Table 4 Correlation rates of the GWAS-top 0.5%, 1%, 2%, and 3% marker-sets and whole marker-set.
From: GMStool: GWAS-based marker selection tool for genomic prediction from genomic data
Data | Phenotype | Selected markersa | RRB (train/val./test) | RF (train/val./test) | DNN (train/val./test) | CNN (train/val./test) |
|---|---|---|---|---|---|---|
Rice | DTF | 184 | 0.838/0.777/0.343 | 0.935/0.641/0.330 | 0.914/0.727/0.328 | 0.862/0.686/0.301 |
369 | 0.890/0.709/0.480 | 0.963/0.570/0.464 | 0.945/0.717/0.412 | 0.905/0.656/0.410 | ||
738 | 0.919/0.715/0.478 | 0.968/0.621/0.484 | 0.962/0.726/0.406 | 0.925/0.734/0.468 | ||
1107 | 0.940/0.715/0.448 | 0.968/0.644/0.485 | 0.966/0.713/0.486 | 0.931/0.659/0.439 | ||
All | 0.844/0.412/0.515 | 0.964/0.398/0.529 | 0.899/0.366/0.512 | 0.923/0.363/0.504 | ||
PC | 184 | 0.816/0.744/0.366 | 0.947/0.500/0.376 | 0.851/0.664/0.304 | 0.834/0.680/0.308 | |
369 | 0.871/0.717/0.517 | 0.960/0.524/0.471 | 0.844/0.624/0.486 | 0.872/0.555/0.387 | ||
738 | 0.917/0.761/0.508 | 0.963/0.513/0.521 | 0.874/0.619/0.532 | 0.891/0.708/0.402 | ||
1107 | 0.944/0.760/0.545 | 0.968/0.495/0.537 | 0.958/0.776/0.531 | 0.912/0.732/0.422 | ||
All | 0.874/0.449/0.473 | 0.968/0.326/0.542 | 0.902/0.554/0.521 | 0.917/0.415/0.400 | ||
PH | 184 | 0.914/0.834/0.494 | 0.971/0.787/0.578 | 0.931/0.795/0.492 | 0.944/0.814/0.586 | |
369 | 0.946/0.859/0.571 | 0.976/0.808/0.617 | 0.934/0.823/0.579 | 0.950/0.772/0.643 | ||
738 | 0.970/0.869/0.566 | 0.980/0.830/0.646 | 0.956/0.875/0.527 | 0.952/0.865/0.527 | ||
1107 | 0.982/0.897/0.636 | 0.979/0.849/0.661 | 0.964/0.890/0.603 | 0.955/0.879/0.669 | ||
All | 0.985/0.733/0.631 | 0.972/0.737/0.548 | 0.912/0.765/0.624 | 0.972/0.737/0.548 | ||
SOY | DTF | 478 | 0.641/0.558/0.578 | 0.744/0.644/0.627 | 0.663/0.660/0.628 | 0.566/0.578/0.584 |
957 | 0.832/0.795/0.705 | 0.957/0.778/0.725 | 0.825/0.763/0.705 | 0.634/0.636/0.656 | ||
1914 | 0.905/0.840/0.757 | 0.974/0.775/0.764 | 0.897/0.825/0.747 | 0.846/0.804/0.739 | ||
2871 | 0.944/0.872/0.767 | 0.978/0.809/0.771 | 0.938/0.850/0.746 | 0.810/0.804/0.753 | ||
All | 0.973/0.743/0.753 | 0.976/0.752/0.760 | 0.921/0.751/0.763 | 0.904/0.721/0.748 |
