Uncovering the early and conserved molecular mechanisms of root nitrogen foraging in model and crops

Li, Ying, Patrick, Ryan M, Peacock, Charles, Koenigsfeld, Leo, Rock, Tara M, Bouguyon, Eleonore, Kuhn, Emily, Albert, MarySara, Varala, Kranthi, McCombie, W Richard, Cheng, Chia-Yi, Ruffel, Sandrine, Coruzzi, Gloria (March 2026) Uncovering the early and conserved molecular mechanisms of root nitrogen foraging in model and crops. BMC Genomics, 27 (1). p. 384. ISSN 1471-2164

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Abstract

BACKGROUND: Nitrogen (N) foraging, the ability of plants to promote preferential root growth in N-rich patches of soil, is fundamental to the competitiveness and wellbeing of plants. A unique “split-root” system, where a heterogenous N environment stimulates root foraging, provides a powerful experimental model to study the mechanisms underlying root foraging in model (Arabidopsis) and/or crop plants. RESULTS: We used the split-root set up to capture early molecular events involved in systemic N-signaling after exposure to a heterogeneous N signal, through time-course transcriptomic analysis across shoots and roots of Arabidopsis. We found that a histone methyltransferase, SET DOMAIN GROUP 8 (SDG8), is necessary for root N-foraging, suggesting a previously unknown role for chromatin regulation in mediating the preferential root growth response to colonize N-rich patches. To determine if the underlying molecular mechanism is conserved in evolution, we compared the root foraging behavior from model-to-crop (Arabidopsis, tomato and maize). Our analysis showed the model and crop species shared a root N-foraging growth response, with some variation among specific genotypes. Interestingly, we observed both shared and distinct transcriptional responses to heterogenous N environments among these three species. CONCLUSIONS: Our study has generated insights into the molecular basis of root N-foraging, with the potential to improve nutrient use efficiency in crop plants in a heterogeneous field environment. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-026-12736-5.

Item Type:	Paper
Subjects:	organs, tissues, organelles, cell types and functions organs, tissues, organelles, cell types and functions > tissues types and functions > root organs, tissues, organelles, cell types and functions > tissues types and functions
CSHL Authors:	McCombie, W. Richard
Communities:	CSHL labs > McCombie lab
SWORD Depositor:	CSHL Elements
Depositing User:	CSHL Elements
Date:	10 March 2026
Date Deposited:	12 May 2026 14:38
Last Modified:	12 May 2026 14:38
PMCID:	PMC13085526
Related URLs:	Publisher
URI:	https://repository.cshl.edu/id/eprint/42202

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