Wild rice locus enables microbiome re-domestication for enhanced nitrogen-use efficiency
8 affiliations
- 1State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
- 2Department of Microbial Ecology, Netherlands Institute of Ecology NIOO-KNAW, Wageningen, the Netherlands
- 3Rice National Engineering Research Center (Nanchang), Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang, China
- 4Key Laboratory of Straw Comprehensive Utilization and Black Soil Conservation, Jilin Agricultural University, Changchun, Jilin China
- 5Ecology and Biodiversity, Institute of Environmental Biology, Utrecht University, Utrecht, the Netherlands
- 6College of Landscape Architecture, Changchun University, Changchun, China
- 7Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX USA
- 8School of Agriculture and Biological Technique, Liaocheng University, Liaocheng, China
Abstract
Domestication of crops, such as rice, has resulted in the loss of beneficial root-associated microbiota central to plant nitrogen-use efficiency. Whether these microbes can be inherited through hybridization of wild and cultivated plants and the host genes involved is unclear. Here we used two recombinant inbred line populations, derived from cultivated rice (Oryza sativa) and its wild relative Oryza rufipogon to map host quantitative trait loci associated with core bacterial taxa. Integrating microbiome profiling, quantitative trait loci mapping, population genomics and transgenic validation, we identified 113 candidate plant genes. The receptor-like kinase-encoding gene OsRLK, found predominantly in wild rice, was significantly associated with Acinetobacter, which enhances plant nitrogen uptake. Knockout and overexpression of OsRLK, inoculated with an Acinetobacter synthetic community, validated their role in nitrogen-use efficiency. In field trials, the overexpression line significantly increased yield-related traits. These findings establish the genetic basis of microbiome re-domestication and provide a framework for microbiome-guided breeding of nutrient-efficient crops.
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BibTeX
@article{chang2026wild,
title = {{Wild rice locus enables microbiome re-domestication for enhanced nitrogen-use efficiency}},
author = {Jingjing Chang and Dianwen Wang and Zongmu Yao and Yingnan Pang and Hengfei Zhang and Changji Wang and Yuanbo Xie and Yu Sun and Jianfeng Zhang and Weiqiang Li and Aizhen Liang and Xiangnan Li and Dazhou Chen and Hongping Chen and Xuewen Chen and Enze Wang and Lam-Son Phan Tran and Jilin Wang and Jos M. Raaijmakers and Chunjie Tian and Eiko E. Kuramae},
journal = {Nature Microbiology},
year = {2026},
month = sep,
doi = {10.1038/s41564-026-02498-x},
url = {https://doi.org/10.1038/s41564-026-02498-x},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Wild rice locus enables microbiome re-domestication for enhanced nitrogen-use efficiency
AU - Jingjing Chang
AU - Dianwen Wang
AU - Zongmu Yao
AU - Yingnan Pang
AU - Hengfei Zhang
AU - Changji Wang
AU - Yuanbo Xie
AU - Yu Sun
AU - Jianfeng Zhang
AU - Weiqiang Li
AU - Aizhen Liang
AU - Xiangnan Li
AU - Dazhou Chen
AU - Hongping Chen
AU - Xuewen Chen
AU - Enze Wang
AU - Lam-Son Phan Tran
AU - Jilin Wang
AU - Jos M. Raaijmakers
AU - Chunjie Tian
AU - Eiko E. Kuramae
PY - 2026
DA - 2026/09/30
JO - Nature Microbiology
DO - 10.1038/s41564-026-02498-x
UR - https://doi.org/10.1038/s41564-026-02498-x
AB - Domestication of crops, such as rice, has resulted in the loss of beneficial root-associated microbiota central to plant nitrogen-use efficiency. Whether these microbes can be inherited through hybridization of wild and cultivated plants and the host genes involved is unclear. Here we used two recombinant inbred line populations, derived from cultivated rice (Oryza sativa) and its wild relative Oryza rufipogon to map host quantitative trait loci associated with core bacterial taxa. Integrating microbiome profiling, quantitative trait loci mapping, population genomics and transgenic validation, we identified 113 candidate plant genes. The receptor-like kinase-encoding gene OsRLK, found predominantly in wild rice, was significantly associated with Acinetobacter, which enhances plant nitrogen uptake. Knockout and overexpression of OsRLK, inoculated with an Acinetobacter synthetic community, validated their role in nitrogen-use efficiency. In field trials, the overexpression line significantly increased yield-related traits. These findings establish the genetic basis of microbiome re-domestication and provide a framework for microbiome-guided breeding of nutrient-efficient crops.
SN - 2058-5276
ER -