Table 4.
Prediction accuracy (r ± s) of seven traits using all single nucleotide polymorphisms (SNPs) and different combinations of quantitative trait loci (QTL) identified by different combinations of statistical models. GBLUP was used to estimate r values.
| Traits | Models | Marker Sets | No. of Markers | r ± s |
|---|---|---|---|---|
| YLD | All | QTL of YLD | 361 | 0.892 ± 0.023a |
| BM | QTL of YLD | 323 | 0.885 ± 0.027a | |
| All | QTL for YLD + DTM | 643 | 0.879 ± 0.026a | |
| BM | QTL of all traits | 1208 | 0.862 ± 0.030b | |
| All | QTL of all traits | 1420 | 0.860 ± 0.030b | |
| SS+SM | QTL of all traits | 427 | 0.850 ± 0.031c | |
| - | All SNPs | 17,277 | 0.841 ± 0.035d | |
| SS+SM | QTL of YLD | 53 | 0.807 ± 0.034e | |
| SS | QTL of all traits | 133 | 0.789 ± 0.045f | |
| SS | QTL of YLD | 8 | 0.483 ± 0.085g | |
| DTM | All | QTL of DTM | 351 | 0.730 ± 0.062a |
| SS+SM | QTL of DTM | 71 | 0.720 ± 0.063a | |
| BM | QTL of DTM | 301 | 0.719 ± 0.066a | |
| All | QTL for DTM + YLD | 643 | 0.689 ± 0.076b | |
| BM | QTL of all traits | 1208 | 0.608 ± 0.083b | |
| All | QTL of all traits | 1420 | 0.603 ± 0.088b | |
| SS+SM | QTL of all traits | 427 | 0.599 ± 0.087b | |
| SS | QTL of all traits | 133 | 0.497 ± 0.095c | |
| - | All SNPs | 17,277 | 0.449 ± 0.101d | |
| SS | QTL of DTM | 28 | 0.362 ± 0.125e | |
| PRO | All | QTL of PRO | 269 | 0.894 ± 0.023a |
| BM | QTL of PRO | 220 | 0.890 ± 0.024a | |
| All | QTL for PRO +OIL | 504 | 0.879 ± 0.026ab | |
| SS+SM | QTL of PRO | 51 | 0.877 ± 0.026b | |
| SS+SM | QTL of all traits | 427 | 0.864 ± 0.031c | |
| All | QTL of all traits | 1420 | 0.855 ± 0.031d | |
| BM | QTL of all traits | 1208 | 0.854 ± 0.030d | |
| - | All SNPs | 17,277 | 0.825 ± 0.034e | |
| SS | QTL of all traits | 133 | 0.800 ± 0.042f | |
| SS | QTL of PRO | 31 | 0.681 ± 0.069g | |
| OIL | All | QTL of OIL | 254 | 0.929 ± 0.016a |
| All | QTL for PRO + OIL | 504 | 0.927 ± 0.018a | |
| SS+SM | QTL of OIL | 84 | 0.919 ± 0.017b | |
| BM | QTL of OIL | 186 | 0.911 ± 0.023c | |
| SS+SM | QTL of all traits | 427 | 0.909 ± 0.021c | |
| All | QTL of all traits | 1420 | 0.909 ± 0.023c | |
| BM | QTL of all traits | 1208 | 0.907 ± 0.023c | |
| - | All SNPs | 17,277 | 0.889 ± 0.028d | |
| SS | QTL of all traits | 133 | 0.845 ± 0.042e | |
| SS | QTL of OIL | 10 | 0.762 ± 0.058f | |
| IOD | SS+SM | QTL of IOD | 72 | 0.835 ± 0.041a |
| All | QTL of IOD | 283 | 0.824 ± 0.046a | |
| All | QTL for IOD + LIO + LIN | 468 | 0.825 ± 0.051a | |
| SS+SM | QTL of all traits | 427 | 0.801 ± 0.055b | |
| BM | QTL of IOD | 190 | 0.752 ± 0.066c | |
| SS | QTL of IOD | 71 | 0.746 ± 0.065c | |
| All | QTL of all traits | 1420 | 0.745 ± 0.066c | |
| BM | QTL of all traits | 1208 | 0.717 ± 0.072d | |
| SS | QTL of all traits | 133 | 0.717 ± 0.072d | |
| - | All SNPs | 17,277 | 0.639 ± 0.073e | |
| LIO | All | QTL for IOD + LIO + LIN | 468 | 0.836 ± 0.043a |
| SS+SM | QTL of LIO | 87 | 0.835 ± 0.039a | |
| All | QTL of LIO | 254 | 0.834 ± 0.048a | |
| SS+SM | QTL of all traits | 427 | 0.817 ± 0.049b | |
| BM | QTL of LIO | 152 | 0.812 ± 0.049b | |
| All | QTL of all traits | 1420 | 0.770 ± 0.055c | |
| SS | QTL of LIO | 68 | 0.765 ± 0.056c | |
| BM | QTL of all traits | 1208 | 0.744 ± 0.058d | |
| SS | QTL of all traits | 133 | 0.736 ± 0.066d | |
| - | All SNPs | 17,277 | 0.672 ± 0.063e | |
| LIN | SS+SM | QTL of LIN | 67 | 0.837 ± 0.041a |
| All | QTL of LIN | 256 | 0.833 ± 0.051a | |
| All | QTL for IOD + LIO + LIN | 468 | 0.830 ± 0.047a | |
| SS+SM | QTL of all traits | 427 | 0.809 ± 0.053b | |
| BM | QTL of LIN | 170 | 0.792 ± 0.062c | |
| SS | QTL of LIN | 70 | 0.756 ± 0.062d | |
| All | QTL of all traits | 1420 | 0.755 ± 0.061d | |
| BM | QTL of all traits | 1208 | 0.727 ± 0.066e | |
| SS | QTL of all traits | 133 | 0.725 ± 0.070e | |
| - | All SNPs | 17,277 | 0.649 ± 0.069f |
Letters indicate significant difference at α= 0.05 level. Tukey’s multiple range test was used. The highest prediction accuracy of each trait is highlighted in bold font. SS, SNP-based single-locus model; SM, SNP-based multi-locus model; BM, block-based model; All, SS+SM+BM; seed yield; DTM, days to maturity; PRO, protein content; OIL, oil content; IOD, iodine value; LIO, linoleic acid content; LIN, linolenic acid content.