Host genetic traits underlying the composition/assembly of the citrus microbiome

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 SNP-associated microbial functional traits of leaf and root microbiomes, but not in rhizosphere microbiome, indicating they are important factor for bacteria to colonize inside or on leaf and root tissues, but less so in the rhizosphere. We also uncovered that chemotaxis and flagella genes play critical roles for bacteria colonizing leaf tissues, but not in root tissues and rhizosphere. Microbiome associated host genes were mainly involved in plant immunity, transporters, hormones, cell wall, and 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 genetic traits underneath the mutual selection of citrus and microbes via GWAS analyses