| Summary: | Abstract Background Tassel branch number shapes plant architecture, which is crucial for maize adaptation to high-density planting. Therefore, unrevealing the molecular mechanisms of tassel branching is essential for crop breeding. To gain better insights into this mechanism, we integrated metabolomic and transcriptomic analysis to explore differentially accumulated metabolites (DAMs) and differentially expressed genes (DEGs) between two types of materials with distinct tassel branching numbers. Results We identified a pair of maize sibling lines, unbranched tassel line (UBT) and multibranched tassel line (MBT). UBT has only one spike without branches due to the inhibition of branch meristems, while MBT has multiple branches. Gene Ontology (GO) enrichment analysis of DEGs revealed significant enrichment in organ growth regulation, hormone response and auxin signaling pathway. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of DAMs revealed enrichment in plant hormone signal transduction. Integrated transcriptomic and metabolomic analysis revealed enrichment of the tryptophan metabolism, a crucial auxin biosynthetic pathway, suggesting its potential involvement in tassel branching development. Conclusions The elevated levels of indole-3-acetamide in the tryptophan metabolism pathway suggest an increase in auxin accumulation, which may subsequently suppressed branch meristem formation in UBT through downregulation of BARREN STALK 1 expression and modulation of auxin signaling pathways.
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