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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)