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Table 1 Average (SD) of marker and QTL related statistics of the simulated population presenting high LD

From: Assessing the value of phenotypic information from non-genotyped animals for QTL mapping of complex traits in real and simulated populations

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)
  1. The averages are expressed over the ten replicates, using the Bayes C and weighted single step GBLUP (WssGBLUP) analyses
  2. 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
  3. bGenetic variance (%) explained by the sum of variances accounted by top marker windows (Pvar_topMRKw) and by the NtopQTLs (Pvar_topQTL)
  4. cMaximum genetic variance (%) explained by a top marker window (Pvar_1stMRKw) and by a topQTL (Pvar_1stQTL)
  5. 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)