Skip to main content

Table 4 Number of iterations in PCG of linearly equivalent ssGBLUP MME using marker matrix \({\mathbf{Z}}_m^{vR1}\) (VanRaden 1), convergence tolerance \(10^{-12}\), heritability 0.1, and no preconditioning under different polygenic proportions w

From: Single-step SNP-BLUP with on-the-fly imputed genotypes and residual polygenic effects

MME

Size

Weight \({w}\)

0.00

0.01

0.10

0.20

0.30

1.00

Orig.

73,580

619

622

624

624

623

1

73,580

758

733

701

728

744

2

111,106

736

1005

970

907

836

748

3

181,800

736

3422

3315

3154

2934

623

4

181,800

74

74

72

72

71

71

5

181,800

74

73

72

70

71

70

6

115,054

74

74

72

72

71

71

  1. MME, original ssGBLUP; 1, basic equivalent ssGBLUP; 2, basic RPG ssSNP-BLUP; 3, expanded RPG ssSNP-BLUP; 4, orthogonal ssSNP-BLUP; 5, orthogonal expanded ssSNP-BLUP; 6, reduced orthogonal ssSNP-BLUP