Fruit Phenotype Analysis of <i>SlSAHH2</i>-CRISPR Tomato and Methylation Mechanism of <i>SlSAHH2</i> Promoting Fruit Ripening

S-adenosyl-l-homocysteine hydrolase (SAHH EC 3.3.1.1) is a key enzyme that maintains methylation homeostasis. In this study, the knockout of <i>SlSAHH2</i> delayed tomato fruit ripening. Compared with the wild type (WT), most ripening-related biochemical characteristics were significantly reduced in <i>SlSAHH2</i>-CRISPR fruits. Additionally, the expression of genes related to ethylene synthesis and ripening was generally down-regulated. In transcriptome data, a total of 3701 up-regulated and 3134 down-regulated differentially expressed genes (DEGs) were identified and analyzed. Bisulfite sequencing PCR (BSP) results showed that the methylation levels of the promoters of ethylene-related genes in <i>SlSAHH2</i>-OE fruits were higher. Furthermore, in the presence of a methylation inhibitor, the expression of <i>E4</i>, <i>E8</i>, <i>ACO1</i>, <i>ACO3,</i> and <i>ACS2</i> was generally up- or down-regulated in <i>SlSAHH2</i>-OE or <i>SlSAHH2</i>-CRISPR fruits, respectively. In summary, it can be inferred that in the balance between methylation and ethylene synthesis, <i>SlSAHH2</i> was more inclined to promote the latter process during tomato fruit ripening.