A 13‐kb Deletion in SeAPRR2 Disrupts Chloroplast Development by Dual‐Targeting SeHEMA1/SeLHCB4 for White Peel Formation in Chayote

Fruit peel colour is a critical quality trait in chayote, directly influencing its commercial value. However, the molecular mechanisms underlying peel colour variation remain poorly understood. In this study, we observed higher chlorophyll content in deep green peel (DGP), green peel (GP), and light green peel (LGP) compared to white peel (WP). Additionally, WP exhibited reduced chloroplast number and structural disorganisation, with metabolomics confirming the reduction of galactolipids (DGDG and MGDG) essential for membrane stability. Integrated transcriptomic, resequencing, and WGCNA analyses identified SeAPRR2 as a candidate gene controlling peel colour, with a ~ 13-kb deletion in WP responsible for the white phenotype. This deletion triggered downregulation of DEGs related to chlorophyll biosynthesis and photosynthesis pathways. DAP-Seq revealed that SeAPRR2 binds to the cis-element (AAT(G/C)ATT) in promoters. Through Y1H, DLR, GUS activity, EMSA, and molecular docking assays, we confirmed that SeAPRR2 activates the transcription of SeHEMA1 and SeLHCB4 via promoter binding. Heterologous overexpression of SeAPRR2, SeHEMA1, and SeLHCB4 in tomato significantly elevated chlorophyll content and increased chloroplast number. Collectively, this study establishes SeAPRR2 as a master regulator of peel colour through the SeAPRR2-SeHEMA1/SeLHCB4 module. The large-fragment deletion mechanism provides novel genetic insights for breeding colour traits in cucurbit crops.