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Table 2 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 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

362

358

358

355

357

1

73,580

536

512

536

523

536

2

111,106

646

1203

1085

987

886

536

3

181,800

646

4023

3660

3307

3040

355

4

181,800

193

196

193

191

190

182

5

181,800

193

197

194

192

190

181

6

115,054

193

196

193

191

190

182

  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