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Table 2 Average (SD) of marker and QTL related statistics of the simulated population presenting low 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)

3.95 (0.58)

0.42 (0.10)

1.40 (0.97)

Bayes C (π = 0.999)

36.71 (12.35)

12.39 (11.93)

1.80 (1.62)

WssGBLUP/SIw1

2.73 (0.53)

0.25 (0.08)

2.00 (1.70)

WssGBLUP/SIw2

10.58 (1.59)

1.45 (0.37)

2.10 (1.29)

WssGBLUP/SIw3

26.80 (4.93)

4.51 (1.31)

1.20 (0.63)

WssGBLUP/SIIw1

2.82 (0.35)

0.26 (0.04)

1.90 (1.20)

WssGBLUP/SIIw2

12.05 (1.72)

1.69 (0.38)

1.90 (1.10)

WssGBLUP/SIIw3

31.60 (3.76)

5.66 (2.49)

1.10 (0.88)

True values

Pvar_topQTL(%)b

Pvar_1stQTL (%)c

topQTLd

24.32 (4.92)

3.19 (0.61)

15.4 (2.32)

  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)
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BMC Genomic Data

ISSN: 2730-6844

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