Candidate gene analysis of fruit pedicel length based on genome-wide association study in cucumber (Cucumis sativus L.)

• Fruit pedicel length traits of 266 core cucumber accessions were evaluated. • A Genome-Wide Association Study (GWAS) was performed to identify five significant loci associated with FPL. • CsaV4_2G003418, CsaV4_3G001234, CsaV4_3G004527, and CsaV4_7G000548 were candidate genes that might be involved in FPL. Fruit pedicel length (FPL) is a crucial agronomic trait in cucumber, affecting fruit development, cultivation management, and adaptability to mechanized harvesting. Despite its importance, the genes regulating fruit pedicel length have not been reported yet in cucumber. Here, we phenotyped 266 core cucumber accessions for FPL across two environments and performed a genome-wide association study. Five significant loci associated with FPL were identified: gFPL2.1, gFPL3.1, gFPL3.2, gFPL5.1 and gFPL7.1 . Based on pairwise linkage disequilibrium correlation, sequencing analysis and qRT-PCR analysis of these loci, we identified four candidate genes potentially influencing FPL, including CsaV4_2G003418 (the bZIP transcription factor) for gFPL2.1, CsaV4_3G001234 (the NPF transporter) for gFPL3.1, CsaV4_3G004527 (a subunit of the AP-4 vesicle transport protein complex) for gFPL3.2 , and CsaV4_7G000548 (Mediator, a transcriptional co-regulator complex for RNA polymerase II) for gFPL7.1 . Our findings identified the genetic foundation of cucumber FPL, offering valuable markers for breeding mechanical harvesting-optimized cultivars and a foundation for elucidating the molecular mechanism regulating pedicel elongation.