Table 1 Number of SNPs identified across four major crop species using their most recent public genome releases

Rice (Oryza sativa) Genome size: ~ 400 Mb

GJ-temp: IRGSP

IRGSP

GCF_001433935.1

26,516,112

3,060,410

319,632

232,847

29,622

1,461,451

3048

38,699

2958

GJ-subtrp: CHAO MEO

CM

GCA_009831315.1

27,024,845

3,069,706

356,381

233,761

29,316

1,462,534

3037

38,571

3012

GJ-trop1: Azucena

AZ

GCA_009830595.1

27,316,403

3,081,793

345,485

226,235

28,131

1,473,280

2984

38,824

2925

GJ-trop2: KETAN NANGKA

KN

GCA_009831275.1

27,331,337

3,031,741

335,086

219,831

27,464

1,448,804

3052

38,543

3048

cB: ARC 10497

ARC

GCA_009831255.1

27,286,525

2,984,499

324,769

211,937

26,277

1,425,562

2965

37,501

2984

XI-1A: ZhenShan97RS3

ZS97

GCA_001623345.2

27,439,649

3,504,390

573,128

406,815

53,607

1,664,226

3322

42,456

3344

XI-1B1: IR 64

IR64

GCA_009914875.1

27,084,312

2,822,657

311,142

203,724

25,188

1,342,849

2618

34,958

2729

XI-1B2: PR 106

PR106

GCA_009831045.1

27,461,145

3,029,730

343,797

224,081

27,840

1,443,799

2901

37,805

2926

XI-2A: GOBOL SAIL

GS

GCA_009831025.1

27,608,213

2,885,485

293,846

198,221

24,849

1,388,477

2867

36,840

2909

XI-2B: LARHA MUGAD

LM

GCA_009831355.1

27,974,114

2,921,223

307,604

206,271

25,723

1,402,841

2870

37,200

2961

XI-3A: LIMA

LIMA

GCA_009829395.1

27,053,048

2,838,843

301,480

197,894

24,453

1,360,673

2839

36,103

2867

XI-3B1: KHAO YAI GUANG

KYG

GCA_009831295.1

27,378,477

2,911,252

307,567

201,613

24,948

1,394,212

2840

36,680

2840

XI-3B2: LIU XU

LX

GCA_009829375.1

27,759,204

2,939,867

311,835

213,624

26,747

1,411,721

2943

37,483

3052

XI-adm: MH63RS3

MH63

GCA_001623365.2

27,503,492

3,509,396

603,812

422,385

55,137

1,661,569

3306

41,928

3370

cA1: N22

N22

GCA_001952365.3

27,594,493

3,019,972

328,996

229,046

28,380

1,443,123

2931

37,919

2985

cA2: NATEL BORO

NABO

GCA_009831335.1

28,044,207

2,979,119

312,640

212,806

26,394

1,433,853

2976

38,230

3075

Sorghum (Sorghum bicolor) (Genome size: ~ 600 Mb)

BT623v3.1

-

GCF_000003195.3

32,698,281

1,078,742

793,513

675,414

96,219

593,563

1442

13,124

1349

Tx2783

-

GCA_903166285.1

32,537,001

752,298

327,512

205,336

25,181

434,942

888

15,706

7822

Tx436

-

GCA_903166325.1

32,748,001

868,964

422,070

247,710

30,256

503,717

917

17,873

9090

Tx430

-

GCA_003482435.1

35,102,930

1,194,497

360,556

236,007

28,860

656,657

1527

15,144

1788

Maize (Zea mays) Genome size: ~ 2000 Mb

B73v4

-

GCF_000005005.2

167,604,407

5,789,626

3,758,096

3,413,940

510,132

3,115,092

6621

122,988

6559

B73v5

-

GCA_902167145.1

170,004,877

3,073,808

1,325,232

1,023,768

130,747

1,670,295

3461

58,418

3864

Mo17v2

-

GCA_022117705.1

172,357,693

2,070,795

285,667

184,521

21,221

1,156,699

2433

47,826

2713

Soybean (Glycine max) Genome size: ~ 1000 Mb

Wm82.a2.v1

-

Gmax 275

15,994,704

812,611

267,541

194,096

25,424

500,153

714

14,282

1003

JD17

-

GCA_021733175.1

16,341,705

569,416

213,129

147,393

18,852

335,286

808

10,107

1196