Table 2 Prediction accuracy of phenotypes using selected SNPs compared to all SNPs on Ψ data
From: Exploring the potential of incremental feature selection to improve genomic prediction accuracy
Species | Phenotype | #Selected SNPs (%) | R2 (selected SNPs) | R2 (all SNPs) |
|---|---|---|---|---|
Maize | FT | 446 (0.18%) | 0.486 | 0.364 |
HT | 4021 (1.64%) | 0.237 | 0.203 | |
YLD | 1601 (0.65%) | 0.346 | 0.278 | |
Sorghum | HT | 56,299 (100%) | – | 0.287 |
MO | 27,001 (47.96%) | 0.391 | 0.389 | |
YLD | 8501 (15.10%) | 0.003 | 0.030 | |
Soy | HT | 451 (10.65%) | 0.213 | 0.201 |
R8 | 1001 (23.64%) | 0.206 | 0.196 | |
YLD | 731 (17.27%) | 0.373 | 0.370 | |
Spruce | DBH | 6930 (100%) | – | 0.096 |
DE | 2401 (34.65%) | 0.141 | 0.142 | |
HT | 6930 (100%) | – | 0.143 | |
Switchgrass | AN | 75,001 (34.54%) | 0.767 | 0.754 |
HT | 130,001 (59.87%) | 0.519 | 0.513 | |
ST | 217,150 (100%) | – | 0.512 | |
Pig | T1 | 1 (0.003%) | − 0.021 | 0.013 |
T2 | 9501 (28.06%) | 0.190 | 0.192 | |
T3 | 3201 (9.45%) | 0.080 | 0.079 | |
T4 | 8501 (24.66%) | 0.112 | 0.111 | |
T5 | 7001 (20.31%) | 0.172 | 0.163 | |
Chicken | EW28 | 29,001 (9.84%) | 0.046 | 0.046 |
EW36 | 41,001 (13.91%) | 0.088 | 0.070 | |
EW56 | 50,001 (16.97%) | 0.091 | 0.079 | |
EW66 | 43,001 (14.59%) | 0.116 | 0.102 | |
EW72 | 45,001 (15.27%) | 0.015 | − 0.012 | |
EW80 | 60,001 (20.36%) | 0.060 | 0.055 | |
EWAFE | 40,001 (13.57%) | − 0.010 | − 0.014 |