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Heritable microbiome variation is correlated with source environment in locally adapted maize varieties

Xiaoming He, Danning Wang, Yong Jiang, Meng Li, Manuel Delgado-Baquerizo, Chloee McLaughlin, Caroline Marcon, Li Guo, Marcel Baer, Yudelsy A. T. Moya, et al.
(2024) NATURE PLANTS. 10(4). p.598-617
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Abstract
Beneficial interactions with microorganisms are pivotal for crop performance and resilience. However, it remains unclear how heritable the microbiome is with respect to the host plant genotype and to what extent host genetic mechanisms can modulate plant-microbiota interactions in the face of environmental stresses. Here we surveyed 3,168 root and rhizosphere microbiome samples from 129 accessions of locally adapted Zea, sourced from diverse habitats and grown under control and different stress conditions. We quantified stress treatment and host genotype effects on the microbiome. Plant genotype and source environment were predictive of microbiome abundance. Genome-wide association analysis identified host genetic variants linked to both rhizosphere microbiome abundance and source environment. We identified transposon insertions in a candidate gene linked to both the abundance of a keystone bacterium Massilia in our controlled experiments and total soil nitrogen in the source environment. Isolation and controlled inoculation of Massilia alone can contribute to root development, whole-plant biomass production and adaptation to low nitrogen availability. We conclude that locally adapted maize varieties exert patterns of genetic control on their root and rhizosphere microbiomes that follow variation in their home environments, consistent with a role in tolerance to prevailing stress.
Keywords
Plant Science, ROOT MICROBIOTA, DATA SET, MODEL, ASSOCIATION, COMMUNITIES, EXPRESSION, DIVERSITY, INFERENCE, SELECTION, CLIMATE

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MLA
He, Xiaoming, et al. “Heritable Microbiome Variation Is Correlated with Source Environment in Locally Adapted Maize Varieties.” NATURE PLANTS, vol. 10, no. 4, 2024, pp. 598–617, doi:10.1038/s41477-024-01654-7.
APA
He, X., Wang, D., Jiang, Y., Li, M., Delgado-Baquerizo, M., McLaughlin, C., … Yu, P. (2024). Heritable microbiome variation is correlated with source environment in locally adapted maize varieties. NATURE PLANTS, 10(4), 598–617. https://doi.org/10.1038/s41477-024-01654-7
Chicago author-date
He, Xiaoming, Danning Wang, Yong Jiang, Meng Li, Manuel Delgado-Baquerizo, Chloee McLaughlin, Caroline Marcon, et al. 2024. “Heritable Microbiome Variation Is Correlated with Source Environment in Locally Adapted Maize Varieties.” NATURE PLANTS 10 (4): 598–617. https://doi.org/10.1038/s41477-024-01654-7.
Chicago author-date (all authors)
He, Xiaoming, Danning Wang, Yong Jiang, Meng Li, Manuel Delgado-Baquerizo, Chloee McLaughlin, Caroline Marcon, Li Guo, Marcel Baer, Yudelsy A. T. Moya, Nicolaus von Wirén, Marion Deichmann, Gabriel Schaaf, Hans-Peter Piepho, Zhikai Yang, Jinliang Yang, Bunlong Yim, Kornelia Smalla, Sofie Goormachtig, Franciska T. de Vries, Hubert Hüging, Mareike Baer, Ruairidh J. H. Sawers, Jochen C. Reif, Frank Hochholdinger, Xinping Chen, and Peng Yu. 2024. “Heritable Microbiome Variation Is Correlated with Source Environment in Locally Adapted Maize Varieties.” NATURE PLANTS 10 (4): 598–617. doi:10.1038/s41477-024-01654-7.
Vancouver
1.
He X, Wang D, Jiang Y, Li M, Delgado-Baquerizo M, McLaughlin C, et al. Heritable microbiome variation is correlated with source environment in locally adapted maize varieties. NATURE PLANTS. 2024;10(4):598–617.
IEEE
[1]
X. He et al., “Heritable microbiome variation is correlated with source environment in locally adapted maize varieties,” NATURE PLANTS, vol. 10, no. 4, pp. 598–617, 2024.
@article{01HTPQP3CP2CVX8QN54WP4YZNR,
  abstract     = {{Beneficial interactions with microorganisms are pivotal for crop performance and resilience. However, it remains unclear how heritable the microbiome is with respect to the host plant genotype and to what extent host genetic mechanisms can modulate plant-microbiota interactions in the face of environmental stresses. Here we surveyed 3,168 root and rhizosphere microbiome samples from 129 accessions of locally adapted Zea, sourced from diverse habitats and grown under control and different stress conditions. We quantified stress treatment and host genotype effects on the microbiome. Plant genotype and source environment were predictive of microbiome abundance. Genome-wide association analysis identified host genetic variants linked to both rhizosphere microbiome abundance and source environment. We identified transposon insertions in a candidate gene linked to both the abundance of a keystone bacterium Massilia in our controlled experiments and total soil nitrogen in the source environment. Isolation and controlled inoculation of Massilia alone can contribute to root development, whole-plant biomass production and adaptation to low nitrogen availability. We conclude that locally adapted maize varieties exert patterns of genetic control on their root and rhizosphere microbiomes that follow variation in their home environments, consistent with a role in tolerance to prevailing stress.}},
  author       = {{He, Xiaoming and Wang, Danning and Jiang, Yong and Li, Meng and Delgado-Baquerizo, Manuel and McLaughlin, Chloee and Marcon, Caroline and Guo, Li and Baer, Marcel and Moya, Yudelsy A. T. and von Wirén, Nicolaus and Deichmann, Marion and Schaaf, Gabriel and Piepho, Hans-Peter and Yang, Zhikai and Yang, Jinliang and Yim, Bunlong and Smalla, Kornelia and Goormachtig, Sofie and de Vries, Franciska T. and Hüging, Hubert and Baer, Mareike and Sawers, Ruairidh J. H. and Reif, Jochen C. and Hochholdinger, Frank and Chen, Xinping and Yu, Peng}},
  issn         = {{2055-026X}},
  journal      = {{NATURE PLANTS}},
  keywords     = {{Plant Science,ROOT MICROBIOTA,DATA SET,MODEL,ASSOCIATION,COMMUNITIES,EXPRESSION,DIVERSITY,INFERENCE,SELECTION,CLIMATE}},
  language     = {{eng}},
  number       = {{4}},
  pages        = {{598--617}},
  title        = {{Heritable microbiome variation is correlated with source environment in locally adapted maize varieties}},
  url          = {{http://doi.org/10.1038/s41477-024-01654-7}},
  volume       = {{10}},
  year         = {{2024}},
}
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