---
title: "Root regulatory networks link salicylic acid, jasmonic acid and secondary metabolites to disease‑s"
id: "biorxiv-0-root-gene-regulatory-network-analysis-reveals-roles-for-defense-hormones-and"
canonical_url: "https://medichelpline.com/clinical-feed/biorxiv-0-root-gene-regulatory-network-analysis-reveals-roles-for-defense-hormones-and"
content_type: "clinical_feed_article"
specialty: "General"
source_name: "bioRxiv (Biomedical Preprints)"
source_url: "https://www.biorxiv.org/content/10.64898/2026.10.22.760950v1?rss=1"
published_at: "2026-10-23T12:00:00.000Z"
evidence_level: "Verified Feed"
license: "CC-BY-NC-4.0 / Informational Use"
---
# Root regulatory networks link salicylic acid, jasmonic acid and secondary metabolites to disease‑s
## Provenance & Clinical Metadata
- **Canonical URL:** https://medichelpline.com/clinical-feed/biorxiv-0-root-gene-regulatory-network-analysis-reveals-roles-for-defense-hormones-and
- **Specialty:** [General](https://medichelpline.com/clinical-feed/general.md)
- **Primary Source:** bioRxiv (Biomedical Preprints)
- **Source URL:** [Original Journal Publication](https://www.biorxiv.org/content/10.64898/2026.10.22.760950v1?rss=1)
- **Published At:** 2026-10-23T12:00:00.000Z
- **Evidence Rating:** Verified Feed
## Executive GIST (TL;DR)
- Investigators performed time-series RNA-seq on roots of foliar‑infected Arabidopsis thaliana grown in natural soil over seven days post‑inoculation. The root transcriptional program changed within one day after foliar pathogen challenge. - The cohort showed early upregulation of **salicylic acid (SA)**-associated defense genes and later downregulation of **jasmonic acid (JA)**-responsive and secondary metabolism-related genes. - SA levels rose at 1 day post inoculation; JA levels declined by 3 days post inoculation, according to the authors. - Investigators constructed a gene regulatory network from responding root transcriptomes to identify candidate regulatory hubs and pathways. - The study team validated predicted key components using follow-up functional assays and mutant analyses. These assays indicated contributions of SA, JA, indole glucosinolates, camalexin, and flavonoids to establishment of a disease‑suppressive soil (soil‑borne legacy, SBL). - Transcriptional regulation was concentrated in root tips, with spatial patterns informing the network analysis. - The authors noted that roots undergo rapid systemic reprogramming after foliar infection and that hormone signaling plus secondary metabolism shape SBL beyond canonical defense roles. - Data links molecular root responses to a community-level outcome (SBL), but the preprint status means results have not been peer reviewed; further mechanistic and ecological validation is needed.
## Clinical Analysis & Structured Key Points
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Run Qi 1 Utrecht University; * [Find this author on Google Scholar](https://www.biorxiv.org/lookup/google-scholar?link_type=googlescholar&gs_type=author&author%5B0%5D=Run%2BQi%2B "Open in new tab") * [Find this author on PubMed](https://www.biorxiv.org/lookup/external-ref?access_num=Qi%20R&link_type=AUTHORSEARCH "Open in new tab") * [Search for this author on this site](https://www.biorxiv.org/search/author1%3ARun%2BQi%2B) Ivona Glavincheska 1 Utrecht University; * [Find this author on Google Scholar](https://www.biorxiv.org/lookup/google-scholar?link_type=googlescholar&gs_type=author&author%5B0%5D=Ivona%2BGlavincheska%2B "Open in new tab") * [Find this author on PubMed](https://www.biorxiv.org/lookup/external-ref?access_num=Glavincheska%20I&link_type=AUTHORSEARCH "Open in new tab") * [Search for this author on this site](https://www.biorxiv.org/search/author1%3AIvona%2BGlavincheska%2B) Jelle Spooren 1 Utrecht University; * [Find this author on Google Scholar](https://www.biorxiv.org/lookup/google-scholar?link_type=googlescholar&gs_type=author&author%5B0%5D=Jelle%2BSpooren%2B "Open in new tab") * [Find this author on PubMed](https://www.biorxiv.org/lookup/external-ref?access_num=Spooren%20J&link_type=AUTHORSEARCH "Open in new tab") * [Search for this author on this site](https://www.biorxiv.org/search/author1%3AJelle%2BSpooren%2B) Xiaoyan Liu 1 Utrecht University; * [Find this author on Google Scholar](https://www.biorxiv.org/lookup/google-scholar?link_type=googlescholar&gs_type=author&author%5B0%5D=Xiaoyan%2BLiu%2B "Open in new tab") * [Find this author on PubMed](https://www.biorxiv.org/lookup/external-ref?access_num=Liu%20X&link_type=AUTHORSEARCH "Open in new tab") * [Search for this author on this site](https://www.biorxiv.org/search/author1%3AXiaoyan%2BLiu%2B) Marit Van Laatum 1 Utrecht University; * [Find this author on Google Scholar](https://www.biorxiv.org/lookup/google-scholar?link_type=googlescholar&gs_type=author&author%5B0%5D=Marit%2BVan%2BLaatum%2B "Open in new tab") * [Find this author on PubMed](https://www.biorxiv.org/lookup/external-ref?access_num=Van%20Laatum%20M&link_type=AUTHORSEARCH "Open in new tab") * [Search for this author on this site](https://www.biorxiv.org/search/author1%3AMarit%2BVan%2BLaatum%2B) Francel Verstappen 2 Wageningen University * [Find this author on Google Scholar](https://www.biorxiv.org/lookup/google-scholar?link_type=googlescholar&gs_type=author&author%5B0%5D=Francel%2BVerstappen%2B "Open in new tab") * [Find this author on PubMed](https://www.biorxiv.org/lookup/external-ref?access_num=Verstappen%20F&link_type=AUTHORSEARCH "Open in new tab") * [Search for this author on this site](https://www.biorxiv.org/search/author1%3AFrancel%2BVerstappen%2B) Iris F Kappers 2 Wageningen University * [Find this author on Google Scholar](https://www.biorxiv.org/lookup/google-scholar?link_type=googlescholar&gs_type=author&author%5B0%5D=Iris%2BF%2BKappers%2B "Open in new tab") * [Find this author on PubMed](https://www.biorxiv.org/lookup/external-ref?access_num=Kappers%20IF&link_type=AUTHORSEARCH "Open in new tab") * [Search for this author on this site](https://www.biorxiv.org/search/author1%3AIris%2BF%2BKappers%2B) Roeland L Berendsen 1 Utrecht University; 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In Arabidopsis thaliana, foliar infection by Hyaloperonospora arabidopsidis (Hpa) has been shown to establish a disease-suppressive microbiome that promotes protection against Hpa infection of the subsequent plant generation grown in this conditioned soil - a phenomenon known as soil-borne legacy (SBL). The root responses involved in SBL establishment have remained largely unclear. In this study, time-series RNA-seq of roots from Hpa-infected plants grown in natural soil was conducted over seven days post-inoculation. A gene regulatory network of the responding roots was constructed. The role of predicted key components was verified in follow-up assays. Root transcriptional reprogramming started within one day after foliar infection. Genes associated with salicylic acid (SA)-mediated defense were upregulated, while those linked to secondary metabolism and jasmonic acid (JA) responsiveness were downregulated. SA accumulation increased at 1 dpi, and JA decreased by 3 dpi. Transcriptional regulation occurred primarily in the tips of the roots. Mutant analyses confirmed that SA, JA, indole glucosinolates, camalexin, and flavonoids contribute to SBL establishment. Our findings reveal rapid systemic transcriptional reprogramming in roots upon foliar pathogen attack, uncovering novel roles of hormone signaling and secondary metabolism in shaping a disease-suppressive soil beyond their known defense functions. ### Competing Interest Statement The authors have declared no competing interest. ## Footnotes * ## Funder Information Declared Dutch Research Council, https://ror.org/04jsz6e67, OCENW.GROOT.2019.063 Copyright The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a [CC-BY-ND 4.0 International license](http://creativecommons.org/licenses/by-nd/4.0/). bioRxiv and medRxiv thank the following for their generous financial support: > The Chan Zuckerberg Initiative, Cold Spring Harbor Laboratory, the Sergey Brin Family Foundation, California Institute of Technology, Centre National de la Recherche Scientifique, Fred Hutchinson Cancer Center, Imperial College London, Massachusetts Institute of Technology, Stanford University, The University of Edinburgh, University of Washington, and Vrije Universiteit Amsterdam. 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