Table 2. SPE Genes of the Individual Root Tissues and Their Assignment to Maize Subgenomes.

	No. of Genes	No. of Genes Assigned to Subgenomes	%	Subgenome 1	%	Subgenome 2	%
FGS genesa	39,656	19,365	49	12,190	63	7,175	37
Expressed genes PRT	27,347	17,402	64	10,962	63	6,440	37
Expressed genes WPR	28,113	17,996	64	11,343	63	6,653	37
SPE class
SPE total	2,341	696***	30	429	62	267	38
SPE_C	1,260	310***	25	197	64	113	36
SPE_S	1,287	294***	23	184	63	110	37
SPE_EZ	1,037	226***	22	156	68	71	31
SPE_MZ	1,091	199***	18	113	57	86	43
SPE WPR	946	131***	14	87	66	44	34

In addition to our tissue-specific analysis (PRT), a published WPR data set (Paschold et al., 2012) was reanalyzed using the same method as in this study. Fisher’s exact test was used to determine if more or less SPE genes than expected are assigned to subgenomes (***P < 0.001).

^aFiltered gene set of maize B73.