*2.5. Di*ff*erentially Expressed Genes (DEGs) in Response to N Rate*

To identify the DEG in response to N rate, Cuffdiff [18] program was used in comparing the FPKM of the treatment vs. control according to the following criteria: fold change (FC) |log2| ≥ 1.0 and false discovery rate (FDR, *q*-value) ≤ 0.05. The total DEG in response to N enrichment in NPB were 87 (65 down-regulated and 22 up-regulated), 40 (12 down and 28 up) and 148 (69 down and 79 up) between LN and MN, MN and HN, LN and HN comparisons, respectively (Figure 5A,D). Among them, merely four genes were consistently present in every comparison. The corresponding numbers of DEG were 115 (58 down and 57 up), 162 (80 down and 82 up) and 511 (239 down and 272 up) in YD6, and only 15 genes were commonly present in these comparisons (Figure 5B,E). The number of DEG indicate that more drastic transcriptome changes from LN to HN, rather than from LN to MN, or MN to HN, irrespective of varieties.

**Figure 5.** Profiles of DEGs between the comparisons. (**A**,**D**) DEGs in response to N rate in NPB; (**B**,**E**) DEGs in response to N rate in YD6; (**C**,**F**) DEGs between the varieties; (**G–L**) Fold changes of DEGs related to ribosomal protein (**G**), Protease inhibitor/seed storage/LTP family protein (**H**), F-box domain protein (**I**), retrotransposon protein, transposon protein (**J**), CACTA, En/Spm sub-class protein, transposon protein (**K**), Pong sub-class protein (**L**).

Apparently, the number of DEG in response to N enrichment was much more in the *indica* variety YD6 than in the *japonica* variety NPB. Surprisingly, of those DEG commonly presented in response to N rate in NPB and YD6, only one common gene was found (LOC\_Os01g01660), which putatively encodes an isoflavone reductase-like gene and confers tolerance to reactive oxygen species. This scarce overlapping in the DEGs suggested that the transcriptome responses to N enrichment were very much dependent on the different genetic background. Combination of different sets of background genes may totally alter the transcription profile in response to certain N enrichment.

On the contrary, comparison between NPB and YD6 at each respective N rate revealed that the number of DEG commonly presented at each N level was a majority of 463 genes (Figure 5C,F), much more than those numbers of distinctive DEGs at each N rate. Among these DEGs, we listed

several specific types of genes (Figure 5F–L). This corroborates that the varietal set of DEG was a core determinant in shaping their response to various N enrichment.
