3.3 Limited transcriptomic change induced by eCO2 than by N application rate

To understand the underlying transcriptional changes in response to the eCO2, we employed RNA sequencing approach to compare the gene expression profiles of tissues near the SAM (where the tiller was about to appear) and the third true leaf at leaf-age four. The total number of DEG introduced by tissue type (leaf and SAM), N application rate (N0 and N10), and CO2 treatment (ambient CO2 and eCO2) were strikingly different (Fig. 4A). Tissue had the highest effect, followed by N application rate, and eCO2. The N application had more influences on leaf than SAM, similar to the impact of CO2 (Fig. 4A).
Using the Venn diagram, we found that the universal DEG (commonly altered genes) introduced by tissue was the most (11221, Fig. 4B), followed by N application rate (197, Fig. 4C), and lastly by CO2 effect (5, Fig. 4D). These numbers indicated that the global gene expression profile was overwhelmingly defined by the tissue type, only being altered at limited range by N application rate, and at a very narrow scope by [CO2].