*2.11. Expression Profiles of No Apical Meristem Family Genes, Carbohydrate, and N Metabolism and Transport-Related Genes*

No apical meristem family genes (NAM) are critical for meristem maintenance and floral development [21]. Tillers contain newly branched meristems and therein arise perspective panicles. Rice genome contains 90 putative NAM genes. Among the 76 NAM genes detected in the transcriptome at this stage, 27 had an extremely low expression (FPKM ≤ 0.1). Among the 49 decently expressed NAM genes (FPKM > 0.1), 18 displayed significant varietal differences, 12 being responsive to the N rate, and 10 showed an interaction between the variety and N rate (Figure S10). Among those significantly changed, only 11 of the 18 genes in the varietal comparison and six of the 12 genes responsive to the N rate displayed a twofold or higher change at least once. Apparently, more NAM genes were defined by the variety than to be responsive to the N rate.

Carbohydrates provide basic carbon substrates for multiple primary and secondary metabolic pathways, and are subject to the impact of N availability [22,23]. Among the totally 555 carbohydrate metabolism-related genes we screened for in the transcriptome data, 29 were not detected in the SAM at this stage, and 45 showed an extremely low expression (FPKM < 0.1). Of those 482 decently expressed genes, 200 genes did not show significant (*p* > 0.05) differences in any comparison; 212 showed significant varietal differences (*p* ≤ *0.05*, Figure S11); 128 being responsive to the N rates; and 43 showed significant interaction between the variety and N rate. This corroborates with that more genes were expressing differentially between the varieties than those in response to the N rate. All these specific pathway profile analysis points toward that the expression profile differences were more likely to be determined by a variety rather than the N enrichment.

N enrichment directly affects the N availability, absorption, synthesis and transport of the related amino acids and the downstream N metabolism [2,24]. We screened for 210 genes pertaining to ammonium, nitrate, nitrite, glutamate, glutamine, asparagine, tryptophan, methionine, aspartate, proline, glycine, cysteine and NADH metabolism. We detected 199 genes expressed in the SAM, with 178 showed a decent expression (FPKM > 0.1). Among them, 97 showed significant differences between the varieties; 69 showed responsive to the N rate; 28 displayed significant interaction between the variety and N rate (Figure S12). Comparably, much more genes expressed differentially between the varieties than those being responsive to the N rate. At the same time, we found that the genes related to N metabolism are in different modules and play different roles during this period (Figure 10). The N transporter proteins, *OsNRT1* and *OsNRT2.3*/*OsNRT2.3a*/*OsNRT2.3b*, are in the brown module which positively relate to dry weight of stem and leaf (Table 3). Interestingly, an ammonium transporter protein-coding gene *OsAMT1.2* locates in the turquoise module, which negatively regulates the dry weight of leaf. These results show that the N related genes in rice plant might play very different roles in the absorption, function and distribution of N in response to N rate as well as in tillering regulation.

**Table 3.** Fold change of the expression level of N metabolism and transporter genes between the varieties and their responses to the N rate.


Note: The expression changes are in the form of log2, and significances at their respective probability level. Red and blue color represent scale of up-and down-regulation, respectively.
