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In Salvia miltiorrhiza Bunge (S. miltiorrhiza), an important medicinal plant, the accumulation of its active components is closely related to the level of phosphorus supply, but the molecular regulatory mechanism of phosphorus treatment in the growth and secondary metabolism of S. miltiorrhiza is not clear. In this study, we investigated the effects of low phosphorus (P2), moderate phosphorus (P4), and high phosphorus (P6) treatment on the growth and development of S. miltiorrhiza. seedlings, the accumulation of bioactive compounds, and their transcriptional regulation using transcriptomic and metabolomic analyses, and identified the key regulatory genes in the biosynthesis pathways of tanshinone and salvianolic acid. The findings revealed that S. miltiorrhiza biomass exhibited a \u201cpeaked\u201d response to phosphorus concentration, peaking at 0.625 mmol\u00b7L\u22121. At this optimal concentration, all four batches achieved maximum root length, root weight, and leaf weight: Batch I (11.3 cm, 2.34 g, 1.62 g), Batch II (12.7 cm, 2.67 g, 1.89 g), Batch III (13.8 cm, 2.85 g, 2.04 g), and Batch IV (15.6 cm, 3.51 g, 2.44 g). Both lower and higher concentrations resulted in growth inhibition and reduced bioactive compound accumulation. Transcription factors associated with root growth and development included bHLH, MYB, and WRKY; in particular, the bZIP23 transcription factor was highly expressed under abnormal phosphorus supply conditions. In addition, the biosynthetic pathways of tanshinone and salvianolic acid were elucidated, and key genes related to the synthesis pathways (CPS, KSL, CYP, PAL, HPPR, and RAS) were identified. The expression of several TFs (such as SmCPS1, SmCYP76AH3, SmCYP76AH1, SmGGPPS1, and SmRAS1) was found to be correlated with tanshinone and salvianolic acid synthesis. The present study provides a theoretical basis for further revealing the molecular mechanism of phosphorus regulation of growth, development, and secondary metabolism of S. miltiorrhiza and provides potential targets for efficient cultivation and molecular breeding of S. miltiorrhiza.<\/jats:p>","DOI":"10.3390\/ijms26136253","type":"journal-article","created":{"date-parts":[[2025,7,1]],"date-time":"2025-07-01T05:28:28Z","timestamp":1751347708000},"page":"6253","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Transcriptome- and Metabolome-Based Regulation of Growth, Development, and Bioactive Compounds in Salvia miltiorrhiza (Lamiaceae) Seedlings by Different Phosphorus Levels"],"prefix":"10.3390","volume":"26","author":[{"given":"Kewei","family":"Zuo","sequence":"first","affiliation":[{"name":"School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong 723000, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lingxing","family":"Chen","sequence":"additional","affiliation":[{"name":"School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong 723000, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tian","family":"Li","sequence":"additional","affiliation":[{"name":"School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong 723000, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shuang","family":"Liu","sequence":"additional","affiliation":[{"name":"School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong 723000, China"},{"name":"Collaborative Innovation Center for Comprehensive Development of Biological Resources in Qinba Mountainous Area, Hanzhong 723000, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chenlu","family":"Zhang","sequence":"additional","affiliation":[{"name":"School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong 723000, China"},{"name":"Shaanxi Provincial Key Laboratory of Resource Biology, Hanzhong 723000, China"},{"name":"State Key Laboratory of Biological Resources and Ecology and Environment, School of Biology, School of Biological Science and Engineering, South Campus, Shaanxi University of Technology, Hanzhong 723000, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2025,6,28]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"112384","DOI":"10.1016\/j.plantsci.2025.112384","article-title":"New insights of advanced biotechnological engineering strategies for tanshinone biosynthesis in Salvia miltiorrhiza","volume":"352","author":"Shou","year":"2025","journal-title":"Plant Sci."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"106392","DOI":"10.1016\/j.fitote.2025.106392","article-title":"Three new diterpenes from the roots of Salvia miltiorrhiza and their cytotoxicity","volume":"181","author":"Xia","year":"2025","journal-title":"Fitoterapia"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"120529","DOI":"10.1016\/j.indcrop.2025.120529","article-title":"The impact of soil moisture stress on the growth and biosynthesis of effective components in Salvia miltiorrhiza","volume":"225","author":"Li","year":"2025","journal-title":"Ind. 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