# Root Microbiota: Orchestrating Architecture‐Smart Crops

**Authors:** Qinqin Chen, Yanlai Yao, Huan Chen, Baolei Jia

PMC · DOI: 10.1111/1751-7915.70307 · Microbial Biotechnology · 2026-02-03

## TL;DR

This paper explores how root microbes help shape rice plant structure, offering new ways to breed crops that adapt better to changing environments.

## Contribution

The paper introduces the concept of 'holobiont architecture' for dynamic plant-microbiome interactions in crop breeding.

## Key findings

- Root microbiota directly regulate rice tiller number, a key architectural trait.
- Microbial orchestration enables dynamic fine-tuning of plant architecture.
- The holobiont framework improves phenotypic plasticity and environmental resilience in crops.

## Abstract

Crops depend on microbial partners for their growth, development, and overall resilience. A pivotal understanding has emerged showing the direct involvement of the root microbiota in regulating the tiller number of rice, a crucial architecture that influences yield. Novel frontiers in microbiological applications for agriculture highlight the profound role of the root microbiota in shaping crop architecture to boost productivity. We propose that improvements in crop production are moving from a genetic perspective on “architecture” to embracing “holobiont architecture.” As such, microbial orchestration provides a dynamic fine‐tune function for breeding “architecture‐smart crops” characterised by phenotypic plasticity under environmental uncertainty.

Root‐associated microbiota play an important role in shaping crop architecture. The concept of “holobiont architecture” is proposed, in which plant architecture is dynamically fine‐tuned through synergistic plant–microbiome interactions. This framework offers novel avenues for breeding architecture‐smart crops with improved phenotypic plasticity and environmental resilience.

## Full-text entities

- **Genes:** AT1G72180 (Leucine-rich receptor-like protein kinase family protein) [NCBI Gene 843550] {aka C-terminally encoded peptide receptor 2, CEPR2, T9N14.3, T9N14_3}, IAA34 (indole-3-acetic acid inducible 34) [NCBI Gene 838070] {aka T15D22.10, T15D22_10, indole-3-acetic acid inducible 34}, PUCHI (Integrase-type DNA-binding superfamily protein) [NCBI Gene 831974] {aka T28N17.40, T28N17_40}
- **Chemicals:** SL (MESH:C000591191), Cyclo (-), dipeptide (MESH:D004151), Cyclo(Leu-Pro) (MESH:C445694), ethylene (MESH:C036216), Auxin (MESH:D007210), Leu-Pro (MESH:C043937), carbon (MESH:D002244)
- **Species:** Urochloa brizantha (bread grass, species) [taxon 240448], Arabidopsis thaliana (mouse-ear cress, species) [taxon 3702], Oryza sativa (Asian cultivated rice, species) [taxon 4530], Glycine max (soybean, species) [taxon 3847], Bacillus velezensis SQR9 (strain) [taxon 1423138], Pseudomonas fluorescens (species) [taxon 294]

## Full text

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## Figures

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## References

17 references — full list in the complete paper: https://tomesphere.com/paper/PMC12868375/full.md

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Source: https://tomesphere.com/paper/PMC12868375