Table 2.
Assignment of Gene Regulatory Modes by Comparisons of F1 DNA, F1 RNA, and 1:1 RNA Mix Sample
| Result of t Test (P < 0.05)a | Inferred Mechanism | B73 × Mo17 (Immature Ear)b | B73 × Mo17 (Embryo)b | B73 × Mo17 (Seedling)b | B84 × B73 (Seedling) | B37 × B73 (Seedling) | Oh43 × B73 (Seedling) | Oh43 × Mo17 (Seedling) | Total |
|---|---|---|---|---|---|---|---|---|---|
| Differentially expressed genes (1:1 RNA mix ≠ F1 DNA) | |||||||||
| 1:1 RNA mix ≈ F1 RNA ≠ F1 DNA | cis-regulatory variation | 88 | 106 | 91 | 23 | 38 | 35 | 43 | 424 (34.5%) |
| 1:1 RNA mix ≠ F1 RNA ≈ F1 DNA | trans-regulatory variation | 10 | 5 | 4 | 2 | 6 | 3 | 4 | 34 (2.8%) |
| 1:1 RNA mix ≠ F1 RNA ≠ F1 DNA | cis- and trans- variation | 22 | 24 | 19 | 0 | 1 | 7 | 8 | 81 (6.6%) |
| 1:1 RNA mix ≈ F1 RNA ≈ F1 DNA | Unknown | 5 | 15 | 10 | 5 | 3 | 6 | 8 | 52 (4.2%) |
| Nondifferentially expressed genes (1:1 RNA mix ≈ F1 DNA) | |||||||||
| 1:1 RNA mix ≈ F1 RNA ≈ F1 DNA | No variation | 76 | 97 | 91 | 29 | 32 | 37 | 43 | 405 (32.9%) |
| 1:1 RNA mix ≈ F1 RNA ≠ F1 DNA | Low levels of cis-variation | 54 | 25 | 36 | 5 | 10 | 9 | 10 | 149 (12.1%) |
| 1:1 RNA mix ≠ F1 RNA ≈ F1 DNA | F1 variation | 17 | 8 | 7 | 1 | 0 | 1 | 4 | 38 (3.1%) |
| 1:1 RNA mix ≠ F1 RNA ≠ F1 DNA | Unknown | 18 | 5 | 8 | 2 | 6 | 3 | 5 | 47 (3.8%) |
| Total by tissue and genotype | 290 | 285 | 266 | 67 | 96 | 101 | 125 | 1230 | |
a
1:1 RNA mix refers to an equal mix of the RNA from the parent inbred lines; F1 refers to the RNA isolated from the F1 hybrid; F1 DNA refers to genomic DNA from the hybrid that will contain equal amounts of the two alleles.
b
The regulatory modes for the B73 × Mo17 columns were actually determined using data from both of the reciprocal hybrids (B73 × Mo17 and Mo17 × B73).