Skip to main content

Table 5 Boundaries of the validated regions that are additively significant on calving interval as well as the most significant SNPs and their associated genes within these regions in discovery and validation populations

From: Validation of markers with non-additive effects on milk yield and fertility in Holstein and Jersey cows

  

Most strongly associated SNP in discovery

Most strongly associated SNP in validation

 

BTCa

Interval (Mbp)b

SNP

Position (bP)

-log10 (P)

Effect ± SE

MAFc

\( \frac{\sigma_a^2}{\sigma_p^2} \) (%)d

SNP

Position (bp)

-log10 (P)

Effect ± SE

MAF

\( \frac{\sigma_a^2}{\sigma_p^2} \) (%)

Genes

5

12.551 - 13.463

rs133249083

13027942

4.139

2.462 ± 0.620

0.329

0.095

rs135584613

13270757

3.229

−3.077 ± 0.893

0.325

0.140

NA

5

88.607 - 89.159

rs135833682

88822777

4.076

−2.191 ± 0.556

0.417

0.083

rs133539520

88861488

2.679

−2.784 ± 0.934

0.313

0.112

ABCC9

9

55.233 - 55.657

rs134339497

55233033

4.325

−2.364 ± 0.580

0.402

0.096

rs136630637

55637401

2.399

−2.559 ± 0.887

0.337

0.098

NA

9

57.397 - 57.735

rs137407787

57396816

4.130

−2.346 ± 0.591

0.358

0.091

rs42550144

57723628

2.408

−2.685 ± 0.929

0.290

0.100

EPHA7

9

60.121 - 60.477

rs43600502

60477358

5.195

−2.642 ± 0.584

0.352

0.114

rs133175600

60130790

2.127

2.813 ± 1.05

0.212

0.087

LOC101902479

11

20.620 – 21.274

rs133774241

20994163

4.318

−2.706 ± 0.665

0.241

0.096

rs137059194

20898669

2.410

−2.467 ± 0.8529

0.458

0.101

LOC783737

11

39.466 - 39.772

rs109315341

39466071

4.126

−2.971 ± 0.749

0.177

0.092

rs133126268

39747182

2.408

−3.706 ± 1.284

0.115

0.094

NA

11

40.896 - 41.299

rs133462686

41298588

4.491

−3.036 ± 0.729

0.182

0.098

rs109834745

40895791

2.414

3.554 ± 1.228

0.139

0.101

LOC101903002

18

4.541 - 4.810

rs109920290

4541123

4.326

2.4 ± 0.589

0.391

0.098

rs110689012

4810082

2.044

3.37 ± 1.29

0.119

0.080

NA

18

37.446 - 37.925

rs41875426

37446338

4.061

2.679 ± 0.682

0.213

0.086

rs137407722

37925382

3.142

4.111 ± 1.213

0.147

0.142

NA

18

53.789 - 54.605

rs41891477

54232476

4.180

−2.302 ± 0.576

0.399

0.091

rs109907036

54028686

3.680

4.065 ± 1.094

0.186

0.168

PRKD2 / PPP5C

18

57.109 - 58.052

rs110801791

57516245

4.675

−3.508 ± 0.824

0.136

0.103

rs41895542

57269152

2.496

3.6 ± 1.219

0.133

0.100

NA

18

61.922 - 62.150

rs133761590

62115202

4.661

2.525 ± 0.594

0.369

0.106

rs137170802

62143810

2.736

−3.018 ± 0.966

0.255

0.116

CACNG6 / VSTM1

22

4.979 - 5.598

rs41996522

5028345

6.076

−2.784 ± 0.564

0.442

0.137

rs41995585

5133660

2.168

−3.028 ± 1.117

0.168

0.086

NA

27

41.873 - 42.109

rs134294374

42079983

5.581

−2.76 ± 0.586

0.367

0.127

rs41586304

41872925

2.295

3.105 ± 1.107

0.176

0.094

NR1D2

27

43.595 - 44.261

rs110746407

43914360

6.075

−2.781 ± 0.564

0.441

0.136

 

rs43064076

43595406

2.873

−3.831 ± 1.192

0.146

0.123

NA

X

139.211 - 139.509

rs136627433

139508886

4.679

−2.606 ± 0.6098

0.394

0.116

 

rs110719178

139490243

2.320

−3.327 ± 1.175

0.163

0.101

NA

  1. aBTC: Bos Taurus chromosome
  2. bIntervals containing individually validated SNPs are in bold
  3. c MAF minor allele frequency
  4. d σ 2 a = additive variance; σ 2 p = phenotypic variance