Transcriptomic and Metabolomic Analyses Reveal Mechanisms of Sexual Differentiation and Dimorphism in Morus macroura

<i>Morus macroura</i> 'Panzhihua No. 1' is a dual-purpose cultivar valued for its edible leaves and fruits. Derived from an ancient mulberry tree, it is a unique local germplasm resource. During asexual propagation, <i>M. macroura</i> exhibits sexual variation closely associated with fruit and leaf yield. To explore the molecular mechanisms of sexual dimorphism and its effects on nutritional traits, we integrated transcriptomic and metabolomic analyses of male and female inflorescences and leaves. Key sex-biased genes were enriched in plant hormone signaling, flavonoid biosynthesis, and carbohydrate metabolism pathways. Female plants had elevated expression of ethylene-responsive transcription factor 1 (<i>ERF1</i>), EIN3-binding F-box proteins (<i>EBF1/2</i>), and Chalcone synthase (<i>CHS</i>) genes and higher levels of bioactive flavonoids, including isoquercitrin and kaempferol derivatives. In contrast, male plants had increased expression of gibberellin 20-oxidase (<i>GA20ox</i>) and <i>DELLA</i> genes and accumulated glycosides, which are beneficial for leaf development. These findings reveal how sex-linked metabolic networks shape mulberry tissue functional profiles, providing molecular targets for breeding.