Association analyses of host genetics, root-colonizing microbes, and plant phenotypes under different nitrogen conditions in maize

Authors

Michael A. Meier, University of Nebraska-Lincoln
Gen Xu, University of Nebraska-LincolnFollow
Martha G. Lopez-Guerrero, University of Nebraska-Lincoln
Guangyong Li, University of Nebraska-LincolnFollow
Christine Smith, University of Nebraska-Lincoln
Brandi Sigmon, University of Nebraska-LincolnFollow
Joshua R. Herr, University of Nebraska-Lincoln
James R. Alfano, University of Nebraska-Lincoln
Yufeng Ge, University of Nebraska-LincolnFollow
James C. Schnable, University of Nebraska-LincolnFollow
Jinliang Yang, University of Nebraska - LincolnFollow

Document Type

Article

Date of this Version

7-27-2022

Citation

Meier et al. eLife 2022;11:e75790. DOI: https://doi.org/10.7554/eLife.75790

Comments

article is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use and redistribution provided that the original author and source are credited.

Abstract

The root-associated microbiome (rhizobiome) affects plant health, stress tolerance, and nutrient use efficiency. However, it remains unclear to what extent the composition of the rhizobiome is governed by intraspecific variation in host plant genetics in the field and the degree to which host plant selection can reshape the composition of the rhizobiome. Here, we quantify the rhizosphere microbial communities associated with a replicated diversity panel of 230 maize (Zea mays L.) genotypes grown in agronomically relevant conditions under high N (+N) and low N (-N) treatments. We analyze the maize rhizobiome in terms of 150 abundant and consistently reproducible microbial groups and we show that the abundance of many root-associated microbes is explainable by natural genetic variation in the host plant, with a greater proportion of microbial variance attributable to plant genetic variation in -N conditions. Population genetic approaches identify signatures of purifying selection in the maize genome associated with the abundance of several groups of microbes in the maize rhizobiome. Genome-wide association study was conducted using the abundance of microbial groups as rhizobiome traits, and n=622 plant loci were identified that are linked to the abundance of n=104 microbial groups in the maize rhizosphere. In 62/104 cases, which is more than expected by chance, the abundance of these same microbial groups was correlated with variation in plant vigor indicators derived from high throughput phenotyping of the same field experiment. We provide comprehensive datasets about the three-way interaction of host genetics, microbe abundance, and plant performance under two N treatments to facilitate targeted experiments toward harnessing the full potential of root-associated microbial symbionts in maize production.