Transcriptomics and Hormone-Targeted Metabolomics Reveal the Mechanisms Underlying Special Branching in Loquat

Branching traits play a critical role in shaping the tree structure of fruit crops and directly influence both yield and fruit quality. Effective and well-managed branching is crucial for maximizing productivity. However, loquat trees typically exhibit weak branching ability, characterized by fewer and longer bearing shoots, along with terminal flower buds, which collectively result in lower yields per unit area. Despite their significance, research on branching characteristics in loquat remains limited. To clarify the factors influencing branching and to provide a rational and effective direction for improving the inherently weak branching performance of current loquat cultivars, we selected the loquat varieties ‘Dawuxing’ and ‘Chunhua 1’, which exhibit significant differences in leaf and branch growth. Compared to ‘Dawuxing’, ‘Chunhua 1’ has longer branches, wider stem and leaf angles, fewer lateral branches, and a looser leaf cell structure. Transcriptome analysis of terminal buds at different developmental stages revealed that differentially expressed genes in the terminal buds of central branches from the spring and summer shoots of the two cultivars were enriched in the plant hormone signal transduction pathway. Hormone-targeted metabolomics identified significant differences in the levels of abscisic acid, auxins, cytokinins, gibberellins, jasmonic acid, and strigolactones in the terminal buds of both cultivars. Through integrated analysis, two candidate genes were identified as potential regulators of branching differences between the two cultivars: EVM0025028 (EjSAPK1), SnRK2 gene a core component of the abscisic acid signaling pathway, and EVM0040331 (EjRMS3), a D14 gene involved in encoding a strigolactone receptor. These findings provide valuable genetic resources for future research on branching regulation in Eriobotrya species and offer a theoretical foundation for enhancing branching management in loquat cultivation.