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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.