Expression profiling of Auxin and GA signaling genes during fruit set in Zanthoxylum armatum

Zanthoxylum armatum DC. is an important economic crop in Southwest China, but severe fruit drop and low fruit set rate reduce yields. Identification of key genes regulating fruit set in Z. armatum could provide new insights for addressing fruit abscission. In this study, we examined the morphological and anatomical characteristics of pistils and young fruits in two Z. armatum cultivars, ‘Jiuyeqing’ and ‘Prickleless’. Both cultivars exhibited unisexual flowers with apomictic traits and similar fruit morphology as well as anatomy. Transcriptome data were utilized to identify auxin and gibberellin biosynthetic and signaling genes. A total of 21 Aux/IAAs, 19 ARFs, 2 GA20oxs, 3 GA2OXs, GID1, and 6 DELLA genes were differentially expressed in male and female flowers, suggesting their candidate roles in regulating fruit set. Phylogenetic analysis revealed that Aux/IAA family members clustered into two clades with seven subfamilies, while ARFs were divided into four subclasses. ZaGA20oxs, ZaGA2oxs, ZaGID1, and ZaDELLAs showed high homology to their orthologs in tomato and cucumber. Quantitative real-time PCR (qRT-PCR) analysis showed that auxin-related ZaIAA8, ZaIAA11, ZaIAA20, ZaARF1, ZaARF5, and ZaARF10 exhibited similar expression trends during fruit set in both cultivars, whereas other genes (e.g., ZaIAA6, ZaIAA7, ZaARF9, ZaARF18) displayed divergent expression. Gibberellin-related ZaGA20ox2, ZaGA2OX2, ZaGA2OX4, ZaDELLA1, and ZaDELLA3 were significantly differentially expressed during pistil development and fruit initiation across cultivars. This study provides insights into the molecular mechanisms of phytohormone-mediated fruit development and offers a theoretical foundation for breeding high-yield varieties.