TABLE 4.
Loss of accuracy of GEBVs with genotyping of selected low-density (SLD) SNPs as a percentage of the accuracy obtained by high-density BayesB in generations after training and with 100, 500, and 1000 simulated QTL
| No. of simulated QTL | Generation
|
|||
|---|---|---|---|---|
| Method | 2 | 3 | 4 | |
| SLD-BB-110 | 1.1 (±3.2) | 0.8 (±3.2) | 0.7 (±4.2) | |
| 100 | SLD-BB-40 | 3.1 (±3.1) | 2.0 (±3.2) | 1.7 (±4.2) |
| SLD-FSS-0.01 | 9.0 (±2.4) | 8.1 (±3.3) | 8.7 (±4.0) | |
| SLD-FSS-110 | 18.2 (±3.2) | 23.1 (±3.2) | 24.9 (±4.2) | |
| SLD-BB-110 | 2.5 (±3.2) | 1.9 (±4.8) | 1.5 (±5.4) | |
| 500 | SLD-BB-40 | 7.8 (±3.2) | 6.5 (±4.8) | 4.02 (±5.0) |
| SLD-FSS-0.01 | 10.7 (±2.7) | 10.6 (±4.0) | 12.1 (±4.1) | |
| SLD-FSS-110 | 12.5 (±2.8) | 14.2 (±2.8) | 18.8 (±4.3) | |
| SLD-BB-110 | 3.0 (±3.3) | 2.6 (±3.8) | 2.3 (±4.9) | |
| 1000 | SLD-BB-40 | 9.2 (±3.3) | 9.7 (±3.7) | 8.4 (±4.9) |
| SLD-FSS-0.01 | 12.8 (±3.2) | 17.7 (±4.1) | 21.0 (±4.6) | |
| SLD-FSS-110 | 13.7 (±3.5) | 18.4 (±3.8) | 22.0 (±4.2) | |
One thousand individuals were used to estimate HD-SNP effects (±SE, based on 25 replicates). SLD-BB-110 and SLD-BB-40 refer to selection of 110 and 40 SNPs using BayesB; SLD-FSS-0.01 and SLD-FSS-110 refer to selection of SNPs by forward stepwise selection with a significance level of 0.01 or with a total of 110 SNPs selected.