 Durga EC14437 X Durga JNKKV, Sehore, Jabalpur I C
9 Gaurav D60-9647 X EC7034 JNKKV, Sehore, Jabalpur I C
10 GS-1 Selection from Punjab 1 I C
11 GS-2 Selection from Geduld variety I C
12 Hardee D49-772 X Improved Pelican MACS, Pune I C
13 Hara soya Himso 1520 9 Bragg HPKVV, Palampur I C
14 Indirasoya-9 Secondary selection 8021 IGKVV, Raipur I C
15 Improved Pelican Tanloxi X PI 60406 MACS, Pune I C
16 JS-2 Selection from Tehari Garhwal material JNKKV, Sehore, Jabalpur I C
17 JS-71-05 Selection from Lee type exotic material JNKKV, Sehore, Jabalpur I D
18 JS-75-46 Improved Pelican X Semmes JNKKV, Sehore, Jabalpur I D
19 JS-76-205 Kalitur X Bragg JNKKV, Sehore, Jabalpur IV E
20 JS-79-81 Bragg X Hara soya-deciduous JNKKV, Sehore, Jabalpur IV E
21 JS-80-21 JS 75-1 X PK 7394 JNKKV, Sehore, Jabalpur I E
22 JS-90-41 PS 73-7 X Hark JNKKV, Sehore, Jabalpur IV E
23 JS-93-05 Secondary selection from PS-73-22 JNKKV, Sehore, Jabalpur V E
24 JS-335 JS78-77 X JS 75-5 JNKKV, Sehore, Jabalpur V E
25 Kalitur Indigenous Native Variety JNKKV, Sehore, Jabalpur V E
26 KB-79 Hardee X Monetta GKVI, Bangalore V E
27 KHSB-2 Manloxi X EC 39821 GKVI, Bangalore V E
28 Lee S-100 X CNS V E
29 LSB-1 Selection from MACS 330 ANGRAU, Hyderabad V E
30 MACS-13 Hampton X EC 7034 MACS, Pune V E
31 MACS-57 JS 2 X Improved Pelican MACS, Pune V E
32 MACS-58 JS 2 X Improved Pelican MACS, Pune V E
33 MACS-124 JS 2 X Improved Pelican MACS, Pune V E
34 MACS-450 Bragg X MACS 111 MACS, Pune V E
35 MAUS-1 Mutant from DS 87-14 MAUS, Parbhani V E
36 MAUS-2 Selection from 84 to 14 MAUS, Parbhani V E
37 MAUS-32 Selection from JS 80-21 MAUS, Parbhani V E
38 MAUS-47 PS 73-7 X Hark MAUS, Parbhani V E
39 MAUS-61 JS 71-1 X PK 7394 MAUS, Parbhani V E
40 MAUS-61-2 JS 80-21 X KB 60 MAUS, Parbhani II A
41 MAUS-71 JS 71-05 X JS 8738 MAUS, Parbhani II A
42 MAUS-81 KB74 X JS335 MAUS, Parbhani II A
43 Monetta Exotic X Variety EC 2587 MACS, Pune II A
44 NRC-2 Induced Mutant of Bragg DSR, Indore II A
45 NRC-7 Selection from S 6996 DSR, Indore II A
46 NRC-12 Induced Mutant of Bragg DSR, Indore II A
47 NRC-37 Gaurav X Punjab 1 DSR, Indore II A
48 Palam Soya JS72-451 X Punjab1 HPKVV, Palampur II D

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Table 1 continued
S. no. Name of the varieties Pedigree Releasing center Cluster Sub-population

49 PK-262 UPSM 97 X Hardee GBPUAT, Pantnagar II D

50 PK-308 T 31 X Hardee GBPUAT, Pantnagar II D
51 PK-327 UPSM 82 X Semmes GBPUAT, Pantnagar II A
52 PK-416 UPSM 534 X S38 GBPUAT, Pantnagar II A
53 PK-471 Hardee X Punjab 1 GBPUAT, Pantnagar II A
54 PK-472 Hardee X Punjab 1 GBPUAT, Pantnagar II D
55 PS-1024 PK 308 X PK 317 GBPUAT, Pantnagar II A
56 PS-1029 PK 262 X PK 317 GBPUAT, Pantnagar II A
57 PS-1042 Bragg X PK 416 GBPUAT, Pantnagar II A
58 PS-1092 PK 327 X PK 416 GBPUAT, Pantnagar II A
59 PS-1241 EC 7965 X Bragg GBPUAT, Pantnagar II D
60 Punjab-1 Selection from Nanking Variety PAU, Ludhiana III D
61 Pusa-16 CNS X Lee IARI, New Delhi III D
62 Pusa-22 Punjab 1 X Clark 63 IARI, New Delhi III D
63 Pusa-20 Bragg X Lee IARI, New Delhi III B
64 Pusa-24 Shelby X Bragg IARI, New Delhi III B
65 Pusa-37 Bragg X Java 16 IARI, New Delhi III D
66 Pusa-40 8-3 X Lee IARI, New Delhi III B
67 RAUS-5 Pusa 16 X JS 335 MPUA&T, Udaipur III D
68 Shilajeet Selection from 9309 GBPUAT, Pantnagar III D
69 Shivalik Selection from Segregating PK 73-55 HPKVV, Palampur III B
70 SL-96 Botato X JS 3 PAU, Ludhiana III B
71 SL-295 PK 416 X PS 564 PAU, Ludhiana III B
72 SL-525 PK 416 X PK 1023 PAU, Ludhiana III B
73 Type-49 Selection from Indigenous material MACS, Pune III B
74 VLS-1 Mutant of Bragg VPKAS, Almora III B
75 VLS-2 Selection from VHC 856007 VPKAS, Almora III B
76 VLS-21 Selection from VHC 3055 VPKAS, Almora III B
77 VLS-47 Selection from KHSF-3-1-1 VPKAS, Almora III B
78 Samrat Farmers variety III B

calculated [24]. The Jaccards similarity index was run for range of genetic clusters from value of K = 210
calculated using NTSYS-pc version 2.02e (Applied Bio- using a model without admixture and correlated allele
Statistics, Inc., Setauket, NY, USA) package to compute frequencies. The authors used the burn-in period of
pairwise Jaccards similarity coefficients [25] and this 100,000 and Monte Carlo Markov Chain replicates of
similarity matrix was used in cluster analysis using an 100,000 [28] and the analysis was repeated five times. Ln
Unweighted Pair-Group Method with Arithmetic averages (PD) was derived for each K and then plotted to find the
(UPGMA) to obtain a dendrogram. NTSYS pc version 2.02 plateau of the K values [29].
[26] was also used to perform Principal Coordinate
Analysis (PCoA) to identify multidimensional
relationship that describes portions of the genetic Results and Discussion
variance in the data set. Genetic similarity coefficient
was calculated for each pair of cultivars [3] to determine SSR Polymorphism
the effectiveness of the group of SSR loci in distinguishing
each of the 78 varieties. In the present study, 39 STMS markers were used to
Model-based cluster analysis was performed to infer genotype 78 soybean varieties. The authors have used
genetic structure and to define the number of clusters (gene single locus SSR markers since they provide more reliable
pools) in the dataset using the software STRUCTURE scoring of genotypes as compared to multi-locus SSRs.
version 2.3.4 [27]. The membership of each genotype was Reproducibility of the amplification patterns was checked

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Understanding genetic relationship and population structure of Indian soybean varieties

Table 2 Locus, linkage group, chromosome number, range of allele size, no. of alleles per locus, PIC values, major allelic frequency, Dp, MI
and Rp
S. no. Locus Linkage Chromosome Range of No. of PIC Major allelic Discrimination Marker Resolving
group number alleles size alleles values frequency power index power

1 Satt211 A1 5 150190 3 0.628 0.438 0.637 1.885 1.999

2 Satt276 A1 5 310400 4 0.685 0.378 0.697 2.743 1.999
3 Satt493 A2 8 250275 4 0.678 0.467 0.687 2.714 1.999
4 Satt415 B1 11 300380 3 0.073 0.962 0.038 0.219 0.151
5 Satt426 B1 11 200230 4 0.653 0.513 0.652 2.613 1.955
6 Satt063 B2 14 100155 7 0.735 0.218 0.851 5.149 1.999
7 Satt126 B2 14 125155 2 0.813 0.703 0.399 1.626 1.081
8 Satt194 C1 4 210250 4 0.401 0.75 0.406 1.602 0.999
9 Satt524 C1 4 175 1 0 1 0 0
10 Satt100 C2 6 140165 3 0.578 0.461 0.583 0.192 1.998
11 Satt170 C2 6 7590 3 0.184 0.911 0.165 0.554 0.352
12 Sat_114 D2 17 260315 4 0.668 0.426 0.669 2.673 1.998
13 Satt498 D2 17 200250 2 0.025 0.974 0.506 0.051 0.102
14 Satt129 D1a 1 110150 4 0.672 0.387 0.678 2.688 1.999
15 Satt184 D1a 1 150180 4 0.597 0.583 0.567 2.389 1.666
16 Satt216 D1b 2 140220 4 0.632 0.5 0.633 2.531 1.999
17 Satt459 D1b 2 200 1 0 1 0 0
18 Satt231 E 15 100110 2 0.496 0.544 0.502 0.992 1.818
19 Satt411 E 15 100165 6 0.795 0.359 0.781 4.77 1.999
20 Satt072 F 13 200 1 0 1 0 0
21 SOYHSP176 F 13 110150 7 0.793 0.328 0.806 5.556 1.999
22 Satt038 G 18 155190 4 0.609 0.545 0.617 2.436 1.817
23 Sat_187 G 18 1 0 1 0 0
24 Sat_127 H 12 210300 6 0.759 0.381 0.771 4.558 1.999
25 Satt434 H 12 310360 6 0.749 0.351 0.759 4.499 1.999
26 Sat_105 I 20 220275 4 0.851 0.375 0.721 3.403 1.994
27 Satt587 I 20 125 1 0 1 0 0
28 Satt046 J 16 180 1 0 1 0 0
29 Satt431 J 16 190260 6 0.778 0.302 0.797 4.671 1.999
30 Satt539 K 9 175195 5 0.721 0.407 0.725 3.604 1.999
31 SOYPRP1 K 9 120150 3 0.338 0.8 0.342 1.015 0.799
32 Sat_099 L 19 210285 5 0.481 0.417 0.659 2.407 1.999
33 Satt278 L 19 200280 2 0.264 0.842 0.268 0.529 0.628
34 Satt346 M 7 195210 2 0.396 0.739 0.391 0.793 1.041
35 Sat_084 N 3 175195 5 0.931 0.553 0.637 4.659 1.783
36 GMABABE N 3 155180 4 0.591 0.536 0.579 2.364 2.086
37 Satt109 O 10 170300 6 0.773 0.3 0.801 4.639 1.997
38 Satt132 O 10 150200 3 0.53 0.521 0.52 1.591 1.912
39 GMSC51 150180 3 0.616 0.421 0.637 1.848 1.999
Average 3.59 0.59 0.54 0.59 2.54 1.64

by performing two independent reactions for each primer alleles per marker (Table 2). The highest number of alleles
pair. The amplification profile of these markers was con- was detected at locus Satt063 and SOYSHP176 with a total
sistent uniformly and no new differences were detected. A of 7 alleles. The respective values for overall genetic
total of 140 alleles were scored from these 39 primer pairs variability for Polymorphism Information Content (PIC),
and 84.61% were found polymorphic. The number of Resolving Power (Rp), Major allelic frequency, Marker
alleles per locus varied from 2 to 7, with an average of 3.59 index (MI) and Discrimination Power (Dp) across all the

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 D. K. Chauhan et al.

78 genotypes are given in Table 2. PIC values ranged from marker. In another study, a lower mean Rp value (1.0) was
0.073 (Satt415) to 0.932 (Satt084), with an average value reported in genetic diversity analysis in emmer wheat using
of 0.59. The present study reported that the genetic diver- SSR markers [39]. The frequency of major alleles was also
sity index is positively correlated with the number of calculated which ranged from 0.218 to 1 with an average
alleles at a given locus, similar to that earlier reported [30]. value of 0.54. Discrimination power (Dp) was calculated
The genetic diversity observed in the present study is for all the polymorphic markers, and varied from 0.038
comparable to those reported in earlier studies [31], 4 (Satt415) to 0.851 (Satt063) with an average of 0.59.
alleles per locus were detected with an average PIC value
of 0.58. In another study, an average of 4.78 alleles per Phylogenetic Relationships Among the Soybean
locus was observed among 92 soybean accessions of Hubei Varieties
using SSR markers [32]. A slightly higher SSR diversity
among soybean accessions was also reported, where 6.91 The genetic relationship among the soybean varieties was
and 6.3 alleles per locus and an average polymorphic assessed by a cluster analysis of the similarity matrix using
information content of 0.68 and 0.63, respectively, were SSR data. A UPGMA cluster diagram grouped all the 78
reported [33, 34]. In another study, a lower SSR diversity soybean varieties into five major clusters, I, II, III, IV and
was observed, where they detected 3.23 alleles per locus V (Fig. 1) and the clusters were comprised of 19, 20, 19, 3
and an average PIC value of 0.38 in 48 vegetable soybean and 17 genotypes, respectively. The genetic similarity
accession using 22 polymorphic EST-SSRs [35]. The coefficients found in the cultivar comparison matrix were
possible explanation for this observation is that ESR-SSRs relatively low. The cluster I is further divided into two sub-
are mostly conserved sequences and show lesser variations clusters, and possesses genotypes released from different
across genotypes, whereas, in the present study, genomic- breeding centers viz., Pantnagar, Jabalpur and Pune, but
SSRs for genetic diversity evaluation were used. MI values their parentages were based on US introductions. Cluster II
ranged from 0.051 (Satt498) to 5.556 (SOYSHP176) with consists of all the varieties of PK, PS and NRC series
an average value of 2.54. In the present study, the average released from Pantnagar and Indore, respectively and are
genetic similarity (GS) among the 78 soybean genotypes grouped into different, but same sub-cluster of cluster II.
was found to be 0.41 and most of the values lied between Genotypes such as MAUS61-2, MAUS71 and MAUS81
0.2 and 0.5, reflecting relatively high degree of genetic released from Marathwada Agricultural University
diversity among the genotypes. The levels of average GS (MAUS), Parbhani are also grouped together in cluster II.
observed was lower as compared to those earlier reported Similarly, all the genotypes released from New Delhi,
[31], where an average GS value of 0.70 was observed and Ludhiana and Almora are grouped into different sub-clus-
42% of the accessions were having values higher than 0.75 ters of cluster III, respectively. Cluster IV consists of only
among 23 soybean genotypes representing several inde- the genotypes released from Jabalpur (JS series). All the
pendent breeding sources from Southeastern Europe and varieties of MACS series released from Maharashtra
five plant introductions from Western Europe and Canada, Academy for Cultivation of Sciences (MACS), Pune,
using 20 SSR markers. A slightly higher average genetic belong to same sub-cluster of cluster V. Genotypes
similarity values were also reported [36], where the aver- released from Parbhani viz., MAUS1, MAUS2, MAUS32,
age genetic similarities of 0.44 and 0.50 were observed for MAUS47 and MAUS61 are also clustered together in
40 plant introductions from several Asian and European cluster V. Thus, genotypes released from various parts of
countries and 39 North American elite cultivars, respec- India showed diverse clustering patterns. This may be due
tively. On the other hand, an average genetic dissimilarity to the use of diverse parents and breeding material for the
coefficient of 0.63 and 0.815 was reported for 186 development of these varieties. Principal coordinate anal-
Brazilian soybean cultivars, and for 45 Canadian soybean ysis (PCoA) which is used to show multiple dimensions of
cultivars and 37 exotic germplasm accessions, respectively the distribution of the genotypes in a scatter-plot (Fig. 2)
[34, 37], which was similar to GS reported in the present which was at par with that of grouping as shown in den-
study. Similar results based on AFLP were reported earlier drogram (Fig. 1).
[38], where they recorded an average GS of 0.563. The varieties Pusa-16, Pusa-20, Pusa-22, Pusa-40,
The resolving power (Rp), a feature of marker that Pusa-24 and Pusa-37 released from IARI, New Delhi are
indicates the discriminatory potential of the primer, ranged clustered in the same sub sub-cluster because they have
from 0.102 (satt498) to 2.086 (GMABABE) with an been derived either from Lee or Bragg varieties. Simi-
average value of 1.64 (Table 2). Rp value takes into larly, the varieties PK-262, PK-308, PK-472 derived
account the number of polymorphic bands in a pattern and from Hardee variety and released from Pantnagar are
the informative value of each individual polymorphic band, clustered in the same sub sub-cluster of dendrogram. The
thus provides a measure of discriminatory power of a PS-1024, PS-1029, PS-1024, PS-1092 varieties derived

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Understanding genetic relationship and population structure of Indian soybean varieties

Fig. 1 UPGMA dendrogram showing genetic relationship among soybean varieties based on SSR markers

from either PK-317 or PK416 and released from Pant- Population Structure
nagar also fall in the same sub sub-cluster. The varieties
MACS-57, MACS-58, MACS-124 and MACS-450 The SSR marker data were used for model-based clustering
released from Pune, derived from common parents viz., using the software STRUCTURE version 2.3.4 for deter-
JS-2 and Improved pelican, are clustered into same sub- mining the genetic structure among the 78 soybean vari-
cluster of cluster V. Similarly, varieties of the MAUS, eties. Based on maximum likelihood and delta K (DK)
NRC, VLS, JS and SL series are clustered in same sub values, the number of optimum subgroups was five. The
sub-cluster of the dendrogram based on their origin, level of genetic differentiation or Wrights fixation index
pedigree and releasing center. It is because the con- (Fst) was calculated through STRUCTURE programme
cerned breeding centre has used the similar plant mate- between the five soybean sub-populations assigned to the
rial for the breeding of these varieties. The seven SSR corresponding AE and the inferred population structure is
markers viz., Satt063, SOYHSP176, Satt411, Sat_127, given in Fig. 3. The sub-populations (AE) had an Fst
Satt434, Satt431 and Satt109, which are reported to value of 0.339, 0.338, 0.251, 0.275 and 0.201, respectively,
produce the maximum number of alleles/marker, having with an average value of 0.281, indicating moderate pop-
high discrimination potential and together are effective ulation structure. The first inferred population A consists of
to differentiate, discriminate and identify all the soybean genotypes released from Indore, Pantnagar and Parbhani.
varieties used in the present study, thus providing con- The sub-population B includes varieties belonging to VLS,
cluding evidence about the use of SSR markers for PUSA and SL series released from Almora, New Delhi and
genetic differentiation and identification of soybean Ludhiana, respectively. The sub-population C consists of
varieties. varieties released from different breeding centers viz.,

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 D. K. Chauhan et al.

Fig. 2 3-D principal

component analysis depicting
genetic relationship among 78
soybean varieties

Pantnagar, Jabalpur, Coimbatore and Pune, but their sub-population A have been developed using different
parentages were based on US introductions. Varieties breeding material having diverse origin, where as the
released mostly from New Delhi and Pantnagar belong to genotypes of sub-population E have originated from simi-
sub-population D. Similarly, varieties released from Pune, lar breeding material released from Jabalpur. Thus,
Parbhani, Bangalore and Jabalpur are grouped into sub- groupings of soybean varieties through STRUCTURE
population E. Sub-population A were found to be geneti- analysis are well in agreement with the distance-based
cally more differentiated followed by B, D, C and E, based clustering and PCoA, classifying the genotypes on the basis
on Fst value. The reason lies that varieties belonging to of origin, pedigree and releasing centre.

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Understanding genetic relationship and population structure of Indian soybean varieties

Fig. 3 The population structure of 78 soybean varieties as obtained from STRUCTURE 2.3.4 software

In summary, the results of STRUCTURE and Fst anal- Compliance with Ethical Standards
ysis were in good agreement with the results obtained
Conflict of interest The authors declare that they have no conflict of
through phylogenetic tree-based, similarity coefficient interest.
distribution and PCoA analyses, grouping the genotypes on
the basis of origin, pedigree and releasing centre and
confirmed the presence of statistically high genetic diver- References
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