Host Genetic Traits Underlying the Composition and Assembly of the Citrus Microbiome

Abstract

Although plant genotypes are known to be a determinant of microbiome composition, the genetic mechanisms underlying how genotypes affect the microbiome are poorly understood. Citrus is an important, perennial fruit crop that normally contains scion grafted on the rootstock. Here, we investigated the genetic traits underlying the citrus microbiome. We sequenced the metagenome of leaf, root, and rhizosphere soil samples and the genome of corresponding citrus genotypes, which included 66 unique rootstock–scion combinations (56 scion genotypes and 9 rootstock genotypes) from one location using deep shotgun sequencing. Using a genome-wide association study (GWAS) analysis, we identified significant associations between citrus genes and a subset of genera and functional traits of the microbiome. Intriguingly, we found that bacterial secretion systems and mobility-related genes were present in single-nucleotide polymorphism-associated microbial functional traits of leaf and root microbiomes but not in the rhizosphere microbiome, indicating that they are important factors for bacteria to colonize inside or on leaf and root tissues but less so in the rhizosphere. We also discovered that chemotaxis and flagella genes play critical roles for bacteria colonizing leaf tissues but not in root tissues and the rhizosphere. Microbiome-associated host genes were mainly involved in plant immunity, transporters, hormones, cell walls, and the metabolism of carbohydrates, amino acids, and nitrogen. We identified genetic determinants that are associated with the abundance of Bacillus, Bradyrhizobium, Burkholderia, and Cellvibrio, genera that are known to comprise many beneficial bacteria for citrus. This study unraveled the genetic traits underneath the mutual selection of citrus and microbes via GWAS analyses. This study provides useful information that aids the utilization of genotypes and key members of a healthy microbiota for microbiome engineering as well as the editing of specific genes to improve host microbiota. [Graphic: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Keywords

• endophytes
• genomics
• metagenomics
• microbiome
• rhizosphere and phyllosphere