Multi-omics analysis reveals changes in lignin metabolism and hormonal regulation in Acacia melanoxylon stems under low boron stress

• Low boron stress disrupts apical dominance in Acacia melanoxylon ; • Low boron stress in Acacia melanoxylon activates phenylpropanoid and flavonoid biosynthesis pathways; • Low boron stress changes hormone levels, and induces an increase in lateral branches. Acacia melanoxylon , a valuable and versatile evergreen tree species, plays a critical ecological and economic role; but its molecular and metabolic responses to boron stress have yet to be completely elucidated. In this paper, we investigated the response mechanisms of one-year-old A. melanoxylon stems to chronic low boron stress imposed continuously throughout their first year of growth, using integrated physiological, transcriptomic, metabolomic, and hormonal analyses. Low boron stress significantly reduced tree height and average internode length while increasing the number of dead branches. It also induced significant increases in malondialdehyde (MDA) content and antioxidant enzyme activity, alongside pronounced anatomical and compositional changes in A. melanoxylon stems. Integrated transcriptomic and metabolomic analyses revealed significant enrichment of genes and metabolites linked to phenylpropanoid and flavonoid biosynthesis pathways in A. melanoxylon stems under low boron stress. Furthermore, hormonal analyses further identified reduced auxin levels alongside increases in abscisic acid, cytokinin, jasmonic acid, and salicylic acid. The alterations in phenylpropanoid and flavonoid biosynthesis pathways, coupled with shifts in hormonal homeostasis are key responses that contribute to internode shortening in A. melanoxylon under low boron stress, facilitating the emergence of lateral branches on the main stem. This study provides novel insights into the mechanisms by which woody plants adapt to low boron stress through the interaction between secondary metabolites and hormones.