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.

与微生物的有益相互作用对于作物性能和恢复力至关重要。然而，目前尚不清楚微生物组相对于宿主植物基因型的遗传性如何，以及宿主遗传机制在面对环境胁迫时可以在多大程度上调节植物与微生物群的相互作用。在这里，我们调查了 3,168 个根和根际微生物组样本，这些样本来自 129 个当地适应的玉米品种，这些样本来自不同的栖息地，并在控制和不同的胁迫条件下生长。我们量化了应激治疗和宿主基因型对微生物组的影响。植物基因型和来源环境可以预测微生物组丰度。全基因组关联分析确定了与根际微生物丰度和来源环境相关的宿主遗传变异。我们在一个候选基因中发现了转座子插入，该插入与我们的对照实验中关键细菌Massilia的丰度以及源环境中的土壤总氮有关。单独分离和控制接种Massilia就可以促进根系发育、全株生物量生产和适应低氮利用率。我们的结论是，适应当地情况的玉米品种对其根部和根际微生物群施加遗传控制模式，这些微生物群遵循其家园环境的变化，这与对普遍胁迫的耐受性作用一致。