Single-step SNP-BLUP with on-the-fly imputed genotypes and residual polygenic effects

Table 1 Number of rows (\(N_r\)), columns (\(N_c\)), non-zeros (\(N_z\)), and mean number of non-zeros on row or column (\(M_z\)) by matrix used in MME coefficient matrices in the test case with 73,579 animals

Matrix	\(N_r\)	\(N_c\)	\(N_z\)	\(M_z\)
\({\mathbf{A}}^{-1}\)	73,579	73,579	235,669^a	3.20^a
\({\mathbf{A}}^{11}\)	70,694	70,694	168,818^a	2.39^a
\({\mathbf{A}}^{12}\)	70,694	2885	62,489	0.88/21.66
\({\mathbf{A}}^{22}\)	2885	2885	4362^a	1.51^a
\({\mathbf{L}}\)	73,579	73,579	191,026	2.60
\({\mathbf{L}}_1\)	70,694	70,694	181,536	2.57
\({\widehat{{\mathbf{A}}}}^{-1}\)	6833	6833	22,612^a	3.31^a
\(\widehat{{\mathbf{L}}}\)	6833	6833	18,173	2.66

\({\mathbf{L}}\) and \({\mathbf{L}}_1\) are Cholesky decomposition matrices of \({\mathbf{A}}^{-1}\) (inverse of pedigree relationship matrix) and \({\mathbf{A}}^{11}\) (submatrix of \({\mathbf{A}}^{-1}\)), respectively. \(\widehat{{\mathbf{A}}}\) and \(\widehat{{\mathbf{L}}}\) are the corresponding matrices for smaller pedigree of genotyped animals and their ancestors
^aNon-zeros of symmetric matrices counted from the lower/upper triangular region only

ISSN: 1297-9686