Single-step genomic BLUP with genetic groups and automatic adjustment for allele coding

Table 2 Number of iterations until convergence in single-step GBLUP when the centering of the markers for the genomic relationship matrix used base population allele frequencies (before the “/” sign) or an allele frequency of 0.5 for all markers (after the “/” sign)

Model	Groups	Groups + J1	Groups + JQ
Reg, dense	1999/2908	1646/1531	2979/2448
Reg, sparse	1991/2929	1647/1555	2961/2426
QP	1990/2134	2149/2051	2227/2207

Groups: the model had genetic groups; Groups + J1: the model had genetic groups and a single J factor; Groups + JQ: the model had genetic groups and group-wise J factors; reg, dense: regression coefficients for genetic groups and J factors in a dense matrix; reg, sparse: regression coefficients for genetic groups in a sparse matrix and J factors in a dense matrix; QP: genetic groups and J factors by QP transformation

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