Clustered Expansins modulate pedicel length by regulating cell elongation in tomato

The pedicel plays a crucial structural and physiological role in connecting fruits to plants, facilitating the transport of photosynthates essential for fruit development. Pedicel length (PL) significantly influences fruit growth, harvesting efficiency, and postharvest handling. However, the genetic basis of PL in tomato remains poorly understood. In this study, we integrated genome-wide association studies and bulked segregant analysis to identify a high-confidence loci TPL3 (Tomato Pedicel Length 3), which harbors a cluster of six Expansins (EXPs) that regulate pedicel elongation from flower to red ripe fruit. Homozygous mutants harboring various combinations of EXP gene mutations were generated using CRISPR/Cas9. Analysis of PL in exps mutants revealed that the EXPs cluster regulates pedicel elongation in both the cortex and pith cells throughout reproductive stages, with dose-dependent effects. Biochemical and transcriptomic analyses showed reduced cellulose content, increased cellulase expression, and altered expression of lignin biosynthesis and cell wall remodeling genes in exps pedicels. These findings highlight the role of the EXPs cluster in regulating cell wall composition and structure, ultimately affecting pedicel elongation. Phenotypic correlations further revealed a coordinated relationship between PL and reproductive organ development, including a positive association with fruit weight. Population genetics analyses detected strong selection signatures at TPL3 during evolution by hitchhiking with fw3.2. Using natural variation at indel_5 (ch03_65074685), we developed a molecular marker for PL that achieved 94.2% genotyping efficiency across 120 tomato accessions and exhibited high utility for distinguishing PL phenotypes in commercial cultivars. This study reveals the genetic basis of pedicel elongation and offers an efficient molecular marker for breeding tomatoes with optimized PL.