Increasing evidence has revealed that plant secretory peptides are involved in the long-distance signaling pathways that help to regulate plant development and signal stress responses. In this study, we purified small peptides from soybean () xylem sap via hlorophenol extraction and conducted an in-depth peptidomic analysis using a mass spectrometry (MS) and bioinformatics approach. We successfully identified 14 post-translationally modified peptide groups belonging to the peptide families CEP (C-terminally encoded peptides), CLE (CLAVATA3/embryo surrounding region-related), PSY (plant peptides containing tyrosine sulfation), and XAP (xylem sap-associated peptides). Quantitative PCR (qPCR) analysis showed unique tissue expression patterns among the peptide-encoding genes. Further qPCR analysis of some of the peptide-encoding genes showed differential stress-response profiles toward various abiotic stress factors. Targeted MS-based quantification of the nitrogen deficiency-responsive peptides, GmXAP6a and GmCEP-XSP1, demonstrated upregulation of peptide translocation in xylem sap under nitrogen-deficiency stress. Quantitative proteomic analysis of overexpression in hairy soybean roots revealed that significantly impacts stress response-related proteins. This study provides new insights that root-to-shoot peptide signaling plays important roles in regulating plant stress-response mechanisms.
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