Stage-specific metabolic divergence in flavonoid biosynthesis correlates with embryogenic capacity in rubber tree (Hevea brasiliensis)

Our results provide comprehensive metabolomic evidence for stage-dependent metabolic reprogramming during SE in <i>H. brasiliensis</i>. The contrasting patterns of flavonoid metabolism between genotypes at the callus-to-differentiation transition-systematic downregulation in the HE genotype versus sustained activation in the LE genotype-are consistent with the hypothesis that a timely reallocation of metabolic flux from secondary to primary metabolism may favor somatic embryo development. This study identifies the callus-to-differentiation transition as a critical metabolic checkpoint and suggests flavonoid biosynthesis genes, particularly <i>CHS</i> and glycosyltransferases, as potential targets for improving SE efficiency in recalcitrant genotypes.