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Table 3 Average Linkage Disequilibrium (r2) for different distances between closely located SNP pairs.

From: Accuracy of genomic selection in simulated populations mimicking the extent of linkage disequilibrium in beef cattle

  

POP1 (40 k)

POP2 (800 k)

h2

Distance

range (Mb)

Pairs

r2(SD)

Frequency

r2 > 0.30 (%)

Pairs

r2 (SD)

Frequency

r2 > 0.30 (%)

 

0.00-0.10

5049

0.23 (0.24)

1512 (29.95)

4275

0.24 (0.25)

1272 (29.75)

 

0.10-0.20

5074

0.17 (0.19)

1063 (20.95)

4474

0.18 (0.20)

919 (20.54)

 

0.20-0.30

6265

0.14 (0.16)

885 (14.13)

4290

0.14 (0.16)

644 (15.01)

 

0.30-0.40

4938

0.12 (0.14)

510 (10.33)

4358

0.12 (0.14)

493 (11.31)

 

0.40-0.50

5042

0.10 (0.13)

425 (8.43)

4280

0.10 (0.13)

359 (8.39)

0.10

0.50-0.60

6199

0.09 (0.11)

370 (5.97)

4196

0.09 (0.12)

279 (6.65)

 

0.60-0.70

4994

0.08 (0.10)

228 (4.57)

4208

0.09 (0.11)

242 (5.75)

 

0.70-0.80

5975

0.07 (0.09)

187 (3.69)

4268

0.08 (0.10)

190 (4.45)

 

0.80-0.90

6183

0.07 (0.09)

167 (2.70)

4334

0.07 (0.10)

170 (3.92)

 

0.90-1.00

4917

0.06 (0.08)

128 (2.60)

4163

0.07 (0.09)

149 (3.58)

 

Overall

3932610

0.008 (0.03)

6151 (0.16)

3126250

0.01 (0.03)

6062 (0.19)

 

0.00-0.10

5248

0.22 (0.24)

1495 (28.49)

4494

0.24 (0.25)

1375 (30.60)

 

0.10-0.20

5224

0.17 (0.19)

1077 (20.62)

4740

0.18 (0.20)

1006 (21.22)

 

0.20-0.30

6528

0.13 (0.16)

855 (13.10)

4630

0.14 (0.17)

724 (15.64)

 

0.30-0.40

5147

0.11 (0.14)

461 (8.96)

4560

0.12 (0.14)

488 (10.70)

 

0.40-0.50

5112

0.09 (0.12)

315 (6.16)

4596

0.11 (0.13)

406 (8.83)

0.25

0.50-0.60

6466

0.08 (0.11)

343 (5.31)

4469

0.10 (0.12)

333 (7.45)

 

0.60-0.70

5146

0.07 (0.09)

186 (3.61)

4418

0.09 (0.11)

250 (5.66)

 

0.70-0.80

5227

0.07 (0.09)

139 (2.66)

4502

0.08 (0.10)

226 (5.02)

 

0.80-0.90

6431

0.06 (0.08)

178 (2.77)

4359

0.08 (0.10)

207 (4.75)

 

0.90-1.00

5129

0.06 (0.08)

95 (1.85)

4416

0.07 (0.09)

154 (3.49)

 

Overall

4096952

0.006 (0.03)

5689 (0.14)

3283438

0.011 (0.03)

6543 (0.20)

 

0.00-0.10

5439

0.22 (0.24)

1517 (27.89)

4191

0.24 (0.24)

1265 (30.18)

 

0.10-0.20

5468

0.17 (0.19)

1070 (19.57)

4225

0.17 (0.20)

865 (20.47)

 

0.20-0.30

6801

0.13 (0.16)

886 (13.03)

4263

0.14 (0.16)

621 (14.57)

 

0.30-0.40

5435

0.11 (0.14)

543 (9.99)

4251

0.12 (0.14)

457 (10.75)

 

0.40-0.50

5444

0.09 (0.12)

361 (6.63)

4286

0.10 (0.12)

333 (7.77)

0.40

0.50-0.60

6782

0.08 (0.10)

293 (4.32)

4284

0.09 (0.11)

270 (6.30)

 

0.60-0.70

5377

0.07 (0.09)

176 (3.27)

4103

0.09 (0.11)

232 (5.65)

 

0.70-0.80

5374

0.07 (0.09)

150 (2.79)

4260

0.08 (0.10)

205 (4.81)

 

0.80-0.90

6733

0.06 (0.08)

155 (2.30)

4285

0.07 (0.09)

136 (3.17)

 

0.90-1.00

5342

0.06 (0.07)

75 (1.40)

4199

0.06 (0.08)

104 (2.48)

 

Overall

4290985

0.006 (0.03)

5710 (0.13)

3072154

0.010 (0.03)

5305 (0.17)

  1. The results are for chromosome 1 in the recent generations for three heritability levels and POP1 (40 k) and POP2 (800 k) for one replicate. For POP2 (800 k), 40 k markers were randomly sampled to represent the 800 k panel.
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BMC Genomic Data

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