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Table 2 Cross-validation correlations between observed and predicted phenotype

From: Differentially penalized regression to predict agronomic traits from metabolites and markers in wheat

Trait

D

UM

EM

D + UM

D + EM

DiPR D + UM

DiPR D + EM

w DiPR D + UM

w DiPR D + EM

Heading date

0.528

0.568

0.550

0.594

0.570

0.574

0.589

0.464

0.251

Plant height

0.609

0.534

0.587

0.615

0.655

0.621

0.660

0.688

0.349

Yield

0.234

0.226

0.310

0.301

0.295

0.315

0.268

0.699

0.015

Thousand kernel weight

0.465

0.462

0.486

0.531

0.481

0.521

0.483

0.453

0.105

Protein

0.221

0.600

0.666

0.537

0.378

0.600

0.666

0.000

0.000

Gluten content

0.391

0.581

0.635

0.574

0.462

0.558

0.635

0.287

0.000

Water absorption

0.145

0.412

0.486

0.373

0.235

0.400

0.486

0.043

0.000

Starch content

0.181

0.580

0.631

0.549

0.385

0.578

0.620

0.007

0.024

Moisture content

0.095

0.304

0.283

0.312

0.161

0.323

0.195

0.353

0.129

Zeleny sedimentation1

0.446

0.590

0.591

0.615

0.515

0.619

0.604

0.400

0.111

Hardness Index

0.145

0.384

0.401

0.383

0.222

0.379

0.393

0.351

0.048

Test weight

0.648

0.662

0.684

0.689

0.689

0.678

0.662

0.456

0.296

Zeleny sedimentation2

0.570

failed

failed

0.492

0.566

0.570

0.566

1.000

0.996

Protein content1

0.462

0.505

0.538

0.542

0.520

0.522

0.610

0.399

0.100

Protein content2

0.323

0.603

0.584

0.568

0.456

0.593

0.581

0.101

0.051

kernel weight

0.528

0.391

0.460

0.555

0.545

0.542

0.563

0.557

0.250

kernel diameter

0.539

0.440

0.466

0.589

0.565

0.584

0.607

0.549

0.202

Hardness Index

0.229

0.540

0.666

0.418

0.263

0.538

0.688

0.020

0.050

Moisture content

0.207

0.362

0.350

0.304

0.227

0.362

0.350

0.000

0.000

Gluten content

0.163

0.547

0.586

0.448

0.307

0.547

0.586

0.000

0.000

Gluten Index

0.449

0.026

0.183

0.379

0.461

0.385

0.464

0.790

0.300

Falling Number

0.102

0.783

0.783

0.753

0.627

0.782

0.788

0.001

0.152

flour yield

−0.068

0.285

0.483

0.152

0.018

0.285

0.483

0.000

0.000

bran yield

0.541

0.360

0.315

0.525

0.549

0.544

0.537

0.464

0.251

Average

0.340

0.467

0.510

0.492

0.423

0.517

0.545

0.351

0.164

Maximum

0.648

0.783

0.783

0.753

0.689

0.782

0.788

1.000

0.996

Minimum

−0.068

0.026

0.183

0.152

0.018

0.285

0.195

0.000

0.000

  1. Each of 151 varieties was dropped in turn; a prediction equation computed with drop-one cross-validation from the remaining set of 150 was then used to predict the phenotype of the missing variety. The reported correlations are between 151 observed and predicted phenotypes. D: DArT markers.UM: unextracted metabolites. EM: extracted metabolites. DiPR: differentially penalized regression. w: weighting factor for DiPR. Bold: maximum cross-validation correlation. Italics: w = 0, 0.5 or 1, equivalent to standard ridge regression on metabolites, metabolites + markers, and markers, respectively.