Open Access

Analysis of Population Structure and Genetic Diversity in Rice Germplasm Using SSR Markers: An Initiative Towards Association Mapping of Agronomic Traits in Oryza Sativa

  • Vishnu Varthini Nachimuthu1Email author,
  • Raveendran Muthurajan3,
  • Sudhakar Duraialaguraja3,
  • Rajeswari Sivakami2,
  • Balaji Aravindhan Pandian2,
  • Govinthraj Ponniah5,
  • Karthika Gunasekaran4,
  • Manonmani Swaminathan2,
  • Suji K K3 and
  • Robin Sabariappan6
Rice20158:30

https://doi.org/10.1186/s12284-015-0062-5

Received: 30 October 2014

Accepted: 8 August 2015

Published: 26 September 2015

Abstract

Background

Genetic diversity is the main source of variability in any crop improvement program. It serves as a reservoir for identifying superior alleles controlling key agronomic and quality traits through allele mining/association mapping. Association mapping based on LD (Linkage dis-equilibrium), non-random associations between causative loci and phenotype in natural population is highly useful in dissecting out genetic basis of complex traits. For any successful association mapping program, understanding the population structure and assessing the kinship relatedness is essential before making correlation between superior alleles and traits. The present study was aimed at evaluating the genetic variation and population structure in a collection of 192 rice germplasm lines including local landraces, improved varieties and exotic lines from diverse origin.

Results

A set of 192 diverse rice germplasm lines were genotyped using 61 genome wide SSR markers to assess the molecular genetic diversity and genetic relatedness. Genotyping of 192 rice lines using 61 SSRs produced a total of 205 alleles with the PIC value of 0.756. Population structure analysis using model based and distance based approaches revealed that the germplasm lines were grouped into two distinct subgroups. AMOVA analysis has explained that 14 % of variation was due to difference between with the remaining 86 % variation may be attributed by difference within groups.

Conclusions

Based on these above analysis viz., population structure and genetic relatedness, a core collection of 150 rice germplasm lines were assembled as an association mapping panel for establishing marker trait associations.

Keywords

RiceGenetic diversityPopulation structurePolymorphism information contentMolecular varianceAssociation mapping

Background

Rice, being the staple food crop for more than 50 % of the world population is cultivated in 163 million hectares with the production of 491 million tonnes. About 90 % of the world’s rice is produced in Asia and India contributes 20 % of the world’s production. This record level production and productivity is due to the availability and exploitation of rich genetic diversity existing in rice germplasm of India. For precise genetic manipulation of complex quantitative traits like, yield, tolerance against biotic/abiotic stresses, quality etc., understanding the genetic/molecular basis of target traits needs to be investigated thoroughly.

The genetic basis of important agronomic traits has been unraveled through Quantitative Trait Loci (QTL) mapping either through linkage mapping (bi-parental mapping populations) or through LD mapping (natural populations). Although traditional linkage based QTL-mapping has become an important tool in gene tagging of crops, it has few limitations viz., 1) classical linkage mapping involves very high cost; 2) it has low resolution as it can resolve only a few alleles and 3) it has limitations towards fine mapping of QTLs as it needs BC-NILs. These limitations can be overcome by the LD based approach of “Association Mapping” using the natural populations. Association mapping serves as a tool to mine the elite genes by structuring the natural variation present in a germplasm. It was successfully exploited in various crops such as rice, maize, barley, durum wheat, spring wheat, sorghum, sugarcane, sugarbeet, soybean, grape, forest tree species and forage grasses (Abdurakhmonov and Abdukarimov 2008).

Before performing an association analysis in a population, it is essential to determine the population structure which can reduce type I and II errors in association mapping due to unequal allele frequency distribution between subgroups that causes spurious association between molecular markers and trait of interest (Pritchard et al. 2000). Similar attempts were recently undertaken to define population structure in rice using different germplasm lines and by developing core collection from national collections and international collections (Ebana et al. 2008; Jin et al. 2010; Zhang et al. 2011; Agrama et al. 2010 and Liakat Ali et al. 2011). Simple Sequence repeat (SSR) markers have been commonly used in genetic diversity studies in rice because of high level of polymorphism which helps to establish the relationship among the individuals even with less number of markers (McCouch et al. 1997). For similar studies, SSR markers were used alone by Jin et al. (2010); Hesham et al. (2008); Sow et al. (2014); Das et al. (2013) and Choudhury et al. (2013) or along with SNP markers by Courtois et al. (2012) and Zhao et al. (2011). The objectives of this present study were to evaluate the genetic variation and to examine the population structure of 192 rice germplasm accessions that comprises of local landraces, improved varieties and exotic lines from diverse origin.

Results

Genetic Diversity

All the 192 rice germplasm lines were genotyped using 61 SSR (microsatellite) markers which produced a total of 205 alleles (Additional file 1: Figure S1). Among these 205 alleles, 5 % were considered as rare (showed an allele frequency of < 5 %). The number of alleles per loci varied from 2 to 7 with an average of 3 alleles per locus. The highest number of alleles were detected for the loci RM316 (7) and the lowest was detected for a group of markers viz., RM171, RM284, RM455, RM514, RM277, RM 5795, HvSSR0247, RM 559, RM416 and RM1227. PIC value represents the relative informativeness of each marker and in the present study, the average PIC value was found to be 0.468. The highest genetic diversity is explained by the landraces included in this study with the mean PIC value of 0.416. PIC values ranged between 0.146 for RM17616 to 0.756 for RM316. Heterozygosity was found to be very low which may be due to autogamous nature of rice. Expected heterozygosity or Gene diversity (He) computed according to Nei (1973) varied from 0.16 (RM17616) to 0.75 (RM287) with the average of 0.52 (Table 1).
Table 1

Details of SSR loci used for genotyping in the 192 rice accessions and their genetic diversity parameters

S. no

Marker

Chromosome no.

SSR MOTIF

Min molecular weight

Maximum molecular weight

Number of alleles

Gene diversity

Heterozygosity

PIC value

1

RM237

1

(CT)18

110

143

4

0.61

0.89

0.545

2

RM1

1

(GA)26

70

105

3

0.63

0.12

0.552

3

RM5

1

(GA)14

105

115

3

0.64

0.6

0.557

4

RM312

1

(ATTT)4(GT)9

95

105

3

0.3

0.03

0.281

5

RM283

1

(GA)18

149

155

3

0.42

0.02

0.377

6

RM452

2

(GTC)9

195

245

3

0.54

0.83

0.448

7

HvSSR0247

2

 

395

400

2

0.5

0.18

0.373

8

RM555

2

(AG)11

135

145

3

0.59

0.04

0.517

9

RM211

2

(TC)3A(TC)18

140

160

3

0.52

0.08

0.463

10

RM324

2

(CAT)21

135

180

5

0.74

0.06

0.695

11

RM514

3

(AC)12

245

252

2

0.19

0

0.171

12

RM55

3

(GA)17

220

225

3

0.44

0.07

0.4

13

RM231

3

(CT)16

170

200

3

0.59

0.12

0.511

14

RM416

3

(GA)9

110

115

2

0.42

0.01

0.335

15

RM442

3

(AAG)10

260

275

3

0.5

0.03

0.448

16

RM 16643

4

(GGGA)5

165

200

5

0.73

0.05

0.685

17

RM 559

4

(AACA)6

160

165

2

0.39

0.01

0.311

18

RM17377

4

(AG)25

140

175

4

0.67

0.04

0.625

19

RM7585

4

(TCTT)6

140

160

4

0.46

0.02

0.422

20

RM17616

4

(TC)14

165

180

3

0.16

0

0.146

21

RM413

5

(AG)11

75

100

4

0.59

0.25

0.548

22

RM178

5

(GA)5(AG)8

110

115

3

0.39

0.04

0.35

23

RM 161

5

(AG)20

160

180

3

0.29

0.04

0.258

24

RM7293

5

(ATGT)6

140

150

3

0.64

0.1

0.558

25

RM1024

5

(AC)13

125

140

3

0.32

0.02

0.298

26

RM 162

6

(AC)20

220

240

3

0.37

0.03

0.34

27

RM7434

6

(GTAT)10

120

145

5

0.66

0.19

0.614

28

RM19620

6

(GTG)7

160

177

3

0.21

0.03

0.204

29

RM5963

6

(CAG)9

160

175

3

0.48

0.15

0.38

30

RM11

7

(GA)17

120

150

4

0.71

0.72

0.661

31

RM118

7

(GA)8

155

185

4

0.62

0.77

0.543

32

RM125

7

(GCT)8

105

130

4

0.61

0.89

0.544

33

RM455

7

(TTCT)5

130

135

2

0.24

0.02

0.208

34

HvSSR0740

7

 

340

400

4

0.7

0.21

0.65

35

RM44

8

(GA)16

95

107

4

0.62

0.77

0.559

36

RM433

8

(AG)13

235

270

3

0.55

0.81

0.446

37

RM447

8

(CTT)8

105

120

4

0.64

0.16

0.572

38

RM284

8

(GA)8

140

145

2

0.21

0.02

0.189

39

RM408

8

(CT)13

120

125

3

0.52

0.01

0.465

40

RM25

8

(GA)18

120

140

4

0.73

0.37

0.679

41

RM256

8

(CT)21

125

140

4

0.73

0

0.681

42

RM105

9

(CCT)6

100

140

3

0.41

0.48

0.37

43

RM107

9

(GA)7

280

300

3

0.48

0

0.425

44

RM 215

9

(CT)16

140

150

3

0.6

0.01

0.528

45

RM 316

9

(GT)8-(TG)9(TTTG)4(TG)4

160

235

7

0.79

0.75

0.756

46

RM205

9

(CT)25

110

140

4

0.72

0

0.665

47

RM171

10

(GATG)5

320

330

2

0.24

0.02

0.211

48

RM271

10

(GA)15

90

99

3

0.66

0.19

0.588

49

RM590

10

(TCT)10

120

140

4

0.57

0.04

0.516

50

RM474

10

(AT)13

240

280

3

0.61

0

0.537

51

RM222

10

(CT)18

200

220

3

0.63

0.02

0.557

52

RM144

11

(ATT)11

160

240

5

0.69

0.18

0.644

53

RM287

11

(GA)21

95

110

5

0.75

0.2

0.706

54

RM 536

11

(CT)16

240

270

5

0.74

0.06

0.701

55

RM224

11

(AAG)8(AG)13

120

155

5

0.65

0.07

0.617

56

RM206

11

(CT)21

130

145

4

0.34

0

0.319

57

RM277

12

(GA)11

115

120

2

0.45

0.08

0.35

58

RM 5795

12

(AGC)8

140

145

2

0.5

0.03

0.374

59

RM1227

12

(AG)15

160

180

2

0.31

0.02

0.262

60

RM20A

12

(ATT)14

220

240

3

0.54

0

0.476

61

RM2197

12

(AT)23

135

140

2

0.44

0

0.341

 

Average

    

3

0.52

0.18

0.468

STRUCTURE Analysis

Population structure of the 192 germplasm lines was analysed by Bayesian based approach. The estimated membership fractions of 192 accessions for different values of k ranged between 2 and 5 (Fig. 1). The log likelihood revealed by structure showed the optimum value as 2 (K = 2). Similarly the maximum of adhoc measure ΔK was found to be K = 2 (Fig. 2), which indicated that the entire population can be grouped into two subgroups (SG1 and SG2). Based on the membership fractions, the accessions with the probability of ≥ 80 % were assigned to corresponding subgroups with others categorized as admixture (Fig. 3).
Fig. 1

Pattern of variation of 192 accessions based on 61 SSR markers. The K values are based on the run with highest likelihood. Bar length represent the membership probability of accessions belonging to different subgroups

Fig. 2

Population structure of 192 accessions based on 61 SSR markers (K = 2) and Graph of estimated membership fraction for K = 2. The maximum of adhoc measure ΔK determined by structure harvester was found to be K = 2, which indicated that the entire population can be grouped into two subgroups (SG1 and SG2)

Fig. 3

Population structure of 192 accessions arranged based on inferred ancestry. Based on the membership fractions, the accessions with the probability of ≥ 80 % were assigned to corresponding subgroups with others categorized as admixture

SG1 consisted of 134 accessions with most of the landraces and varieties of Indian origin and SG2 consisted of 38 accessions which composed of non Indian accessions. Twenty accessions were retained to be admixture. The subgroup SG1 was dominated by indica subtype whereas the subgroup SG2 consisted mostly of japonica group. When the number of subgroups increased from two to five, the accessions in both the subgroups were classified into sub-sub groups (Table 2). As SG1 consisted of 134 accessions mostly of Indian origin, an independent STRUCTURE analysis was performed for this subgroup. ΔK showed its maximum value for K =3 which indicated that SG1 could be further classified into three sub-sub groups (Fig. 4). The differentiation in origin and seasonal differentiation of rice varieties contributed for this clustering.
Table 2

Population structure group of accessions based on Inferred ancestry values

G. no.

Genotypes

Inferred ancestry

Structure group

Subtype

  

Q1

Q2

  

RG1

Mapillai samba

0.977

0.023

SG1

Indica

RG2

CK 275

0.991

0.009

SG1

Indica

RG3

Senkar

0.992

0.008

SG1

Indica

RG4

Murugankar

0.964

0.036

SG1

Indica

RG5

CHIR 6

0.811

0.189

SG1

Indica

RG6

CHIR 5

0.989

0.011

SG1

Indica

RG7

Kudai vazhai

0.975

0.025

SG1

Indica

RG8

CHIR 8

0.759

0.241

SG1

Indica

RG9

Kuruvai kalanjiyam

0.971

0.029

SG1

Indica

RG10

Nava konmani

0.99

0.01

SG1

Indica

RG11

CHIR 10

0.869

0.131

SG1

Indica

RG12

Vellai chithiraikar

0.802

0.198

SG1

Indica

RG13

CHIR 2

0.983

0.017

SG1

Indica

RG14

Jothi

0.992

0.008

SG1

indica

RG15

Palkachaka

0.962

0.038

SG1

indica

RG16

Thooyala

0.934

0.066

SG1

indica

RG17

Chivapu chithiraikar

0.994

0.006

SG1

indica

RG18

CHIR 11

0.976

0.024

SG1

indica

RG19

Koolavalai

0.99

0.01

SG1

indica

RG20

Kalvalai

0.982

0.018

SG1

indica

RG21

Mohini samba

0.963

0.037

SG1

indica

RG22

IR 36

0.989

0.011

SG1

indica

RG23

Koombalai

0.975

0.025

SG1

indica

RG24

Tadukan

0.674

0.326

AD

indica

RG25

Sorna kuruvai

0.986

0.014

SG1

indica

RG26

Rascadam

0.637

0.363

AD

indica

RG27

Muzhi karuppan

0.991

0.009

SG1

indica

RG28

Kaatukuthalam

0.828

0.172

SG1

indica

RG29

Vellaikattai

0.987

0.013

SG1

indica

RG30

Poongar

0.987

0.013

SG1

indica

RG31

Chinthamani

0.985

0.015

SG1

indica

RG32

Thogai samba

0.975

0.025

SG1

indica

RG33

Malayalathan samba

0.701

0.299

AD

indica

RG34

RPHP 125

0.986

0.014

SG1

indica

RG35

CK 143

0.993

0.007

SG1

indica

RG36

Kattikar

0.913

0.087

SG1

indica

RG37

Shenmolagai

0.994

0.006

SG1

indica

RG38

Velli samba

0.887

0.113

SG1

indica

RG39

Kaatu ponni

0.975

0.025

SG1

indica

RG40

kakarathan

0.989

0.011

SG1

indica

RG41

Godavari samba

0.941

0.059

SG1

indica

RG42

Earapalli samba

0.978

0.022

SG1

indica

RG43

RPHP 129

0.01

0.99

SG2

indica

RG44

Mangam samba

0.968

0.032

SG1

indica

RG45

RPHP 105

0.943

0.057

SG1

indica

RG46

IG 4(EC 729639- 121695)

0.977

0.023

SG1

indica

RG47

Machakantha

0.976

0.024

SG1

indica

RG48

Kalarkar

0.992

0.008

SG1

indica

RG49

Valanchennai

0.972

0.028

SG1

indica

RG50

Sornavari

0.957

0.043

SG1

indica

RG51

RPHP 134

0.909

0.091

SG1

indica

RG52

ARB 58

0.987

0.013

SG1

indica

RG53

IR 68144-2B-2-2-3-1-127

0.708

0.292

AD

indica

RG54

PTB 19

0.981

0.019

SG1

indica

RG55

IG 67(EC 729050- 120988)

0.957

0.043

SG1

indica

RG56

RPHP 59

0.031

0.969

SG2

Aromatic

RG57

RPHP 103

0.656

0.344

AD

Aromatic

RG58

Kodaikuluthan

0.828

0.172

SG1

indica

RG59

RPHP 68

0.981

0.019

SG1

indica

RG60

Rama kuruvaikar

0.985

0.015

SG1

indica

RG61

Kallundai

0.939

0.061

SG1

indica

RG62

Purple puttu

0.994

0.006

SG1

indica

RG63

IG 71(EC 728651- 117588)

0.823

0.177

SG1

aus

RG64

Ottadaiyan

0.994

0.006

SG1

indica

RG65

IG 56(EC 728700- 117658

0.435

0.565

AD

Aromatic

RG66

Jeevan samba

0.876

0.124

SG1

indica

RG67

RPHP 106

0.915

0.085

SG1

indica

RG68

IG 63(EC 728711- 117674)

0.049

0.951

SG2

Tropical Japonica

RG69

RPHP 48

0.025

0.975

SG2

Aromatic

RG70

Karthi samba

0.987

0.013

SG1

indica

RG71

IG 27(IC 0590934- 121255)

0.444

0.556

AD

indica

RG72

Aarkadu kichili

0.99

0.01

SG1

indica

RG73

Kunthali

0.969

0.031

SG1

indica

RG74

ARB 65

0.83

0.17

SG1

indica

RG75

IG 21(EC 729334- 121355)

0.091

0.909

SG2

japonica

RG76

Matta kuruvai

0.934

0.066

SG1

indica

RG77

Karuthakar

0.994

0.006

SG1

indica

RG78

RPHP 165

0.99

0.01

SG1

indica

RG79

Manavari

0.704

0.296

AD

indica

RG80

IG 66(EC 729047- 120985)

0.992

0.008

SG1

indica

RG81

CB-07-701-252

0.977

0.023

SG1

indica

RG82

Thooyamalli

0.994

0.006

SG1

indica

RG83

RPHP 93

0.153

0.847

SG2

indica

RG84

Velsamba

0.99

0.01

SG1

indica

RG85

RPHP 104

0.898

0.102

SG1

indica

RG86

RPHP 102

0.993

0.007

SG1

indica

RG87

IG 40(EC 728740- 117705)

0.98

0.02

SG1

indica

RG88

Saranga

0.988

0.012

SG1

indica

RG89

IR 83294-66-2-2-3-2

0.125

0.875

SG2

japonica

RG90

IG 61(EC 728731- 117696)

0.843

0.157

SG1

indica

RG91

IG 23(EC 729391- 121419)

0.852

0.148

SG1

Aus

RG92

IG 49(EC 729102- 121052)

0.945

0.055

SG1

indica

RG93

uppumolagai

0.987

0.013

SG1

indica

RG94

Karthigai samba

0.993

0.007

SG1

indica

RG95

Jeeraga samba

0.685

0.315

SG1

indica

RG96

RP-BIO-226

0.833

0.167

SG1

indica

RG97

Varigarudan samba

0.975

0.025

SG1

indica

RG98

IG 5(EC 729642- 121698)

0.012

0.988

SG2

japonica

RG99

IG 31(EC 728844- 117829)

0.813

0.187

SG1

indica

RG100

IG 7(EC 729598- 121648)

0.008

0.992

SG2

japonica

RG101

RPHP 52

0.991

0.009

SG1

indica

RG102

Varakkal

0.958

0.042

SG1

indica

RG103

Mattaikar

0.732

0.268

AD

indica

RG104

IG 53(EC 728752- 117719)

0.005

0.995

SG2

Temperate japonica

RG105

IG 6(EC 729592- 121642)

0.204

0.796

SG2

Temperate japonica

RG106

Katta samba

0.872

0.128

SG1

indica

RG107

RH2-SM-1-2-1

0.606

0.394

AD

indica

RG108

Red sirumani

0.93

0.07

SG1

indica

RG109

Vadivel

0.977

0.023

SG1

indica

RG110

Norungan

0.991

0.009

SG1

indica

RG111

IG 20(EC 729293- 121310)

0.113

0.887

SG2

indica

RG112

IG 35(EC 728858- 117843)

0.027

0.973

SG2

japonica

RG113

IG 45(EC 728768- 117736)

0.017

0.983

SG2

japonica

RG114

RPHP 159

0.008

0.992

SG2

aromatic rice

RG115

IG 43(EC 728788- 117759)

0.992

0.008

SG1

indica

RG116

RPHP 27

0.52

0.48

AD

Tropical Japonica

RG117

IG 65(EC 729024- 120958)

0.974

0.026

SG1

indica

RG118

Ponmani samba

0.973

0.027

SG1

indica

RG119

Ganthasala

0.993

0.007

SG1

indica

RG120

Thattan samba

0.949

0.051

SG1

indica

RG121

IG 74(EC 728622- 117517)

0.16

0.84

SG2

japonica

RG122

Kaliyan samba

0.245

0.755

AD

indica

RG123

IG 2(EC 729808-121874)

0.56

0.44

AD

japonica

RG124

IG 29(EC 728925- 117920)

0.059

0.941

SG2

Tropical Japonica

RG125

RPHP 55

0.963

0.037

SG1

indica

RG126

Kallimadayan

0.984

0.016

SG1

indica

RG127

IG 10(EC 729686- 121743)

0.066

0.934

SG2

aromatic

RG128

IG 75(EC 728587- 117420)

0.008

0.992

SG2

japonica

RG129

IG 38(EC 728742 - 117707)

0.02

0.98

SG2

Tropical japonica

RG130

IG 39(EC 728779- 117750)

0.012

0.988

SG2

indica

RG131

RPHP 90

0.991

0.009

SG1

indica

RG132

IG 33(EC 728938- 117935)

0.162

0.838

SG2

Tropical Japonica

RG133

IG 42(EC 728798- 117774)

0.495

0.505

AD

indica

RG134

IG 9(EC 729682- 121739)

0.019

0.981

SG2

indica

RG135

RPHP 161

0.849

0.151

SG1

indica

RG136

IG 8(EC 729601- 121651)

0.883

0.117

SG1

indica

RG137

IG 37(EC 728715- 117678)

0.005

0.995

SG2

Tropical Japonica

RG138

Sigappu kuruvikar

0.979

0.021

SG1

indica

RG139

RPHP 138

0.917

0.083

SG1

indica

RG140

Raja mannar

0.989

0.011

SG1

indica

RG141

IG 44(EC 728762- 117729)

0.134

0.866

SG2

indica

RG142

Sasyasree

0.989

0.011

SG1

indica

RG143

IG 46(IC 471826- 117647)

0.073

0.927

SG2

indica

RG144

Chetty samba

0.993

0.007

SG1

indica

RG145

IG 60(EC 728730- 117695)

0.033

0.967

SG2

indica

RG146

IR 75862-206

0.013

0.987

SG2

Tropical Japonica

RG147

IG 58(EC 728725- 117689)

0.011

0.989

SG2

japonica

RG148

Chinna aduku nel

0.798

0.202

SG1

indica

RG149

RH2-SM-2-23

0.296

0.704

AD

indica

RG150

IG 14(IC 517381- 121422)

0.775

0.225

AD

indica

RG151

IG 32(EC 728838- 117823)

0.065

0.935

SG2

japonica

RG152

RPHP 47

0.989

0.011

SG1

indica

RG153

Sembilipiriyan

0.933

0.067

SG1

indica

RG154

IG 48(EC 729203- 121195)

0.006

0.994

SG2

indica

RG155

Sona mahsuri

0.889

0.111

SG1

indica

RG156

IG 12(EC 729626- 121681)

0.405

0.595

AD

indica

RG157

Karungan

0.602

0.398

AD

indica

RG158

IG 13(EC 729640- 121696)

0.143

0.857

SG2

indica

RG159

Sembala

0.934

0.066

SG1

indica

RG160

IG 72(EC 728650- 117587)

0.992

0.008

SG1

indica

RG161

Panamarasamba

0.978

0.022

SG1

indica

RG162

IR 64

0.995

0.005

SG1

indica

RG163

Mikuruvai

0.992

0.008

SG1

indica

RG164

Thillainayagam

0.939

0.061

SG1

indica

RG165

ARB 64

0.843

0.157

SG1

indica

RG166

RPHP 140

0.959

0.041

SG1

indica

RG167

IG 70(EC 729045- 120983)

0.989

0.011

SG1

indica

RG168

Haladichudi

0.993

0.007

SG1

indica

RG169

IG 24(EC 728751- 117718)

0.725

0.275

AD

Aus

RG170

RPHP 42

0.981

0.019

SG1

indica

RG171

RPHP 44

0.951

0.049

SG1

indica

RG172

IG 25(EC 729728- 121785)

0.903

0.097

SG1

Tropical Japonica

RG173

IG 73(EC 728627- 117527)

0.991

0.009

SG1

indica

RG174

IG 51(EC 728772- 117742)

0.008

0.992

SG2

Tropical Japonica

RG175

Vellai kudaivazhai

0.786

0.214

SG1

indica

RG176

Kodai

0.906

0.094

SG1

indica

RG177

Kallundaikar

0.951

0.049

SG1

indica

RG178

IG 17(EC 728900- 117889)

0.993

0.007

SG1

indica

RG179

Avasara samba

0.939

0.061

SG1

indica

RG180

IG 59(EC 728729- 117694)

0.093

0.907

SG2

Tropical Japonica

RG181

IG 52(EC 728756- 117723)

0.026

0.974

SG2

Tropical Japonica

RG182

ARB 59

0.779

0.221

SG1

indica

RG183

RPHP 163

0.995

0.005

SG1

indica

RG184

IG 18(EC 728892- 117880)

0.994

0.006

SG1

indica

RG185

RPHP 36

0.915

0.085

SG1

indica

RG186

IG 28(EC 728920- 117914)

0.009

0.991

SG2

Tropical Japonica

RG187

Vadakathi samba

0.986

0.014

SG1

indica

RG188

RPHP 80

0.986

0.014

SG1

indica

RG189

IG 41(EC 728800- 117776)

0.016

0.984

SG2

Tropical japonica

RG190

IG 26(IC 0590943- 121899)

0.422

0.578

SG2

aromatic

RG191

IG 15(EC 728910- 117901)

0.755

0.245

AD

indica

RG192

Nootri pathu

0.943

0.057

SG1

indica

Fig. 4

Population structure of 134 accessions in sub group-1 and membership probability of assigning genotypes of sub group-1 (K = 3)

Clustering analysis based on Unweighted Pair Group Method with Arithmetic Mean (UPGMA) method using DARwin separated the accessions into two main groups which showed similar results as STRUCTURE analysis. The group I in UPGMA tree consists of both indigenous and agronomically improved varieties whereas the other group consists of exotic accessions. In UPGMA tree, the accessions within group 1 and 2 clustered into smaller sub groups based on their origin and types. Most of the landraces and varieties have been clustered in upper branches of the tree whereas the exotic accessions have been clustered in lower branches of the tree (Fig 5). Hence the clustering analysis by two classification methods revealed high level of similarity in clustering the genotypes. PCoA was used to characterize the subgroups of the germplasm set. A two- dimensional scatter plot involving all 192 accessions has shown that the first two PCA axes accounted for 12.6 and 4.9 % of the genetic variation among populations (Fig 6).
Fig. 5

Unrooted neighbour joining tree of 192 rice varieties. The landraces and varieties used in the study has clustered in the upper branches of the tree whereas the exotic accessions has positioned in the lower branches of the tree

Fig. 6

Principal Coordinates of 192 accessions based on 61 SSR loci. Coord 1 and Coord 2 represent first and second coordinates, respectively. The two PCA axes accounted for 12.6 and 4.9 % of the genetic variation among populations

Genetic Variance Analysis

The hierarchial distribution of molecular variance by AMOVA and pair-wise analysis revealed highly significant genetic differentiation among the groups. It revealed that 14 % of the total variation was between the groups, while 86 % was among individuals within groups (Tables 3 and 4). Calculation of Wright’s F statistic at all SSR loci revealed that FIS was 0.50 and FIT was 0.56. Determination of FST for the polymorphic loci across all accessions has shown FST as 0.14 which implies high genetic variation (Table 4). The pairwise FST estimate among sub-groups has indicated that the two groups are significantly different from each other (Table 3).
Table 3

AMOVA between groups and Pair wise comparison using Fst values (GenAlEx)

Source

df

SS

MS

Est. var.

Percent

Among the population

2

971.922

485.961

9.631

14 %

Within Pops

189

10961.256

57.996

57.996

86 %

Total

191

11933.177

 

67.627

100 %

Pairwise population Fst values

 

SG2

AD

SG1

0.128

0.040

SG2

 

0.061

Table 4

AMOVA between groups and accessions and Fixation indices (Arlequin software)

Source of variation

d.f.

Sum of squares

Variance components

Percentage of variation

Among Populations

2

200.013

1.01840 Va

13.82

Among individuals within Populations

189

1794.771

3.14391 Vb

42.65

Within Individuals

192

616

3.20833 Vc

43.53

 

383

2610.784

7.37064

 

Fixation Indices

FIS

0.49493

FST

0.13817

FIT

0.56471

Discussion

Genetic diversity is the key determinant of germplasm utilization in crop improvement. Population with high level of genetic variation is the valuable resource for broadening the genetic base in any breeding program. The panel of 192 accessions in this study with landraces, varieties as well as breeding lines has different salient agronomic traits. Few landraces included in this study i.e., Mappillai samba (Krishnanunni et al. 2015), Jyothi, Njavara (Deepa et al. 2008), Kavuni (Valarmathi et al. 2015) derived breeding line has therapeutic properties. Many lines included in this study are drought tolerant (Nootripathu, Norungan, Vellaikudaivazhai, kallundaikar, kodai, kalinga 3, Kinandang patong, azucena, mattaikar, IR65907-116-1, karuthakar, mattakuruvai, manavari, kallundai, kodaikulathan, kattikar, poongar, thogai samba, vellaikattai, kattukuthalam, kalvalai, chivapu chithiraikar, vellai chithiraikar, kudaivazhai and murugankar). Few lines have significant level of micronutrients in it (Nachimuthu et al. 2014). This panel has its importance because of its major component as traditional landraces with valuable agronomic traits that are cultivated in the small pockets of Tamil Nadu, India.

Molecular markers help us to understand the level of genetic diversity that exists among traditional races, varieties and exotic accessions which can be exploited in rice breeding programs. The genetic architecture of diverse germplasm lines can be precisely estimated by assessing the STRUCTURE of the population using molecular markers viz., SSRs or SNPs etc., (Horst and Wenzel 2007; Powell et al. 1996; Varshney et al. 2007). In this study, the genetic diversity among the accessions was evaluated by model based clustering and distance based clustering approach using the SSR genotypic data.

Regarding genetic divergence of the population consisting of local landraces, exotic cultivars and breeding lines, 61 polymorphic markers have detected a total of 205 alleles across 192 individuals. The number of alleles varied from 2 to 7 per locus and the average was 3 alleles per locus. Several previous reports have indicated the number of alleles per locus, polymorphic information content and gene diversity of 4.8–14.0, 0.63–0.70 and 6.2–6.8 respectively (Garris et al. 2005; Ram et al. 2007). In the current study, the average number of alleles (3 alleles/locus) is slightly lesser than the average number of alleles (3.88 alleles/ locus) reported by Zhang et al. (2011) in rice core collection with 150 rice varieties from south Asia and Brazil and Jin et al. (2010) who has reported the average alleles per locus as 3.9 in 416 rice accessions collected from China. Using three sets of germplasm lines (Thai (47), IRRI germplasm (53) amd other Oryza species (5)), Chakhonkaen et al. (2012) has reported 127 alleles for all loci, with a mean of 6.68 alleles per locus, and a mean Polymorphic Information Content (PIC) of 0.440 by screening with 19 InDel markers.

Chen et al. (2011) has reported the average gene diversity of 0.358 and polymorphic information content of 0.285 from 300 rice accessions from different rice growing areas of the world with 372 SNP markers. The gene diversity detected in this study (0.52) is comparable to overall gene diversity of rice core collection (0.544) from China, North Korea, Japan, Philippines, Brazil, Celebes, Java, Oceanina and Vietnam (Zhang et al. 2011) and it is higher than US accession panel with average gene diversity of 0.43 (Agrama and Eizenga 2008) and Chinese rice accession panel by Jin et al. (2010) with the average gene diversity of 0.47. The gene diversity reported in our study is lesser than gene diversity (0.68) reported by (Liakat Ali et al. 2011). Most of the diversity panel with global accessions has the gene diversity of 0.5 to 0.7 (Garris et al. 2005; Liakat Ali et al. 2011; Ni et al. 2002). These results on global accessions help to infer that this diversity panel of 192 germplasm lines represents a large proportion of the genetic diversity that exists in major rice growing Asian continent.

The PIC value was 0.468 which varied from 0.146 for RM17616 with only 2 two alleles to 0.756 for RM316 that allowed the amplification of 7 alleles. The PIC value was found to be 0.418 for SG1 which had the majority of indica accessions. The subgroup SG2 dominated by japonica accessions had the PIC value of 0.414. Hence, both the subgroups contribute in a major way for population diversity. As this population encompass different rice materials i.e., landraces, varieties and breeding lines, the molecular diversity is contributed majorly by landraces. These values are similar to those found by Courtois et al. (2012) who reported the PIC value from 0.16 to 0.78 with the average of 0.49 in European rice germplasm collection and in Chinese rice collection of 416 accessions by Jin et al. (2010), who has given similar PIC value of 0.4214. It is also consistent with PIC value (0.48) attained by Zhang et al. (2011). In this study, significant amount of rare alleles was identified which indicates that these rare alleles contribute well to the overall genetic diversity of the population.

Model based approach by STRUCTURE is implemented frequently for studying population structure by various researchers (Agrama et al. 2007, Agrama and Eizenga 2008; Garris et al. 2005; Zhang et al. 2007, 2011; Jin et al. 2010; Liakat Ali et al. 2011, Chakhonkaen et al. 2012 Courtois et al. 2012, Das et al. 2013). Courtois et al. (2012) has successfully detected two subgroups in their study population and assigned rice varieties into two groups with few admixture lines. Jin et al. (2010) has identified seven sub populations among 416 rice accessions from China. Das et al. (2013) has grouped a collection of 91 accessions of rice landraces from eastern and north eastern India into four groups.

Assigning of genotypes to the subgroups based on ancestry threshold vary between different research groups. Zhao et al. (2010) and Courtois et al. (2012) used an ancestry threshold of 80 % to identify accessions belonging to a specific subpopulation. Liakat Ali et al. (2011) has steup the threshold as 60 % and identified 33 accessions as admixtures as the threshold of 80 % consider more genotypes as admixtures. In the current study, a stringent threshold of 80 % ancestry value leaves only 20 genotypes as admixtures.

Population structure analysis in different rice diversity panel has indicated the existence of two to eight sub population in rice (Zhang et al. 2007, Zhang et al. 2009, Zhang et al. 2011, Garris et al. 2005, Agrama et al. 2007, Liakat Ali et al. 2011, Chakhonkaen et al. 2012 and Das et al. 2013). In the current rice diversity panel of 192 accessions based on the criterion of maximum membership probabilities, 134 accessions were assigned to SG1 which is dominated by indica subtype with most of the landraces and varieties of Indian origin and SG2 consisted of 38 accessions which composed mostly of japonica accessions of exotic origin. Similar population structure of two subgroups was observed in previous research by Zhang et al. (2009) in a collection of 3024 rice landraces in China. Zhang et al. (2011) has reported two distinct subgroups in a rice core collection. Courtois et al. (2012) has successfully classified two subgroups as japonica and non japonica accessions in European core collection of rice. The results indicated that two subgroups are due to the different adaptation behavior of accessions to different ecological environment as indica and japonica accessions has independent evolution frame and the origin of Indian rice accessions from indica cultivars. Hence the major criterion for population structure in this panel is indica – japonica subtype. This study includes large number of traditional landraces and varieties from Indian Subcontinent and few exotic accessions randomly selected from IRRI worldwide collection. It clarifies the relationship between Indian germplasm and exotic accessions which indicates that germplasm lines varies based on its ecology and also shows higher level of genetic diversity exists within this population.

Further structure analysis of SG1 that consisted of 134 lines indicated that it can be further subdivided in to three sub sub-groups. The three sub sub-groups classification has the factor of ecosystem and seasonal variation as the major factors for population structure. This results is in accordance with the inference that indica group has higher genetic diversity than japonica accessions which was given by various researchers (Gao et al. 2005; Lu et al. 2005; Lapitan et al. 2007; Caicedo et al. 2007; Liakat Ali et al. 2011; Garris et al. 2005; Qi et al. 2006; Qi et al. 2009); as this subgroup has indica accessions. Liakat Ali et al. (2011) has substantiated this statement with the reason of the indica subpopulation occupying the largest rice growing region which has a varied environments, ecological conditions and soil type.

The result of model based analysis is in accordance with the clustering pattern of Neighbour joining tree and Principal Coordinate Analysis. The first two principal coordinates explained 12.6 and 4.8 % of the molecular variance. Similar pattern of molecular variance explanation was observed by Zhang et al. (2011) for two population subgroups.

Calculation of Wright’s F Statistic at all loci revealed the deviation from Hardy- Weinberg law for molecular variation within the population. The result of Fst indicates higher divergence existing between subgroups of the population. Higher FIT, which is measured at subgroup level in whole population, has indicated lack of equilibrium across the groups and lack of heterozygosity most likely due to the inbreeding nature of rice.

The present study revealed that several unexploited landraces of Tamil Nadu, India which is widely cultivated by the farmers in different parts of the state. Ecological and evolutionary history contributes for the genetic diversity maintained in a population. The varieties with diverse ecosystems and wide eco-geographical conditions contribute for the genetic diversity among rice varieties in this population.

For establishing a core collection for association studies, two step approach followed by Breseghello and Sorrells (2006) and Courtois et al. (2012) was used. This approach involves the determination of population structure and then sampling can be done based on the relatedness of the accessions in the population. Those accessions that show high magnitude of genetic relatedness can be eliminated to develop core collection with diverse representatives. Based on this idea, out of 192 accessions, 150 (Table 5) were selected to form association mapping panel which can be utilized either by genome wide or candidate gene specific association mapping for linking the genotypic and phenotypic variation.
Table 5

Genotypes selected for association mapping panel

G. no

Genotypes

G. no

Genotypes

G. no

Genotypes

G. no

Genotypes

G. no

Genotypes

G. no

Genotypes

RG1

Mapillai samba

RG58

Kodaikuluthan

RG113

IG 45(EC 728768- 117736)

RG154

IG 48(EC 729203- 121195)

RG39

Kaatu ponni

RG95

Jeeraga samba

RG2

CK 275

RG59

RPHP 68

RG114

RPHP 159

RG156

IG 12(EC 729626- 121681)

RG41

Godavari samba

RG96

RP-BIO-226

RG3

Senkar

RG60

Rama kuruvaikar

RG115

IG 43(EC 728788- 117759)

RG157

Karungan

RG42

Earapalli samba

RG98

IG 5(EC 729642- 121698)

RG4

Murugankar

RG62

Purple puttu

RG116

RPHP 27

RG158

IG 13(EC 729640- 121696)

RG43

RPHP 129

RG99

IG 31(EC 728844- 117829)

RG5

CHIR 6

RG63

IG 71(EC 728651- 117588)

RG117

IG 65(EC 729024- 120958)

RG159

Sembala

RG44

Mangam samba

RG100

IG 7(EC 729598- 121648)

RG6

CHIR 5

RG65

IG 56(EC 728700- 117658

RG118

Ponmani samba

RG160

IG 72(EC 728650- 117587)

RG45

RPHP 105

RG101

RPHP 52

RG7

Kudai vazhai

RG66

Jeevan samba

RG120

Thattan samba

RG161

Panamarasamba

RG46

IG 4(EC 729639- 121695)

RG102

Varakkal

RG8

CHIR 8

RG67

RPHP 106

RG121

IG 74(EC 728622- 117517)

RG162

IR 64

RG48

Kalarkar

RG103

Mattaikar

RG9

Kuruvai kalanjiyam

RG68

IG 63(EC 728711- 117674)

RG122

Kaliyan samba

RG163

Mikuruvai

RG50

Sornavari

RG104

IG 53(EC 728752- 117719)

RG12

Vellai chithiraikar

RG69

RPHP 48

RG123

IG 2(EC 729808-121874)

RG164

Thillainayagam

RG51

RPHP 134

RG105

IG 6(EC 729592- 121642)

RG14

Jothi

RG70

Karthi samba

RG124

IG 29(EC 728925- 117920)

RG165

ARB 64

RG52

ARB 58

RG106

Katta samba

RG15

Palkachaka

RG71

IG 27(IC 0590934- 121255)

RG126

Kallimadayan

RG166

RPHP 140

RG53

IR 68144-2B-2-2-3-1-127

RG107

RH2-SM-1-2-1

RG17

Chivapu chithiraikar

RG72

Aarkadu kichili

RG127

IG 10(EC 729686- 121743)

RG168

Haladichudi

RG54

PTB 19

RG108

Red sirumani

RG18

CHIR 11

RG74

ARB 65

RG128

IG 75(EC 728587- 117420)

RG169

IG 24(EC 728751- 117718)

RG55

IG 67(EC 729050- 120988)

RG109

Vadivel

RG20

Kalvalai

RG76

Matta kuruvai

RG129

IG 38(EC 728742 - 117707)

RG170

RPHP 42

RG56

RPHP 59

RG110

Norungan

RG22

IR 36

RG77

Karuthakar

RG130

IG 39(EC 728779- 117750)

RG172

IG 25(EC 729728- 121785)

RG57

RPHP 103

RG112

IG 35(EC 728858- 117843)

RG25

Sorna kuruvai

RG80

IG 66(EC 729047- 120985)

RG131

RPHP 90

RG173

IG 73(EC 728627- 117527)

RG143

IG 46(IC 471826- 117647)

RG184

IG 18(EC 728892- 117880)

RG26

Rascadam

RG81

CB-07-701-252

RG132

IG 33(EC 728938- 117935)

RG174

IG 51(EC 728772- 117742)

RG145

IG 60(EC 728730- 117695)

RG185

RPHP 36

RG31

Chinthamani

RG82

Thooyamalli

RG133

IG 42(EC 728798- 117774)

RG175

Vellai kudaivazhai

RG146

IR 75862-206

RG186

IG 28(EC 728920- 117914)

RG32

Thogai samba

RG83

RPHP 93

RG134

IG 9(EC 729682- 121739)

RG176

Kodai

RG147

IG 58(EC 728725- 117689)

RG187

Vadakathi samba

RG33

Malayalathan samba

RG85

RPHP 104

RG135

RPHP 161

RG178

IG 17(EC 728900- 117889)

RG148

Chinna aduku nel

RG188

RPHP 80

RG34

RPHP 125

RG86

RPHP 102

RG136

IG 8(EC 729601- 121651)

RG180

IG 59(EC 728729- 117694)

RG149

RH2-SM-2-23

RG189

IG 41(EC 728800- 117776)

RG35

CK 143

RG89

IR 83294-66-2-2-3-2

RG137

IG 37(EC 728715- 117678)

RG181

IG 52(EC 728756- 117723)

RG150

IG 14(IC 517381- 121422)

RG190

IG 26(IC 0590943- 121899)

RG36

Kattikar

RG91

IG 23(EC 729391- 121419)

RG141

IG 44(EC 728762- 117729)

RG182

ARB 59

RG151

IG 32(EC 728838- 117823)

RG191

IG 15(EC 728910- 117901)

RG37

Shenmolagai

RG92

IG 49(EC 729102- 121052)

RG142

Sasyasree

RG183

RPHP 163

RG152

RPHP 47

RG192

Nootri pathu

Conclusion

This study analyze the pattern of divergence exists in a population of 192 rice accessions that constitute our rice diversity panel for association mapping. Based on various statistical methods, we identified two sub groups within 192 rice accessions selected for establishing association mapping panel. The average number of alleles per locus and gene diversity has indicated the existence of broad genetic base in this collection. The result of structure analysis is in accordance with clustering method of neighbor joining tree and principal coordinate analysis. Thus, the results of this study which indicates the genetic diversity of the accessions can be utilized to predict approaches such as association analysis, classical mapping population development; parental line selection in breeding programs and hybrid development for exploiting the natural genetic variation exists in this population.

Methods

Plant Material

A collection consisting of 192 rice accessions was used in this study, which consist of land races and varieties collected from nine different states of India as well as from Argentina, Bangladesh, Brazil, Bulgaria, China, Colombia, Indonesia, Philippines, Taiwan, Uruguay, Venezuela and United States (Table 6).
Table 6

Germplasm accessions used in the study

G. no.

Genotype

Parentage

Origin

Type – traditional/Improved

Subtype

Ecosystem IR = irrigated, RL = rainfed lowland; UP = upland

Maturity class: E = early, M = medium, L = late;

Donors/Original providing country

RG1

Mapillai samba

Landrace

Tamil Nadu, India

T

indica

IR

L

India

RG2

CK 275

CO50 X KAVUNI

Tamil Nadu, India

I

indica

IR

L

India

RG3

Senkar

Landrace

Tamil Nadu, India

T

indica

IR

M

India

RG4

Murugankar

Landrace

Tamil Nadu, India

T

indica

UP

L

India

RG5

CHIR 6

Improved chinsurah

West Bengal

I

indica

IR

E

India

RG6

CHIR 5

Improved chinsurah

West Bengal

I

indica

IR

E

India

RG7

Kudai vazhai

Landrace

Tamil Nadu, India

T

indica

UP

E

India

RG8

CHIR 8

Improved chinsurah

West Bengal

I

indica

IR

E

India

RG9

Kuruvai kalanjiyam

Landrace

Tamil Nadu, India

T

indica

IR

E

India

RG10

Nava konmani

Landrace

Tamil Nadu, India

T

indica

RL

M

India

RG11

CHIR 10

Improved chinsurah

West Bengal

I

indica

IR

M

India

RG12

Vellai chithiraikar

Landrace

Tamil Nadu, India

T

indica

RL

E

India

RG13

CHIR 2

Improved chinsurah

West Bengal

I

indica

IR

M

India

RG14

Jyothi

Variety

Kerala, India

T

indica

IR

E

India

RG15

Palkachaka

Landrace

Tamil Nadu, India

T

indica

IR

M

India

RG16

Thooyala

Landrace

Tamil Nadu, India

T

indica

IR

E

India

RG17

Chivapu chithiraikar

Landrace

Tamil Nadu, India

T

indica

RL

E

India

RG18

CHIR 11

Improved chinsurah

West Bengal

I

indica

IR

M

India

RG19

Koolavalai

Landrace

Tamil Nadu, India

T

indica

RL

M

India

RG20

Kalvalai

Landrace

Tamil Nadu, India

T

indica

RL

E

India

RG21

Mohini samba

Landrace

Tamil Nadu, India

T

indica

IR

M

India

RG22

IR 36

IR 1561 X IR 24 X Oryza nivara x CR 94

IRRI, Philippines

I

indica

IR

E

Philippines

RG23

Koombalai

Landrace

Tamil Nadu, India

T

indica

IR

M

India

RG24

Tadukan

Landrace

Philippines

T

indica

UP

M

Philippines

RG25

Sorna kuruvai

Landrace

Tamil Nadu, India

T

indica

IR

M

India

RG26

Rascadam

Landrace

Tamil Nadu, India

T

indica

IR

M

India

RG27

Muzhi karuppan

Landrace

Tamil Nadu, India

T

indica

IR

E

India

RG28

Kaatukuthalam

Landrace

Tamil Nadu, India

T

indica

RL

M

India

RG29

Vellaikattai

Landrace

Tamil Nadu, India

T

indica

RL

M

India

RG30

Poongar

Landrace

Tamil Nadu, India

T

indica

RL

L

India

RG31

Chinthamani

Landrace

Tamil Nadu, India

T

indica

RL

M

India

RG32

Thogai samba

Landrace

Tamil Nadu, India

T

indica

RL

M

India

RG33

Malayalathan samba

Landrace

Tamil Nadu, India

T

indica

IR

E

India

RG34

RPHP125

NDR 2026 (RICHA)

UTTAR PRADHESH

I

indica

IR

E

India

RG35

CK 143

CO50 X KAVUNI

Tamil Nadu, India

I

indica

IR

L

India

RG36

Kattikar

Landrace

Tamil Nadu, India

T

indica

RL

M

India

RG37

Shenmolagai

Landrace

Tamil Nadu, India

T

indica

IR

M

India

RG38

Velli samba

Landrace

Tamil Nadu, India

T

indica

IR

M

India

RG39

Kaatu ponni

Landrace

Tamil Nadu, India

T

indica

IR

M

India

RG40

kakarathan

Landrace

Tamil Nadu, India

T

indica

IR

M

India

RG41

Godavari samba

Landrace

Tamil Nadu, India

T

indica

IR

M

India

RG42

Earapalli samba

Landrace

Tamil Nadu, India

T

indica

IR

M

India

RG43

RPHP 129

Kamad

JAMMU & KASHMIR

T

indica

Scented

E

India

RG44

Mangam samba

Landrace

Tamil Nadu, India

T

indica

IR

M

India

RG45

RPHP 105

Moirang phou

MANIPUR

T

indica

IR

E

India

RG46

IG 4(EC 729639- 121695)

TD2: :IRGC 9148-1

IRRI, Philippines

I

indica

IR

M

Philippines

RG47

Machakantha

Landrace

Orissa, India

T

indica

scented

E

India

RG48

Kalarkar

Landrace

Tamil Nadu, India

T

indica

RL

E

India

RG49

Valanchennai

Landrace

Tamil Nadu, India

T

indica

RL

E

India

RG50

Sornavari

Landrace

Tamil Nadu, India

T

indica

RL

E

India

RG51

RPHP 134

NJAVARA

Kerala

T

indica

RL

E

India

RG52

ARB 58

Variety

Karnataka

I

indica

IR

E

India

RG53

IR 68144-2B-2-2-3-1-127

IR 72 X ZAWA BONDAY

IRRI, Philippines

I

indica

 

E

Philippines

RG54

PTB 19

Variety

Kerala, India

I

indica

IR

M

India

RG55

IG 67(EC 729050- 120988)

IR 77384-12-35-3-12-l-B::IRGC 117299-1

IRRI, Philippines

I

indica

IR

E

Philippines

RG56

RPHP 59

Taroari Basmati/karnal local

HARYANA

T

Aromatic

scented

L

India

RG57

RPHP 103

Pant sugandh dhan -17

UTTARKHAND

I

Aromatic

scented

L

India

RG58

Kodaikuluthan

Landrace

Tamil Nadu, India

T

indica

RL

E

India

RG59

RPHP 68

Subhdra

Orissa, India

I

indica

RL

E

India

RG60

Rama kuruvaikar

Landrace

Tamil Nadu, India

T

indica

IR

E

India

RG61

Kallundai

Landrace

Tamil Nadu, India

T

indica

RL

E

India

RG62

Purple puttu

Landrace

Tamil Nadu, India

T

indica

IR

E

India

RG63

IG 71(EC 728651- 117588)

TEPI BORO::IRGC 27519-1

IRRI, Philippines

I

aus

IR

E

Philippines

RG64

Ottadaiyan

Landrace

Tamil Nadu, India

T

indica

RL

M

India

RG65

IG 56(EC 728700- 117658

BICO BRANCO

Brazil

T

Aromatic

UP

E

Philippines

RG66

Jeevan samba

Landrace

Tamil Nadu, India

T

indica

IR

M

India

RG67

RPHP 106

akut phou

MANIPUR

I

indica

IR

M

India

RG68

IG 63(EC 728711- 117674)

CAAWA/FORTUNA

IRRI, Philippines

I

Tropical Japonica

IR

M

Philippines

RG69

RPHP 48

Bindli

UTTARKHAND

T

Aromatic

Scented

L

India

RG70

Karthi samba

Landrace

Tamil Nadu, India

T

indica

IR

M

India

RG71

IG 27(IC 0590934- 121255)

ARC 11345::IRGC 21336-1

IRRI, Philippines

I

indica

IR

M

Philippines

RG72

Aarkadu kichili

Landrace

Tamil Nadu, India

T

indica

IR

M

India

RG73

Kunthali

Landrace

Tamil Nadu, India

T

indica

IR

E

India

RG74

ARB 65

Variety

Karnataka

I

indica

IR

E

India

RG75

IG 21(EC 729334- 121355)

HONGJEONG::IRGC 73052-1

IRRI, Philippines

I

japonica

IR

E

Philippines

RG76

Matta kuruvai

Landrace

Tamil Nadu, India

T

indica

IR

E

India

RG77

Karuthakar

Landrace

Tamil Nadu, India

T

indica

RL

E

India

RG78

RPHP 165

Tilak kachari

West Bengal

T

indica

IR

E

India

RG79

Manavari

Landrace

Tamil Nadu, India

T

indica

U

E

India

RG80

IG 66(EC 729047- 120985)

IR 71137-243-2-2-3-3::IRGC 99696-1

IRRI, Philippines

I

indica

IR

E

Philippines

RG81

CB-07-701-252

White ponni X Rasi

Tamil Nadu, India

I

indica

IR

E

India

RG82

Thooyamalli

Landrace

Tamil Nadu, India

T

indica

IR

M

India

RG83

RPHP 93

Type-3 (Dehradooni Basmati)

UTTARKHAND

I

indica

Scented

M

India

RG84

Velsamba

Landrace

Tamil Nadu, India

T

indica

IR

M

India

RG85

RPHP 104

Kasturi (IET 8580)

UTTARKHAND

I

indica

IR

M

India

RG86

RPHP 102

Kanchana

Kerala, India

I

indica

Semi Deep Water

L

India

RG87

IG 40(EC 728740- 117705)

DEE GEO WOO GEN

TAIWAN

T

Indica

IR

M

Philippines

RG88

Saranga

Landrace

Tamil Nadu, India

T

indica

IR

E

India

RG89

IR 83294-66-2-2-3-2

DAESANBYEO X IR65564-44-5-1

IRRI, Philippines

I

japonica

RL

M

Philippines

RG90

IG 61(EC 728731- 117696)

CRIOLLO LA FRIA

Venezuela

I

Indica

IR

E

Philippines

RG91

IG 23(EC 729391- 121419)

MAHA PANNITHI::IRGC 51021-1

IRRI, Philippines

I

Aus

IR

M

Philippines

RG92

IG 49(EC 729102- 121052)

MENAKELY ::IRGC 69963-1

Madagascar

I

Indica

RL

M

Philippines

RG93

Uppumolagai

Landrace

Tamil Nadu, India

T

Indica

IR

M

India

RG94

Karthigai samba

Landrace

Tamil Nadu, India

T

Indica

RL

M

India

RG95

Jeeraga samba

Landrace

Tamil Nadu, India

T

Indica

IR

M

India

RG96

RP-BIO-226

IMPROVED SAMBHA MAHSURI

ANDHRA PRADESH

I

Indica

IR

M

India

RG97

Varigarudan samba

Landrace

Tamil Nadu, India

T

Indica

IR

M

India

RG98

IG 5(EC 729642- 121698)

IR 65907-116-1-B::C1

IRRI, Philippines

I

japonica

UP

E

Philippines

RG99

IG 31(EC 728844- 117829)

ORYZICA LLANOS 5

Colombia

T

Indica

IR

M

Philippines

RG100

IG 7(EC 729598- 121648)

VARY MAINTY::IRGC 69910-1

Madagascar

I

japonica

IR

M

Philippines

RG101

RPHP 52

SEBATI

Orissa, India

I

Indica

IR

M

India

RG102

Varakkal

Landrace

Tamil Nadu, India

T

Indica

UP

E

India

RG103

Mattaikar

Landrace

Tamil Nadu, India

T

Indica

RL

L

India

RG104

IG 53(EC 728752- 117719)

CAROLINA RINALDO BARSANI

URUGUAY

I

Temperate japonica

IR

E

Philippines

RG105

IG 6(EC 729592- 121642)

SOM CAU 70 A::IRGC 8227-1

Vietnam

I

Temperate japonica

IR

E

Philippines

RG106

Katta samba

Landrace

Tamil Nadu, India

T

Indica

RL

L

India

RG107

RH2-SM-1-2-1

SWARNA X MOROBERAKAN

Tamil Nadu, India

I

Indica

IR

E

India

RG108

Red sirumani

Landrace

Tamil Nadu, India

T

Indica

RL

E

India

RG109

Vadivel

Landrace

Tamil Nadu, India

T

Indica

IR

M

India

RG110

Norungan

Landrace

Tamil Nadu, India

T

Indica

RL

E

India

RG111

IG 20(EC 729293- 121310)

CHIGYUNGDO::IRGC 55466-1

South Korea

I

Indica

UP

E

Philippines

RG112

IG 35(EC 728858- 117843)

PATE BLANC MN 1

Cote D’Ivoire

I

japonica

UP

M

Philippines

RG113

IG 45(EC 728768- 117736)

FORTUNA

Puerto Rico

T

japonica

IR

M

Philippines

RG114

RPHP 159

Radhuni Pagal

BANGLADESH

I

aromatic rice

Scented

L

India

RG115

IG 43(EC 728788- 117759)

IR-44595

IRRI, Philippines

I

indica

IR

E

Philippines

RG116

RPHP 27

Azucena

IRRI, Philippines

T

Tropical Japonica

RL

E

India

RG117

IG 65(EC 729024- 120958)

GODA HEENATI::IRGC 31393-1

SRILANKA

I

indica

IR

E

Philippines

RG118

Ponmani samba

Landrace

Tamil Nadu, India

T

indica

IR

M

India

RG119

Ganthasala

Landrace

Tamil Nadu, India

T

indica

IR

M

India

RG120

Thattan samba

Landrace

Tamil Nadu, India

T

indica

IR

E

India

RG121

IG 74(EC 728622- 117517)

KINANDANG PATONG::IRGC 23364-1

IRRI, Philippines

I

japonica

RL

M

Philippines

RG122

Kaliyan samba

Landrace

Tamil Nadu, India

T

indica

IR

M

India

RG123

IG 2(EC 729808-121874)

BLUEBONNET 50::IRGC 1811-1

IRRI, Philippines

I

japonica

UP

M

Philippines

RG124

IG 29(EC 728925- 117920)

TOX 782-20-1

NIGERIA

T

Tropical Japonica

IR

E

Philippines

RG125

RPHP 55

Kalinga -3

Orissa

I

indica

RL

E

India

RG126

Kallimadayan

Landrace

Tamil Nadu, India

T

indica

RL

E

India

RG127

IG 10(EC 729686- 121743)

HASAN SERAI

IRRI, Philippines

I

aromatic

IR

E

Philippines

RG128

IG 75(EC 728587- 117420)

AEDAL::IRGC 55441-1

Korea

T

japonica

IR

E

Philippines

RG129

IG 38(EC 728742 - 117707)

DELREX

UNITED STATES

 

Tropical japonica

IR

M

Philippines

RG130

IG 39(EC 728779- 117750)

HONDURAS

HONDURAS

 

indica

IR

M

Philippines

RG131

RPHP 90

182(M)

Andhra Pradesh

I

indica

IR

E

India

RG132

IG 33(EC 728938- 117935)

WC 3397

JAMAICA

 

Tropical Japonica

IR

E

Philippines

RG133

IG 42(EC 728798- 117774)

KALUBALA VEE

SRILANKA

T

indica

IR

E

Philippines

RG134

IG 9(EC 729682- 121739)

GEMJYA JYANAM::IRGC 32411-C1

IRRI, Philippines

I

indica

IR

E

Philippines

RG135

RPHP 161

Champa Khushi

Vietnam

T

indica

UP

E

India

RG136

IG 8(EC 729601- 121651)

XI YOU ZHAN::IRGC 78574-1

China

I

indica

IR

E

Philippines

RG137

IG 37(EC 728715- 117678)

CENIT

ARGENTINA

T

Tropical Japonica

IR

L

Philippines

RG138

Sigappu kuruvikar

Landrace

Tamil Nadu, India

T

indica

RL

E

India

RG139

RPHP 138

EDAVANKUDI POKKALI

Kerala, India

T

indica

Deep water

L

India

RG140

Raja mannar

Landrace

Tamil Nadu, India

T

indica

IR

M

India

RG141

IG 44(EC 728762- 117729)

EDITH

UNITED STATES

T

indica

IR

E

Philippines

RG142

Sasyasree

TKM 6 x IR 8

West Bengal

I

indica

IR

E

India

RG143

IG 46(IC 471826- 117647)

BABER

INDIA

I

indica

IR

E

India

RG144

Chetty samba

Landrace

Tamil Nadu, India

T

indica

IR

E

India

RG145

IG 60(EC 728730- 117695)

CREOLE

Belize

T

indica

IR

M

Philippines

RG146

IR 75862-206

IR 75083 X IR 65600 -81-5-3-2

IRRI, Philippines

I

Tropical Japonica

IR

M

Philippines

RG147

IG 58(EC 728725- 117689)

CI 11011

UNITED STATES

 

japonica

IR

M

Philippines

RG148

Chinna aduku nel

Landrace

Tamil Nadu, India

T

indica

IR

L

India

RG149

RH2-SM-2-23

SWARNA X MOROBERAKAN

Tamil Nadu, India

I

indica

IR

M

India

RG150

IG 14(IC 517381- 121422)

MALACHAN::IRGC 54748-1

India

I

indica

UP

E

Philippines

RG151

IG 32(EC 728838- 117823)

NOVA

United States

I

japonica

IR

M

Philippines

RG152

RPHP 47

Pathara (CO-18 x Hema)

India

I

indica

IR

E

India

RG153

Sembilipiriyan

Landrace

Tamil Nadu, India

T

indica

RL

M

India

RG154

IG 48(EC 729203- 121195)

DINOLORES::IRGC 67431-1

IRRI, Philippines

I

indica

UP

M

Philippines

RG155

Sona mahsuri

Landrace

Tamil Nadu, India

T

indica

IR

E

India

RG156

IG 12(EC 729626- 121681)

SHESTAK::IRGC 32351-1

Iran

I

indica

IR

E

Philippines

RG157

Karungan

Landrace

Tamil Nadu, India

T

indica

IR

E

India

RG158

IG 13(EC 729640- 121696)

CURINCA::C1

BRAZIL

I

indica

IR

E

Philippines

RG159

Sembala

Landrace

Tamil Nadu, India

T

indica

IR

L

India

RG160

IG 72(EC 728650- 117587)

TD 25::IRGC 9146-1

Thailand

I

indica

IR

M

Philippines

RG161

Panamarasamba

Landrace

Tamil Nadu, India

T

indica

IR

M

India

RG162

IR 64

IR-5857-33-2-1 x IR-2061-465-1-5-5

IRRI, Philippines

I

indica

IR

E

Philippines

RG163

Mikuruvai

Landrace

Tamil Nadu, India

T

indica

RL

E

India

RG164

Thillainayagam

Landrace

Tamil Nadu, India

T

indica

IR

M

India

RG165

ARB 64

Variety

Karnataka

I

indica

IR

E

India

RG166

RPHP 140

VYTILLA ANAKOPON

Kerala

T

indica

IR

E

India

RG167

IG 70(EC 729045- 120983)

IR43::IRGC 117005-1

IRRI, Philippines

I

indica

IR

M

Philippines

RG168

Haladichudi

Landrace

Orissa, India

T

indica

IR

E

India

RG169

IG 24(EC 728751- 117718)

DNJ 140

BANGLADESH

I

Aus

IR

E

Philippines

RG170

RPHP 42

Salimar Rice -1

JAMMU & KASHMIR

I

indica

IR

M

India

RG171

RPHP 44

BR- 2655

KARNATAKA

I

indica

IR

L

India

RG172

IG 25(EC 729728- 121785)

LOHAMBITRO 224::GERVEX 5144-C1

Madagascar

I

Tropical Japonica

IR

E

Philippines

RG173

IG 73(EC 728627- 117527)

MAKALIOKA 34::IRGC 6087-1

IRRI, Philippines

I

indica

IR

E

Philippines

RG174

IG 51(EC 728772- 117742)

GOGO LEMPUK

Indonesia

 

Tropical Japonica

IR

M

Philippines

RG175

Vellai kudaivazhai

Landrace

Tamil Nadu, India

T

indica

RL

M

India

RG176

Kodai

Landrace

Tamil Nadu, India

T

indica

RL

E

India

RG177

Kallundaikar

Landrace

Tamil Nadu, India

T

indica

UP

M

India

RG178

IG 17(EC 728900- 117889)

SIGADIS

INDONESIA

T

indica

RL

L

Philippines

RG179

Avasara samba

Landrace

Tamil Nadu, India

T

indica

IR

E

India

RG180

IG 59(EC 728729- 117694)

COPPOCINA

BULGARIA

I

Tropical Japonica

IR

M

Philippines

RG181

IG 52(EC 728756- 117723)

DOURADO AGULHA

BRAZIL

I

Tropical Japonica

IR

M

Philippines

RG182

ARB 59

Variety

Karnataka

I

indica

IR

E

India

RG183

RPHP 163

Seeta sail

West Bengal

T

indica

Scented

M

India

RG184

IG 18(EC 728892- 117880)

SERATOES HARI

INDONESIA

T

indica

IR

E

Philippines

RG185

RPHP 36

TKM-9

Tamil Nadu, India

I

indica

IR

E

India

RG186

IG 28(EC 728920- 117914)

TIA BURA

INDONESIA

T

Tropical Japonica

IR

M

Philippines

RG187

Vadakathi samba

Landrace

Tamil Nadu, India

T

indica

IR

M

India

RG188

RPHP 80

24(K)

Andhra Pradesh

I

indica

IR

E

India

RG189

IG 41(EC 728800- 117776)

KANIRANGA

Indonesia

T

Tropical japonica

IR

M

Philippines

RG190

IG 26(IC 0590943- 121899)

BASMATI 370::IRGC 3750-1

IRRI, Philippines

I

aromatic

IR

E

Philippines

RG191

IG 15(EC 728910- 117901)

SZE GUEN ZIM

CHINA

I

indica

IR

E

Philippines

RG192

Nootri pathu

Landrace

Tamil Nadu, India

T

indica

RL

L

India

IRRI lines - The number after hyphen inside brackets represent IRGC number

Microsatellite Genotyping

DNA Isolation and PCR Amplification

DNA was extracted from leaf tissue by grinding with liquid nitrogen using CTAB method (Saghai-Maroof et al. 1984.). It was diluted to a final concentration of 30 ng μl−1 for enabling polymerase chain reactions. DNA amplification parameters such as specificity, efficiency and fidelity are strongly influenced by the components of the PCR reaction and by thermal cycling conditions (Caetano-Anolles and Brant 1991). Therefore, the careful optimization of reaction components and conditions will ultimately result in more reproducible and efficient amplification. The concentrations of primers, template DNA, Master Mix, and annealing temperature was optimized on eight diverse accessions for 156 SSR markers distributed on the 12 chromosomes by modified Taguchi method (Cobb and CIarkson 1994). Microsatellite primer sequences, annealing temperature and chromosomal locations are obtained from GRAMENE database (http://archive.gramene.org/markers/microsat/). Sixty one SSR primer pairs which produce polymorphic allele amplification were chosen to genotype the entire set of germplasm collection.

The volume of the PCR reaction system was 10 μl. The PCR reaction mixture of 10 μl had 0.4 mM dNTPs, 4 mM of MgCl2, 150 mM of Tris–HCl, 10 pmoles of forward and reverse primer and 0.05 U Taq polymerase with 30 ng of DNA. Polymerase chain reaction was performed in BIORAD THERMAL CYCLER using the following program: 94 °C for 2 min, 35 cycles of 94 °C for 45 sec, 50–60 °C for 1 min, 72 °C for 2 min with a final extension of 72 °C for ten min.

Polyacrylamide Gel Electrophoresis

Amplified products were size separated in native polyacrylamide gel electrophoresis using 6 % (w/v) polyacrylamide gel according to Sambrook et al. (2001) in vertical electrophoresis tank with 1X TBE at 150 V. The gel size was determined using standard molecular weight size markers after the bands were detected by silver staining.

Allele Scoring

The bands were visualized in a cluster of two to six in the stained gels for most of the markers. Based on the expected product size given in the GRAMENE website (Additional file 2: Table S1), the size of the most intensely amplified bands around the expected product size for each microsatellite marker was identified using standard molecular weight size markers (20 bp DNA ladder, GeNeI Company). Then the stained gel was dried and documented using light box. Allele score was given based on the presence of a particular size allele in each of the germplasm. The presence was denoted as 1 and absence of an allele as 0 and it was rechecked manually (Additional file 3: Table S2).

Data Analysis

A 1/0 matrix was constructed based on the presence and absence of alleles for the set of 61 markers. This SSR genotype data was analyzed for genetic diversity and population structure.

Genetic Diversity

For a set of accessions, genetic diversity parameters such as number of alleles per locus, allele frequency, heterozygosity and polymorphic information index (PIC) was estimated using the program POWERMARKER Ver3.25 (Liu and Muse 2005). Allele frequency represents the frequency of particular allele for each marker. Heterozygosity is the proportion of heterozygous individuals in the population. Polymorphic information content that represent the amount of polymorphism within a population was estimated based on Botstein et al. (1980).

To assess genetic structure, model based approach and distance based approach were used. Model based approach was utilized with Structure ver 2.3.4 software (Pritchard et al. 2000). The actual number of subpopulation which is denoted by K was identified by this method. For that, the project was run with the following parameter set: the possibility of admixture and allele frequency correlated. Run length was given as 150,000 burning period length followed by 150,000 Markov Chain Monte Carlo (MCMC) replication. Each k value was run for 10 times with k value varying from 1 to 10. The optimum k value was determined by plotting the mean estimate of the log posterior probability of the data (L (K) against the given K value. True number of subpopulation was identified using the maximal value of L (K). An adhoc quantity ΔK proposed by (Evanno et al. 2005) based on second order rate of change of the likelihood function with respect to K estimated using Structure Harvester (Earl 2012) has also shown a clear peak at the optimal K value.

Distance based approach which is based on calculating pair wise distance matrix was computed by calculating a dissimilarity matrix using a shared allele index with DARwin software (Perrier and Jacquemoud-Collet 2006). An unweighted neighbor joining tree was constructed using the calculated dissimilarity index. The genetic distance between accessions was estimated using NEI coefficient (Nei 1972) with bootstrap procedure of resampling (1000) across markers and individuals from allele frequencies. To determine the association among the accessions, unweighted pair group method with arithmetic mean (UPGMA) tree was also drawn using Powermarker and viewed in MEGA 6.0 software (Tamura et al. 2013).

The presence of molecular variance within and between hierarchical population structure estimated by Structure was assessed via Analysis of molecular variance (AMOVA) by Arlequin (Excoffier et al. 2005). F statistics which include FIT, deviations from Hardy- Weinberg expectation across the whole population, FIS deviation from Hardy- Weinberg expectation within a population and FST, correlation of alleles between subpopulation was calculated using AMOVA approach in Arlequin. AMOVA and Principal Coordinate analysis of the germplasm set was performed based on Nei (Nei 1973) distance matrix using GenAlEx 6.5 (Peakall and Smouse 2012).

Declarations

Acknowledgement

This work was supported by a grant from Department of Biotechnology, Government of India under Rice biofortification with enhanced iron and zinc in high yielding non basmati cultivars through marker assisted breeding and transgenic approaches- Phase II (E28SO) scheme. I thank Dr. Yasodha from Institute of Forest Genetics and Tree Breeding, Coimbatore for helping in the analysis.

Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.

Authors’ Affiliations

(1)
Plant Molecular Biology, Plant Breeding and Genetics Divison, International Rice Research Institute
(2)
Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University
(3)
Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University
(4)
Crop Physiology laboratory, International Crops Research Institute for the Semi-Arid-Tropics
(5)
International Crops Research Institute for the Semi-Arid-Tropics
(6)
Centre of Excellence in Molecular Breeding, Tamil Nadu Agricultural University

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© Nachimuthu et al. 2015