Genome wide association study reveals plant loci controlling heritability of the rhizosphere microbiome

Abstract

45Host genetics has recently been shown to be a driver of plant microbiome composition. However, 46 identifying the underlying genetic loci controlling microbial selection remains challenging. 47 Genome wide association studies (GWAS) represent a potentially powerful, unbiased method to 48 identify microbes sensitive to host genotype, and to connect them with the genetic loci that 49 influence their colonization. Here, we conducted a population-level microbiome analysis of the 50 rhizospheres of 200 sorghum genotypes. Using 16S rRNA amplicon sequencing, we identify 51 rhizosphere-associated bacteria exhibiting heritable associations with plant genotype, and identify 52 significant overlap between these lineages and heritable taxa recently identified in maize. 53Furthermore, we demonstrate that GWAS can identify host loci that correlate with the abundance 54 of specific subsets of the rhizosphere microbiome. Finally, we demonstrate that these results can 55 be used to predict rhizosphere microbiome structure for an independent panel of sorghum 56 genotypes based solely on knowledge of host genotypic information. 57 58 sorghum 60 61Recent work has shown that root-associated microbial communities are in part shaped by host 63 genetics 1-4 . A study comparing the root microbiomes of a broad range of cereal crops has 64 demonstrated a strong correlation between host genetic differences and microbiome composition 4 , 65 suggesting that a subset of the plant microbiome may be influenced by host genotype across a 66 range of plant hosts. In maize, these genotype-sensitive, or "heritable", microbes are 67 phylogenetically clustered within specific taxonomic groups 5 ; however, it is unclear whether the 68 increased genotype sensitivity in these lineages is unique to the maize microbiome or is common 69 to other plant hosts as well. 71Despite consistent evidence of the interaction between host genetics and plant microbiome 72 composition, identifying specific genetic elements driving host-genotype dependent microbiome 73 acquisition and assembly in plants remains a challenge. Recent efforts guided by a priori 74 hypotheses of gene involvement have begun to dissect the impact of individual genes on 75 microbiome composition 6,7 . However, these studies are limited to a small fraction of plant genes 76 predicted to function in microbiome-related processes. Additionally, many plant traits expected to 77 impact microbiome composition and activity, such as root exudation 8 and root system architecture 9 , 78 are inherently complex and potentially governed by a very large number of genes. For these 79 reasons, there is a need for alternative, large-scale and unbiased methods for identifying the genes 80 that regulate host-mediated selection of the microbiome. 82Genome-wide association studies (GWAS) represent a powerful approach to map loci that are 83 associated with complex traits in a genetically diverse population. Though pioneered for use in 84 human genetics, to date the majority of GWAS have been conducted in pla...

Evaluating domestication and ploidy effects on the assembly of the wheat bacterial microbiome

“…This likely is attributable, in part, to varying diversity and rate of plant root exudation across different accessions, species, and growing conditions [ 3 , 69 ]. In addition, other studies provide additional evidence that rhizospheres—which host a more diverse and greater pool of microbes than the root itself to exert influence on—may be ideal for better understanding host contributions to microbiome assembly [ 70 ], including microbiome-based genome-wide association studies [ 71 ]. In order to better understand contributions of ploidy level to microbiome assembly, versus what may be attributable to other genotype dependent differences, we recommend that future work investigate how finer genetic differences across ploidy levels may relate to differences in microbiome composition and activity (e.g.…”

Enabling sustainable agriculture through understanding and enhancement of microbiomes

“…Several genome‐wide association studies (GWAS) have identified candidate plant genes that influence the assembly of plant‐associated microbiota (Walters et al ., 2018; Beilsmith et al ., 2019; Roman‐Reyna et al ., 2019; Deng et al ., 2020). These genes are shared between different plant varieties and are correlated highly with the abundance of specific subsets of the rhizosphere microbiome (Walters et al ., 2018; Deng et al ., 2020). Manipulation of these candidate genes can provide a way forward to generate designer plants with defined microbiomes and their associated benefits (Box 3).…”

Comparative Study of the Rhizospheric Microflora of Sunflower Cultivars Helianthus annuus (Asteráceae, Magnoliópsida) Grown on Soils with Anthropogenic Polyelemental Anomalies

“…Эти различия зарегистрированы при выращивании растений на контрольной незагрязненной почве и особенно выражены при культивировании подсолнечника на техногенно загрязненной почве КМЗ (рисунок, а -в). Обнаруженные различия могут быть обусловлены как свойствами почв и уровнем их загрязнения, так и различиями в составе корневых экссудатов растений двух мутантных культиваров, имеющих приоритетное значение для формирования специфического ризосферного микробиома того или иного растения (Schlemper et al, 2017Deng et al, 2020).…”