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Table 2 Variance components from GBLUP and BayesR for the combined (bull and cow) reference sets

From: Improved precision of QTL mapping using a nonlinear Bayesian method in a multi-breed population leads to greater accuracy of across-breed genomic predictions

Breed

Trait

Pedigree estimate

GBLUP estimate

BayesR estimate

σ 2 P

h 2 a2

σ 2 P

h 2 v

h 2 a

h 2 v /( h 2 v   +  h 2 a )

σ 2 P

h 2 v

h 2 a

h 2 v /( h 2 v   +  h 2 a )

Holstein

FY

437.43

0.428

420.05

0.273

0.122

0.692

416.23

0.242

0.146

0.623

Holstein

MY

341880

0.533

321395

0.361

0.134

0.729

307529

0.312

0.176

0.639

Holstein

PY

272.29

0.469

262.13

0.273

0.142

0.658

263.62

0.255

0.166

0.606

Holstein

F%

0.0839

0.728

0.0776

0.628

0.098

0.865

0.0613

0.473

0.181

0.723

Holstein

P%

0.0148

0.864

0.0132

0.643

0.136

0.825

0.0137

0.597

0.188

0.760

Holstein

FERT

3335

0.014

3260

0.014

0.000

1.000

3269

0.014

0.001

0.948

Holstein

SURV

0.0698

0.025

0.0690

0.019

0.003

0.849

0.0594

0.023

0.009

0.708

Holstein

STAT

1.50

0.244

1.42

0.225

0.007

0.969

1.45

0.225

0.020

0.918

Jersey

FY

359.48

0.534

366.59

0.298

0.175

0.630

358.44

0.276

0.150

0.648

Jersey

MY

226780

0.606

226188

0.402

0.186

0.684

213026

0.371

0.163

0.695

Jersey

PY

219.18

0.539

221.68

0.292

0.182

0.616

220.37

0.281

0.167

0.628

Jersey

F%*

0.1013

0.992

0.1051

0.648

0.335

0.660

0.0735

0.566

0.283

0.666

Jersey

P%

0.0254

0.863

0.0243

0.695

0.188

0.787

0.0219

0.611

0.183

0.770

Jersey

FERT

3975

0.004

3928

0.005

0.000

1.000

3890

0.005

0.001

0.891

Jersey

SURV

0.0456

0.051

0.0455

0.029

0.020

0.587

0.0453

0.028

0.020

0.578

Jersey

STAT

0.76

0.405

0.76

0.297

0.093

0.762

0.75

0.294

0.075

0.796

Hol/Jer

FY

413.96

0.454

404.82

0.276

0.137

0.668

405.77

0.248

0.159

0.610

Hol/Jer

MY

307160

0.556

293243

0.373

0.148

0.715

288223

0.340

0.180

0.654

Hol/Jer

PY

256.40

0.487

250.61

0.276

0.154

0.642

256.90

0.272

0.169

0.617

Hol/Jer

F%

0.0895

0.795

0.0866

0.633

0.143

0.816

0.0688

0.503

0.201

0.714

Hol/Jer

P%

0.0179

0.844

0.0164

0.636

0.159

0.800

0.0178

0.621

0.169

0.786

Hol/Jer

FERT

3530

0.011

3465

0.012

0.000

1.000

3452

0.012

0.000

0.963

Hol/Jer

SURV

0.0627

0.029

0.0622

0.021

0.006

0.761

0.0626

0.021

0.009

0.710

Hol/Jer

STAT

1.20

0.312

1.15

0.267

0.026

0.912

1.19

0.268

0.038

0.877

  1. FY = fat yield (kg/lactation), MY = milk yield (L/lactation), PY = protein yield (kg/lactation), F% = fat percentage (%) and P% = protein percentage in milk (%); STAT = stature; FERT = fertility (calving interval, days); and SURV = daughter survival (annual probability); σ 2 P  = phenotypic variance, and ratios of h 2 v  = σ 2 v /σ 2 P (where σ 2 v  = variance explained by SNPs) and h 2 a  = σ 2 a /σ 2 P (where σ 2 a  = additive genetic variance) or h 2 a2 = σ 2 a2/σ 2 P (where σ 2 a2  = additive genetic variance, when SNPs are not included in the model); *due to singularities, variance components for F% in Jersey using the pedigree were estimated using an unweighted analysis.