## 3 Results
### Manipulating FaHMGR Expression Caused Changes in Strawberry Transcription and Metabolism  
To determine the transcriptional and metabolic regulatory effects of _FaHMGR_ on strawberries, RNA sequencing (RNA-Seq) and metabolic profiling were performed on the strawberries with transient overexpression or suppression of _FaHMGR_ (HMGROE, HMGRR), with the empty vector transformed plants as the control (HMGRC). RNA sequencing generated approximately 6.6 GB of data and an average of 44,377,805 clean reads (Table S3). Mapping to the strawberry genome database yielded a high coverage of 94.77%, suggesting effective detection of transcriptional changes due to overexpression alteration of _FaHMGR_ in strawberries. To validate RNA-Seq reliability, 10 DEGs were randomly selected for qRT-PCR, which revealed consistent expression patterns of these genes with the sequencing results (Figure S1). The PCA of the transcriptome data (Figure 5A) revealed that all samples were positioned along the positive axis of PC1, which explained 32.95% of the variance, indicating a strong association among HMGROE, HMGRR, and HMGRC. HMGROE and HMGRR overlapped along PC1, while minimal differences were observed among the three samples along PC2 (17.74%), with HMGRC positioned in the positive axis. As shown in Figure 5B, the correlation among triplicates for each treatment sample was high, exceeding 0.923. T1 showed slightly lower correlations (below 0.97) with the other two replicates. A total of 3811 DEGs were identified across all samples, with 2713 unique to the comparison pair HMGRR vs. HMGRC and 236 unique to HMGROE vs. HMGRC. There were more downregulated genes than upregulated ones in both comparison pairs (Figure 5C). Of these DEGs, 842 were common between HMGRR vs. HMGRC and HMGRE vs. HMGRC. All DEGs showed four distinct expression patterns and were thereby clustered into four groups comprising 1705, 2049, 54, and 3 genes. Most genes exhibited no significant differences between HMGROE and HMGRR but differed from HMGRC. In contrast, genes in cluster 4, including cold-regulated 413 plasma membrane protein 1 (_AtCOR413-PM1_), were expressed significantly differently between HMGROE and HMGRR (Figure 5D). GO and KEGG enrichment analyses of the DEGs in HMGRR vs. HMGRC and HMGROE vs. HMGRC were performed to identify the functional roles of the DEGs. GO analysis revealed that these DEGs in both the HMGROE vs. HMGRC and HMGRR vs. HMGRC comparisons showed significant enrichment in the item nutrient reservoir activity (Figure 6A, Table S4). KEGG analysis showed significant enrichment of the DEGs in the phenylpropanol biosynthesis pathway for HMGRE vs. HMGRC and in the ribosome, DNA replication, and pyruvate metabolism pathways for the HMGRR vs. HMGRC comparison (Figure 6B, Table S4). Furthermore, WGCNA divided the DEGs into 63 modules (Figure S2). Module-sample relationship analysis identified five modules indicated in Table S5 by the colors dark magenta, honeydew, tan, violet, and white, containing 82, 40, 269, 88, and 102 genes, respectively (Table S5). Genes in each module displayed distinct expression patterns in HMGRR and HMGRE strawberries (Table S5). In the violet module, gene expression was low in HMGRR and high in HMGRE, while the other four modules exhibited the opposite pattern. Notably, two abscisic acid receptors, _PYL11_ and _PYL9_, were identified in the dark magenta and honeydew modules. The tan, violet, and white modules contained several enzymes involved in sugar and acid synthesis pathways. Additionally, transcription factors ERF118 and WRKY12 were found in the white module, suggesting that they may play an important role in _FaHMGR_-mediated effects on fruit quality. By integrating database comparisons, we conducted qualitative and quantitative analyses of metabolites, identifying a total of 501 components in positive ion mode and 312 in negative ion mode (Table S6).