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