Table 2 Genome-wide SNPs selected from A and B subgenomes for development of Axiom_Arachis SNP array and polymorphic SNPs identified in ‘Reference Set’.

From: Development and Evaluation of a High Density Genotyping ‘Axiom_Arachis’ Array with 58 K SNPs for Accelerating Genetics and Breeding in Groundnut

Pseudomolecules of A and B subgenome

Total SNPs on the array

Average SNPs/1 Mb region

Polymorphic SNPs in tetraploid accessions of the ‘Reference Set’

Polymorphic SNPs in diploid accessions of the ‘Reference Set’

Common polymorphic SNPs between tetraploid and diploid accessions of the ‘Reference Set’

Total polymorphic SNPs in the ‘Reference Set’

Average SNPs/1 Mb region

A01

4,714

41.49

379

3,549

297

3,631

33.62

A02

3,167

33.34

736

2,202

499

2,442

25.71

A03

3,478

25.57

558

2,554

333

2,779

20.43

A04

2,693

21.54

617

1,962

435

2,144

17.15

A05

2,624

23.64

475

1,895

303

2,068

18.63

A06

2,764

24.25

487

1,975

308

2,156

18.91

A07

2,303

28.78

406

1,659

243

1,822

22.77

A08

2,921

57.27

401

2,156

244

2,315

45.39

A09

2,790

22.87

483

2,018

298

2,203

18.06

A10

2,529

22.78

346

1,854

204

1,999

18.00

Total A subgenome

29,983

30.15

4,888

21,824

3,164

23,559

23.87

B01

2,405

17.30

361

1,569

181

1,750

12.59

B02

3,112

28.29

617

2,076

400

2,293

20.85

B03

3,443

24.95

523

2,362

287

2,598

18.96

B04

2,588

19.17

516

1,763

311

1,971

14.60

B05

2,576

17.06

395

1,682

204

1,876

12.43

B06

2,793

20.24

433

1,903

236

2,101

15.22

B07

2,638

20.61

384

1,742

193

1,933

15.10

B08

2,671

20.39

323

1,836

180

1,980

15.11

B09

3,152

21.15

479

2,076

270

2,286

15.34

B10

2,872

20.81

393

1,881

199

2,077

15.05

Total B subgenome

28,250

21.00

4,424

18,890

2,461

20,865

15.53

Total

58,233

25.58

9,312

40,714

5,625

44,424

19.50

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