## 2 Results
### Analysis of TFs
Other noteworthy, upregulated genes implicate the involvement of other metabolic processes through genes such as _Aspartic proteinase PC.1_ (10.94), _RNA-binding protein FUS_ (10.81), _Acyltransferase_ (10.35), _Methylesterase 1_ (10.35), _MAP kinase kinase kinase 52_ (10.18), and _Long-chain alcohol oxidase_ (9.76). Conversely, several TFs, including _MYC/MYB_ domain protein (-9.93) and _Heat shock TT_ (\(-\)10.03), were downregulated, potentially disrupting the regulatory networks critical for fruit development and ripening. The downregulation of _late embryogenesis abundant protein_ (_LEA_) (\(-\)10.11) suggests reduced stress tolerance. Furthermore, the decreased expression of _Indole-3-acetic acid-amido synthetase 3_-3 (\(-\)10.13) and _Sugar transporter protein 10_ (\(-\)11.24) suggests alterations in auxin and sugar metabolism, respectively. Additional downregulated genes, including _Glutaredoxin-C9_ (\(-\)10.33), _Alcohol dehydrogenase ADH_ (\(-\)10.36), _Glutamate decarboxylase_ (\(-\)10.86), _Chitinase_ (\(-\)10.91), _Heme-binding-like protein_ (\(-\)11.14), _Cell attachment protein in somatic embryogenesis_ (\(-\)11.16), and _non-symbiotic hemoglobin-like protein_ (\(-\)15.12), likely contribute to the distinct ripening characteristics observed in the M7_5 fruits. The top 30 upregulated genes in M29_2 are involved in a variety of BPs, including secondary metabolism, redox reactions, and transcriptional regulation (Figure 6C, Supplementary Table S2). Among the upregulated genes, two _CHS_ genes (_Solvc053505350.3_ and _Solvc09s091510.3_) were identified, which are the key enzymes in the biosynthesis of flavonoids, a class of secondary metabolites with diverse biological activities. Additionally, several genes involved in redox reactions, such as _NAD(P)H-quinone oxidoreductase subunit I_ (_Solvc11g021220.2_) and _dihydroflavound-4-reductase_ (_Solvc10g018140.2_), were also upregulated, suggesting a potential role of these genes in the response to oxidative stress. Furthermore, several TFs were found to be upregulated, including _ERF5_ (_Solvc03g093550.1_) and a _letcin-domain receptor-like kinase_ (_Solvc07g055690.2_), indicating a potential role of these genes in the regulation of downstream genes. On the other hand, the top 30 downregulated genes in M29_2 are involved in various cellular processes, including protein degradation, cell wall modification, and signaling transduction. Among the downregulated genes, a nuclear migration protein _nudC_ (_Solvc06g051950.3_) was identified, which is involved in the regulation of nuclear movement during cell division. Additionally, several genes involved in protein degradation, such as a _pectinesterase inhibitor-like_ (_Solvc06g005460.1_) and a RING-type _E3 ubiquitin transferase_ (_Solvc06g074140.1_), were also downregulated, suggesting a potential role of these genes in the regulation of protein turnover. Furthermore, several genes involved in cell wall modification, such as a _pectin acetylesterase_ (_Solvc03g025580.1_) and an _expansin-like_ (_Solvc08g007090.2_), were found to be downregulated, indicating a potential role of these genes in the regulation of cell wall dynamics. Interestingly, the transcriptomic analysis of the fruit from the _I114_ mutant lines M7_5 and M29_2 revealed a set of DEGs with contrasting expression patterns. A significant number of genes were upregulated in line M7_5 (M7_5 UP) while they were simultaneously downregulated in line M29_2 (M29_2 DOWN) (Supplementary Table S3). These DEGs encompass a diverse range of functions, including metabolism (e.g., alcohol dehydrogenase and hydroxysteroid dehydrogenase), stress response (e.g., dehydration and late embryogenesis abundant proteins), protein processing (e.g., vacuolar-processing enzyme and cysteine proteinase), and transport (e.g., ABC transporter and sodium/hydrogen exchanger). Several genes encode proteins with roles in seed storage (e.g., 11S globulin, 2S albumin, and victim-like proteins), suggesting potential alterations in fruit nutritional composition.