## 3 Results
### Functional Analysis of DEGs, GSEA and KEGG Pathways Analysis  
In GO analysis a total of 37,653 DEGs were enriched, among which 14,393 DEGs were upregulated and 23,260 DEGs were downregulated. As far as P treatments are concerned, 5297 upregulated and 1471 downregulated DEGS were found in the P0 treatment, 4689 upregulated and 2242 downregulated DEGs were found in the P1 treatment, and 4407 upregulated and 792 downregulated DEGs were found in P2. The number of GO terms for each comparison made among the different seed maturity stages is shown in Table 4. GO analysis indicated the top 15 enriched GO terms according to the 3 GO domains: molecular function, biological process and cellular component (Figure 6, Tables 4 and S1). \begin{table}
\begin{tabular}{c c c c} \hline  & & **Downregulated DEGs** & **Upregulated DEGs** \\ \hline \multirow{3}{*}{P0} & S1–S2 & 4175 & 2921 \\  & S1–S3 & 8044 & 4680 \\  & S2–S3 & 6083 & 3485 \\  & S1–S2 & 5539 & 3029 \\ P1 & S1–S3 & 7669 & 4524 \\  & S2–S3 & 4315 & 3057 \\  & S1–S2 & 3074 & 1943 \\ P2 & S1–S3 & 7408 & 4252 \\  & S2–S3 & 5739 & 3723 \\  & Total DEGs & 52,046 & 31,614 \\ \hline \end{tabular}
\end{table} 
Table 3: Total upregulated and downregulated genes were found to be significantly differentially expressed (\(\,\)log2(fold-change) \(\mid\)\(\,\)\(\,\)\(\,\)\(\,\)\(\,\)\(\,\)\(\,\)\(\,\)\(\,\)\(\,\)\(\,\)\(\,\)\(\,\,\)\(\,\)\(\,\,\)\(\  
Figure 4: Individual heatmaps outlining the DEGs (DEGs) in P0 (**A**), P1 (**B**) and P2 (**C**) conditions. The expression is reported in log2(fold change) with z-score normalization. The hierarchical clustering was performed utilizing the Euclidean distance metric, and the clustering method includes the DEGs with expression levels in terms of \(-1\geq\) log2(fold-change) \(\geq 1\), while also ensuring their significance using a cut-off of an adjusted \(p\)-value \(\leq 0.05\). DEGs were clustered together according to seed maturity stage (S1, S2 and S3), and the z-scores from \(1\) to \(-1\) indicate the intensity linked with normalized expression. The darker the red color is, the more upregulated the genes are, and the darker the blue, the more downregulated the genes are. \begin{table}
\begin{tabular}{c c c c} \hline  & \multicolumn{2}{c}{**GO Terms for Upregulationed DEGs**} & \multicolumn{1}{c}{**GO Terms for Downregulated GEGs**} \\ \hline  & S1–S2 & 1167 & 1471 \\ P0 & S1–S3 & 2350 & 3847 \\  & S2–S3 & 1780 & 2892 \\  & S1–S2 & 1341 & 2242 \\ P1 & S1–S3 & 2156 & 3752 \\  & S2–S3 & 1192 & 1943 \\  & S1–S2 & 580 & 792 \\ P2 & S1–S3 & 2044 & 3600 \\  & S2–S3 & 1783 & 2721 \\ \hline \end{tabular}
\end{table} 
Table 4: Total GO terms found for the upregulated and downregulated genes in each condition. Figure 5: Overall Heatmap illustrates the DEGs (DEGs) in all comparisons among the seed maturity stages in all three P treatments. Hierarchical clustering with Euclidean distance and normalized counts with z-scores. DEGs are considered the genes with \(-1\geq\) log2(fold-change) \(\geq\) 1 and adjusted \(p\)-value \(\leq\) 0.05. Figure 6: The butterfly charts indicate the number of upregulated and downregulated DEGs corresponding to the top 15 GO terms in each GO category (biological process (**A**), cellular component (**B**) and molecular function (**C**)). GO terms and annotations were investigated to identify changes in enriched DEGs that are related to processes that are either determined or affected by P. These changes were studied in the comparisons among the seed maturity stages in each P treatment. A notable finding is that the most enriched DEGs in the GO terms related to P were mainly downregulated and, in most annotations, the highest number of DEGs belonged to the S1-S3 comparison. For instance, in \"phosphorus metabolic process\" (GO:0006793) and \"phosphate-containing compound metabolic process\" (GO:0006796) the number of both upregulated and downregulated enriched DEGs appeared to be perceptibly higher in S1-S3 comparison in all three treatments.