Table 2. Transcriptome Expression Variation across Six Tissues in the Context of B73 and PH207 Annotated Genes.

	B73a	PH207a
Expression competence
Never expressed	6,180	5,885
Expressed in ≥1 tissue	33,121	34,672
Differential expression between genotypes
Always differentially expressed	1,655	1,968
Sometimes differentially expressed	18,913	19,363
Never differentially expressed	18,733	19,226
Genotype-specific expression pattern
Always genotype specific if expressed	3,532	3,964
Sometimes genotype specific	8,719	9,910
Never genotype specific	27,050	26,683

B73 and PH207 RNA-seq reads were mapped to both their cognate genome and the reciprocal genome, and expression was summarized as read counts in each of the mapping scenarios. Tissues included in this analysis were leaf blade, root cortical parenchyma, root stele, germinating kernel, root tip, and whole seedling.

^aThe total number of genes in each genotype are 39,301 (B73) and 40,557 (PH207).