Skip to main content

Table 1 List of HvSSR primers used for genotyping of 729 rice varieties along with their chromosomal position, product size, No. of alleles amplified, gene diversity, heterozygosity and PIC value

From: Genetic diversity trend in Indian rice varieties: an analysis using SSR markers

Chr. No.

Primer ID

Size (bp)

Forward primer

Reverse primer

Major allele frequency

Allele no

Gene diversity

Heterozygosity

PIC

1

HvSSR01-32

250

AAACTGGAGATGAACTCGAA

GTAACGAACTAGAGCATGGG

0.9445

2.0000

0.1048

0.0340

0.0993

 

HvSSR01-41

348

TGAGTGAGACTTGACAGTGC

AGTTAACACCAATGCTGACC

0.5943

3.0000

0.5405

0.2340

0.4638

 

HvSSR01-53

274

TGTCGTCCACGTAGTAGGAG

ACACTCCTCCTCTGTTCTCA

0.8894

2.0000

0.1968

0.0030

0.1774

2

HvSSR02-01

312

AAGAGATGAGAAGAGCAATGA

CAACTTAGAGGAAGAAGGAGG

0.7813

2.0000

0.3417

0.0892

0.2834

 

HvSSR02-33

355

TAATGCACGCACAACTTTAC

TATAGAATGCTGACTGGGCT

0.7976

2.0000

0.3228

0.0923

0.2707

 

HvSSR02-50

195

TTTCAGGAATCTGATGCTTT

TTAATCAAAGCCCTAACAGC

0.6579

3.0000

0.5077

0.1445

0.4547

3

HvSSR03-02

228

TAGCGGAGTTGGAATAACAC

CTGCACTGCATACCTCATAA

0.5346

4.0000

0.5737

0.9224

0.4922

 

HvSSR03-10

280

GTACACAACGTCACAACAGC

ACTGTGGCATATGTTCGATT

0.7566

2.0000

0.3683

0.1468

0.3005

 

HvSSR03-19

230

AATTCAGTTCACGCATTCTT

AGCTGTTCGTCTGCATAGTT

0.8968

2.0000

0.1851

0.0577

0.1680

 

HvSSR03-37

386

GGAAATCGTCAAGAACGTC

TAATTGTATACCACTCCGCC

0.3780

3.0000

0.6610

0.3013

0.5868

 

HvSSR03-54

352

GCCTATCAGGCTATCATCAC

GTGATCGACATTGAGGAGTT

0.8168

2.0000

0.2993

0.0049

0.2545

4

HvSSR04-19

265

TCGTGGAGTATCCTGTATCC

TTATAACTTGGAGCTCAGGC

0.9127

3.0000

0.1631

0.1041

0.1566

 

HvSSR04-27

318

ATGGATTTAGGCTTGTTTGA

ATACTGCGAAGGTGAAGAGA

0.7150

4.0000

0.4609

0.2629

0.4319

 

HvSSR04-46

179

GGCGCGCTTATATATGTACT

CGATTGCGTGGTGTAACTAT

0.7774

4.0000

0.3712

0.1475

0.3413

5

HvSSR05-09

335

CTCTCCATCTTGCAATCTTC

TGCATGACTCTATCAACCAG

0.5331

3.0000

0.5509

0.0768

0.4558

 

HvSSR05-15

275

CCATGTCAAACGGTTACTTT

GGGAGAAGTGAGAAAGAGGT

0.9366

3.0000

0.1205

0.0975

0.1166

 

HvSSR05-30

353

TACGACGGACGATTAAAGTT

GCTAACTCATTCATCTCGCT

0.7962

2.0000

0.3245

0.0000

0.2719

6

HvSSR06-03

212

CTAGGGAATCAGCGGTTAG

GCTCTCTTGTCCTTCTTCTTC

0.9582

3.0000

0.0802

0.0099

0.0771

 

HvSSR06-16

368

TCTGAAATGCTGTCATCAAG

GAGCAGAGTAGGACATGAGC

0.9767

2.0000

0.0454

0.0186

0.0444

 

HvSSR06-40

385

CTCTTCCGTGGTTAAAGAAA

CACTGGTATGATCTCCGACT

0.5405

3.0000

0.5285

0.2859

0.4232

7

HvSSR07-18

343

GGTGTGTTGTCGAATCTCTC

ATGCCATTGTCCTTACATTC

0.5436

3.0000

0.5383

0.1317

0.4392

 

HvSSR07-51

341

CGAGCATGTCTGTCAAGTAA

GTTCGAATGTAATGTTGGCT

0.8503

3.0000

0.2645

0.0349

0.2464

8

HvSSR08-14

295

TCCACTTTACATCGTCACAA

CTACCTCTTAACCGCACATT

0.5996

3.0000

0.5401

0.0736

0.4661

 

HvSSR08-19

221

CATCTCTTGAGAAATCTGCC

TGTGCATTTCGTCTTTCATA

0.4944

4.0000

0.5183

0.1278

0.4022

9

HvSSR09-11

366

TGCAGAATTTCTTCCTTCAT

ACCAGAATCTCCCAAATGTA

0.7632

5.0000

0.3981

0.0371

0.3752

 

HvSSR09-26

331

TGGGCATCTGGTACTATCTT

AGCTCATTCCACAGGTTAGA

0.9594

2.0000

0.0779

0.0056

0.0749

 

HvSSR09-55

382

TTACTCCGCATATATCCATGT

ATTTGACACCAAGTTGATCC

0.5925

4.0000

0.5090

0.7326

0.4105

10

HvSSR10-03

289

TCTTTCCCAAATTCCAGATA

CATTAGTTGTTTGTGGCAGA

0.9081

3.0000

0.1711

0.0883

0.1641

 

HvSSR10-13

169

CAGGGAATCAACATCAAAGT

AGCAAGGCAAGTCATCTCTA

0.5795

4.0000

0.5292

0.4003

0.4378

 

HvSSR10-34

202

TAGACCGAGGAATTGAAAGA

TTTGGGCTTATTGTCAGTTT

0.9060

4.0000

0.1749

0.0982

0.1681

11

HvSSR11-13

285

TGAAACCACAATGAGTCAAA

GCCCTAAACCCAAATAGAAG

0.7532

2.0000

0.3718

0.1062

0.3027

 

HvSSR11-21

291

TACGCTATAACCATGAAGCA

CTCCCGTTATTGTCCTTACA

0.8305

5.0000

0.2962

0.2161

0.2766

 

HvSSR11-58

371

ACTGAATCCTTACTGGAGCA

GGAGATAAGCATTTGGAAGA

0.7881

5.0000

0.3639

0.1607

0.3451

12

HvSSR12-01

271

GATTTGCAACACGTACGATA

GATCATCCACTCTGAGCAAT

0.9203

2.0000

0.1467

0.0986

0.1360

 

HvSSR12-13

388

ACCTTAGGGCTGAGTTCTTT

TTAGGCTTGTCTCTTCCTCA

0.9048

5.0000

0.1782

0.0710

0.1733

 

HvSSR12-39

289

ATCTAACAACAACAATCCCG

CATCTTCATCCCTCGTGTAT

0.8793

4.0000

0.2211

0.1142

0.2124

 

Mean

   

0.7630

3.1111

0.3346

0.1536

0.2917

Back to article page

BMC Genomic Data

ISSN: 2730-6844

Contact us