3.4 Tiller genes displayed a more wide-scale change by eCO2 than by N application rate

To elaborate their responses to eCO2 and N application rate, we extracted the transcription data of 65 tiller-related genes from the transcriptome. Among the 51 genes that showed decent expression (FPKM>0.1) in leaf and/or SAM at 4th true leaf emerging stage, there were 50 genes varied between tissues (leaf and SAM), 29 genes being altered by [CO2], and 24 genes being significantly affected by N application (Table 1). This further corroborated that tissue type (organ) predominantly defines the gene expression profile. However, as there were more tiller genes being responsive to [CO2] than N application, the [CO2] was more influential in regulating the tiller-related genes than the N application. Of the 29 [CO2] responsive tiller-genes and 24 N application responsive tiller-genes, there were 16 genes being commonly responsive to both factors. Eight out of the 22 (36.4%) tiller genes were not responsive to [CO2] but to N application, whereas 13 out of 27 (48.1%) tiller genes were not responsive to N but to CO2. This further supported that the [CO2] was more effective in specifically altering tiller-related genes than the N application, contrary to their differential influences to the global transcriptomic profile.
The relative FPKM changes of these tiller genes introduced by N application (N10/N0), and by [CO2] (eCO2/Ambient) in different tissues were shown in Table 2. N application caused more dramatic change in the leaf than in the SAM: 14 (7 up, 7 down) and 12 (11 up, 1 down) tiller genes surpassed two-fold threshold to be DEG under the ambient and the eCO2 conditions in the leaf, respectively. In the SAM, these numbers were three (all down) and 0 for the ambient and eCO2, respectively. Direct comparison of the [CO2] effect showed that 16 (8 up and 8 down) and seven (down) tiller-genes surpassed two-fold in leaf at N0 and N10, respectively; while these values were seven (6 up and 1 down) and two (up) in SAM. These indicated that either most of them were not participating in the tillering response to eCO2, or the scale of change did not need to surpass the two-fold to affect tillering. This also implies that other genes might be involved in tillering promotion in response to eCO2.