How to consider UPG in ssGBLUP (BLUPF90)
The renumbering software in BLUPF90 (renumf90) can create UPG based on year of birth or can recognize UPG in the pedigree.
For more details, check renumf90 and extra options. Independently on how UPG is included in the pedigree file, UPG in ssGBLUP can be considered for $\mathbf{A}^{-1}$, $\mathbf{A}^{-1}$ and $\mathbf{A}_{22}^{-1}$, or $\mathbf{A}^{-1}$, $\mathbf{G}^{-1}$, and $\mathbf{A}_{22}^{-1}$. For research on this topic, check Misztal et al., 2013, Tsuruta et al., 2019, Cesarani et al., 2021, and Masuda et al., 2022
UPG are considered fixed. Click here for details on how to switch to random UPG.
UPG in $\mathbf{A}^{-1}$
This is automatically done when UPG are in the renumbered pedigree and RANDOM_TYPE is add_an_upginb
UPG in $\mathbf{A}^{-1}$, $\mathbf{G}^{-1}$, and $\mathbf{A}_{22}^{-1}$
OPTION exact_upg
UPG in $\mathbf{A}^{-1}$ and $\mathbf{A}_{22}^{-1}$
OPTION exact_upg OPTION TauOmegaQ2 0.0 1.0
The last option is used to assign $\mathbf{Q}_{2}$ (the incidence matrix relating genotyped animals to unknown parent groups) only to $\mathbf{A}_{22}^{-1}$.
Page Tools
