Table 2

Average number of SNPs (#SNP) fitted in the model, estimated variance components, and estimated heritability (Heritability).

Methods

#SNP

Estimated variance components

Heritability


Marker

Polygenic

Genetic1

Residual

Total


True value2

51.76

51.76

103.52

0.500

P-BLUP

54.44

54.44

48.68

103.12

0.528

G-BLUP

10031

No Poly

44.54

44.54

54.84

99.38

0.448

Poly

38.53

12.09

50.62

49.04

99.66

0.508

BayesB, π = 0.75

2508

No Poly

44.28

44.28

54.08

98.36

0.450

Poly

39.05

11.06

50.11

48.32

98.43

0.509

BayesB, π = 0.95

502

No Poly

43.96

43.96

54.16

98.12

0.448

Poly

38.05

12.80

50.85

47.59

98.44

0.517

BayesB, π = 0.99

100

No Poly

43.44

43.44

54.58

98.02

0.443

Poly

37.43

12.35

49.78

48.30

98.09

0.508

BayesCπ

No Poly

124

45.68

45.68

53.63

99.31

0.460

Poly

80

40.21

10.33

50.54

48.58

99.12

0.510

BayesCπ gen 53

No Poly

92

47.13

47.13

53.48

100.61

0.468


Results are based on training on the first three generations and validation on generation 4 using P-BLUP, G-BLUP, BayesB with different π’s, and BayesCπ, and without (No Poly) and with (Poly) polygenic effects.

1Total genetic variance = marker variance + polygenic variance.

2Total QTL variance = residual variance = 51.76 in the QTLMAS2010 dataset.

3Training on the first 4 generations.

Sun et al. BMC Proceedings 2011 5(Suppl 3):S13   doi:10.1186/1753-6561-5-S3-S13

Open Data