*3.4. GO and KEGG Enrichment Analysis of DEGs*

Next, GO analysis was carried out using the identified DEGs in the three main GO categories: biological process, cellular component, and molecular function (Figure 4A). KEGG pathway analysis showed that the DEGs involved in N metabolism were enriched in all of the four libraries (Figure 4B). The DEGs involved in nitrogen metabolism were then intensively analyzed. The DEGs associated with nitrate transportation, assimilation, and remobilization processes were detected in each genotype (Figure 5 and Figure S1A–D). The genes of the nitrate transporter family were up-regulated, especially in the roots, while N assimilation systems were suppressed. The genes participating in N remobilization were also enhanced. Overall, the expression patterns of the DEGs involved in N metabolism were similar in both genotypes. Thus, further analysis is needed to find clues governing different NUEs between the two genotypes examined.

**Figure 4.** Function classifications of DEGs. (**A**): GO functional enrichment analysis of DEGs. The X-axis represents GO functional classification, and the Y-axis represents the number of up-regulated and down-regulated genes in each corresponding GO term. (**B**): Pathway enrichment analysis of DEGs. The X-axis represents enrichment factor values, and Y-axis represents pathway names.


**Figure 5.** Heatmap of the DEGs involved in N metabolism. L1, TCL1 vs. TTL3; R2, TCR2 vs. TTR4; L3, TCL5 vs. TTL7; R4, TCR6 vs. TTR8.
