Multi-omics analysis of the maize ear diameter mutant3 (zmed3) provides insights into female inflorescence development

The ear is a crucial component of grain yield in maize. Studying the mechanisms underlying ear development is therefore essential for genetic improvement and molecular breeding programs. Among various yield-influencing factors, ear development plays a central role, as it is orchestrated by the inflorescence meristem. This meristematic structure directly regulates key yield-related traits, including ear size, kernel number, and row arrangement. Here, we analyzed the zmed3 mutant, which shows flattened ear tip and disordered kernel rows, and is a single recessive mutation isolated from the Lx9801 breeding population. Using integrated transcriptomic, proteomic, and metabolomic analyses at the 4 mm stage of developing ears, we identified 1,589 differentially expressed genes (DEGs), 181 differentially accumulated proteins (DAPs), and 122 differentially accumulated metabolites (DAMs) in zmed3 mutants compared with normal siblings. These global omics changes were primarily associated with central carbon metabolism. Mutant zmed3 inflorescence meristems (IMs) were initially enlarged, switched to a more fasciated pattern, and finally led to impaired spikelet meristems (SMs). Transcriptomics suggested activation of the jasmonic acid signaling pathway, potentially affecting spikelet cell elongation. Proteomics indicated disruption of the MAPK signaling pathway, likely affecting spikelet cell polarity. Metabolomics demonstrated deficiencies in the tricarboxylic acid cycle and phenylpropanoid synthesis pathway, which in turn alter meristem cells differentiation and cell wall remodeling. Multi-omics integration uncovered a regulatory network involving cell cycle initiation, jasmonic acid signaling, and metabolic flux homeostasis, and pinpointed several candidate genes for future functional characterization. Our study not only identifies potential molecular mechanisms underlying maize ear development but also pinpoints precise targets for genetic improvement. These findings deepen our understanding of inflorescence biology and provide a theoretical framework for optimizing yield-related traits, thereby offering actionable insights for the design of molecular breeding strategies to enhance maize productivity.