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Table 3 Number of iterations in PCG of linearly equivalent ssGBLUP MME using marker matrix \({\mathbf{Z}}_m^{vR1}\) (VanRaden 1), convergence tolerance \(10^{-12}\), heritability 0.5, and diagonal 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

93

62

59

57

57

1

73,580

152

153

158

158

171

2

111,106

847

1176

1099

1007

950

171

3

181,800

847

4058

3658

3195

2873

57

4

181,800

442

443

702

853

920

283

5

181,800

442

455

720

868

917

124

6

115,054

442

443

702

853

920

283

  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