## 3 Results
### Transcriptome Analysis  
We performed transcriptome analysis to identify differentially expressed genes (DEGs) between wild type (WT) and _OsVTC1-1_ RNAi lines. The RNA-seq data revealed that the raw reads and clean reads in each sample ranging from 39,859,454 to 43,623,072 reads and 19,704,679 to 23,321,544, respectively. The total mapped reads varied between 90.7% and 93.0% (Table S1). There were 25 and 19 down-regulated DEGs in RII-2 and RII-3, respectively. The down-regulated DEGs in RII-2 and RII-3 are listed in Table 2. Eleven down-regulated genes were common between RII-2 and RII-3 including _thionin-like peptide_, _aspartokinase_, _aspartokinase_/_homoserine dehydrogenase 2_, _CBL-interacting protein kinase 14_ (_CIPK14_), _ARK protein_, _kinase_, _pheophorbide an oxygenase_ and _photosystem II 10 kDa polypeptide_. There were 100 and 256 up-regulated DEGs in RII-2 and RII-3, respectively. A list of the top 20 DEGs ranked by the log2 FC value is listed in Table S2. _F-box protein_, _jasmonate-induced protein_, _amino acid transporter_ and _glycosyl transferase_ were found to be common in the top 20 up-regulated DEGs among RII-2 and RII-3 lines (Table S2). Heat map representing 100 common genes from WT and _OsVTC1-1_ RNAi lines correspond to the fragments per kilobase of transcript per million fragments (FPKM) value was generated using GraphPad Prism version 9.0.0 to evaluate the similarity among three replicates. The results showed that the expression profiles of most genes were similar among three replicates (Figure S2, Table S3). The principal component analysis (PCA) was also performed using FPKM values. PCA plots declared that the WT samples were grouped together, whereas six replicates of _OsVTC1-1_ RNAi lines were also clustered together with two replicates (RII-2_3 and RII-3_3) spaced a bit further apart (Figure S3). \begin{table}
\begin{tabular}{c c c} \hline \hline  & **Downregulated DEGs of RII-2** & \\ \hline
**No.** & **Gene ID** & **Gene Description** & **Log2 FC** \\ \hline
1 & OS07G0677200 & Peroxidase & \(-\)5.186 \\
2 & OS07G0432201 & Similar to thionion-like peptide & \(-\)4.666 \\
3 & OS02G0139500 & Similar to beta-amyrin synthase & \(-\)3.203 \\
4 & OS12G0583300 & Peptide aspartic, catalytic domain containing protein & \(-\)3.163 \\
5 & OS03G0850400 & Similar to aspartokinase & \(-\)3.157 \\
6 & OS09G0294000 & Similar to bifunctional aspartokinase/homoserine dehydrogenase & \(-\)2.759 \\
7 & OS10G0562900 & Non-protein coding transcript & \(-\)2.656 \\
8 & OS01G0791033 & Similar to ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit & \(-\)2.433 \\
9 & OS12G0628600 & Similar to thuamatin-like pathogenesis-related protein 3 precursor & \(-\)2.352 \\
10 & OS03G0355300 & Protein of unknown function DUF1618 domain containing protein & \(-\)2.136 \\
11 & OS09G0541600 & Conserved hypothetical protein & \(-\)2.089 \\
12 & OS12G0113500 & Similar to CBL-interacting protein kinase 14 & \(-\)2.045 \\
13 & OS01G0117200 & OsRLCK16 Similar to ARK protein (Fragment) & \(-\)1.984 \\
14 & OS07G0475900 & Similar to kinase family protein & \(-\)1.951 \\
15 & OS06G0581500 & Protein kinase, core domain containing protein & \(-\)1.801 \\
16 & OS12G0141400 & Conserved hypothetical protein & \(-\)1.761 \\
17 & OS12G0428000 & Similar to senescence-associated protein DIN1 & \(-\)1.753 \\
18 & OS03G085060 & Similar to pheophorbide _a oxygenase_ & \(-\)1.514 \\
19 & OS07G0109700 & Conserved hypothetical protein & \(-\)1.421 \\
20 & OS07G0147500 & Similar to photosystem II 10 kDa polypeptide, chloroplast precursor & \(-\)1.341 \\
21 & OS01G0762300 & Similar to predicted protein & \(-\)1.340 \\
22 & OS02G0202200 & SPX domain-containing protein & \(-\)1.270 \\
23 & OS08G0117200 & Similar to 40S ribosomal protein S13 (Fragment) & \(-\)1.246 \\
24 & OS10G0465800 & Similar to 60S ribosomal protein L21 & \(-\)1.229 \\
25 & OS01G0949300 & EF-Hand type domain containing protein & \(-\)1.113 \\ \hline \hline \end{tabular}
\end{table}