Natural Variation in CYCLIC NUCLEOTIDE-GATED ION CHANNEL 16 Controls Fruit Weight in Tomato

Fruit weight is a crucial agronomic trait influencing yield and quality in tomato domestication. Although numerous quantitative trait loci (QTLs) controlling fruit weight have been reported, the underlying molecular mechanisms remain largely unresolved. Here, we identify natural variation in the promoter region of CYCLIC NUCLEOTIDE-GATED ION CHANNEL 16 (CNGC16) associated with both fruit weight and gene expression differences via genome-wide association study (GWAS) in tomato accessions. Geographical and subpopulation analyses reveal that the large-fruit CNGC16 haplotype was selectively favoured during domestication and may contribute to local environmental adaptation. Functional assays demonstrate that CNGC16 regulates fruit weight by promoting cell division and maintaining cytosolic Ca²⁺ homeostasis in fruit cells. Mechanistically, CNGC16 physically and genetically interacts with calmodulin 6 (CaM6) to mediate calcium signalling that controls fruit size. These findings uncover a novel calcium-dependent pathway regulating tomato fruit weight and propose CNGC16 and CaM6 as promising molecular targets for crop improvement.