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

Table 1 Single-step model names and model differences in the mixed model equations

Name	J factor	Mixed model equations
reg	None	Regression effects for genetic groups
regJ1	\({\mathbf{Q}}_{\mathrm{c}}={\mathbf{1}}\)	Regression effects for genetic groups and one J factor
regJQ	\({\mathbf{Q}}_{\mathrm{c}}={\mathbf{Q}}_{2}\)	Regression effects for genetic groups and many J factors
QP	None	QP transformation of genetic groups
QPJ1	\({\mathbf{Q}}_{\mathrm{c}}={\mathbf{1}}\)	QP transformation of genetic groups and an absorbed J factor
QPJQ	\({\mathbf{Q}}_{\mathrm{c}}={\mathbf{Q}}_{2}\)	QP transformation of genetic groups and absorbed J factors

The models had either no J factors (None), one J factor (\({\mathbf{Q}}_{\mathrm{c}}={\mathbf{1}}\)) or multiple J factors as defined by the genetic groups (\({\mathbf{Q}}_{\mathrm{c}}={\mathbf{Q}}_{2}\))

ISSN: 1297-9686