A single-nucleotide mutation in <i>SCPL29</i> , encoding a serine carboxypeptidase, regulates fruit length in pepper ( <i>Capsicum annuum</i> L.)

Abstract Fruit length is a key agronomic trait that determines yield and commercial value in pepper, yet the underlying genetic regulatory mechanisms remain largely unknown. Here, we isolated a short-fruit mutant, 205, through EMS mutagenesis, which exhibits abnormal ovary enlargement and significantly reduced fruit length. Genetic mapping revealed that a recessive missense mutation in SCPL29, a gene encoding a serine carboxypeptidase highly expressed at the floral bud stage, is responsible for this phenotype. This point mutation alters the subcellular localization of SCPL29 and induces the formation of punctate autophagic structures. Functional validation via virus-induced gene silencing (VIGS) confirmed that SCPL29 positively regulates fruit length in pepper. Furthermore, we demonstrated that SCPL29 physically interacts with CLAVATA1, and together they coordinately regulate ovary development and final fruit length. Mechanistic investigations further revealed that SCPL29 modulates fruit length via the auxin signaling pathway. Collectively, these findings uncover a serine carboxypeptidase as a determinant of fruit morphology and establish SCPL29 as a potential target for breeding elite pepper varieties with improved fruit length.