Multi-omics analysis reveals the phenylalanine pathway associated with stem development under organic and compound fertilizers in Setaria italica

Introduction To explore the mechanism underlying the effects of combined application of organic fertilizer and compound fertilizer on stem development of foxtail millet, this study used ‘ Jiza Jinmiao 3 ’ as the test material and set up three treatments: sole application of organic manure (Control1), sole application of compound fertilizer (Control2), and combined application of cattle manure-based organic fertilizer and compound fertilizer (Treatment). Methods The effects of different fertilizer treatments were analyzed by integrating phenotypic determination, microscopic observation of stem structure, and multi-omics analyses including transcriptomics, metabolomics, and proteomics. Results The results showed that compared with the sole application treatments, the combined application treatment significantly promoted phenotypic indicators of foxtail millet such as plant height, stem diameter, and stem fresh weight, and also significantly increased the cross-sectional area of stem vessels, the cell wall thickness of basic tissues, and the stem puncture strength. Multi-omics analyses revealed that differentially expressed genes (DEGs), differentially accumulated metabolites (DAMs), and differentially expressed proteins (DEPs) under the combined application treatment were significantly enriched in pathways related to cell wall development, such as phenylalanine metabolism and phenylpropanoid biosynthesis. Specifically, mapped to the phenylalanine pathway, the expression levels of key genes, metabolites, and proteins including Phenylalanine Ammonia - Lyase ( PAL ), Phenylalanine / Tyrosine Ammonia - Lyase ( PTAL ), and Peroxidase gene ( PRDX6 ) were significantly upregulated, and the content of phenylalanine was increased. Discussion This study suggests that the combined application of organic fertilizer and compound fertilizer is associated with enhanced stem structural properties (including increased vascular area, cell wall thickness, and stem puncture strength) potentially linked to improved lodging resistance, with the phenylalanine pathway emerging as a candidate pathway, providing a theoretical basis and technical support for optimizing fertilization strategies and improving yield stability in the high-yield cultivation of foxtail millet.