Table 2.

Number of lines, number of groups and compression level of the full 2480 × 2480 kinship matrix, and proportion of total line mean variance explained by additive relationship matrix from the four mixed-linear model (MLM) analyses

	N a	Groups b	Compression c	${\left(\frac{{\hat{\mathbf{\sigma }}}_{\mathbf{G}}^{\mathbf{2}}}{{\hat{\mathbf{\sigma }}}_{\mathbf{G}}^{\mathbf{2}}\mathbf{+}{\hat{\mathbf{\sigma }}}^{\mathbf{2}}}\right)}^{\mathit{d}}$
Full inbred panel	1687	2100	1.18	0.31
Filtered inbred panel	734	2000	1.24	0.42
B47 topcrosses	243	1760	1.41	0.31
PHZ51 topcrosses	313	1770	1.40	0.39

^aTotal number of entries included in the analysis.

^bNumber of groups determined by optimum compression (note that the complete kinship matrix for 2480 lines was used for all analyses).

^cCompression level is the average number of individuals per group.

^dPolygenic additive background genetic variance divided by total phenotypic variance. This ratio was estimated in GAPIT by fitting the kinship matrix (K) in the mixed linear model without any SNP marker effects.