Table 1.
Average (SD) of marker and QTL related statistics of the simulated population presenting high LD
| Method/Scenarioa | Pvar_topMRKw(%)b | Pvar_1stMRKw(%)c | NtrueQTLd |
|---|---|---|---|
| Bayes C (π = 0.99) | 7.78 (0.99) | 1.19 (0.63) | 2.20 (1.23) |
| Bayes C (π = 0.999) | 46.13 (14.13) | 16.45 (17.86) | 1.90 (1.29) |
| WssGBLUP/SIw1 | 5.16 (0.74) | 0.54 (0.17) | 2.90 (1.66) |
| WssGBLUP/SIw2 | 17.03 (3.11) | 2.29 (0.94) | 2.90 (1.79) |
| WssGBLUP/SIw3 | 38.07 (6.27) | 7.30 (3.30) | 1.30 (1.16) |
| WssGBLUP/SIIw1 | 5.30 (0.63) | 0.59 (0.19) | 2.00 (1.49) |
| WssGBLUP/SIIw2 | 18.76 (1.70) | 2.65 (0.93) | 1.90 (1.29) |
| WssGBLUP/SIIw3 | 39.31 (7.47) | 7.82 (5.80) | 0.90 (0.74) |
| True values | Pvar_topQTL(%)b | Pvar_1stQTL (%)c | NtopQTLd |
| 29.74 (4.88) | 5.07 (2.36) | 16.7 (2.83) |
The averages are expressed over the ten replicates, using the Bayes C and weighted single step GBLUP (WssGBLUP) analyses
aGWAS using (SI) or ignoring (SII) phenotypic information of non-genotyped animals, applying different weights (w1, w2 and w3) for the SNP effects in the WssGBLUP method. And using π = 0.99 and π = 0.999 in the Bayes C method
bGenetic variance (%) explained by the sum of variances accounted by top marker windows (Pvar_topMRKw) and by the NtopQTLs (Pvar_topQTL)
cMaximum genetic variance (%) explained by a top marker window (Pvar_1stMRKw) and by a topQTL (Pvar_1stQTL)
dEstimated number of true QTLs explaining 1 % or more of the genetic variance (NtopQTL), and number of NtopQTLs identified by a top marker window distant no more than 1 Mb from a NtopQTL (NtrueQTL)