Genome-wide association study of Arabidopsis thaliana leaf microbial community

Abstract

Identifying the factors that influence the outcome of host-microbial interactions is critical to protecting biodiversity, minimizing agricultural losses, and improving human health. A few genes that determine symbiosis or resistance to infectious disease have been identified in model species, but a comprehensive examination of how a host's genotype influences the structure of its microbial community is lacking. Here we report the results of a field experiment with the model plant Arabidopsis thaliana to identify the fungi and bacteria that colonize its leaves and the host loci that influence the microbes’ numbers. The composition of this community differs among accessions of A. thaliana. Genome-wide association studies (GWAS) suggest that plant loci responsible for defense and cell wall integrity affect variation in this community. Furthermore, species richness in the bacterial community is shaped by host genetic variation, notably at loci that also influence the reproduction of viruses, trichome branching and morphogenesis.

Bacterial populations in juvenile maize rhizospheres originate from both seed and soil

“…Based on previous experiments using similar methods (Johnston-Monje et al 2014), we had expected that bacterial diversity in root endospheres would be more influenced by plant genotype than by soil, however in this experiment we saw neither genotype nor soil effects, perhaps because the plants were not genetically different enough (i.e., they are both tropical varieties of domesticated Zea mays). We were likewise surprised to observe that leaf and stem surfaces weren't influenced by plant genotype or soil either; although little is understood regarding the origin of phyllosphere microbes (Bulgarelli et al 2013), genotype is thought to play a major role in shaping the phyllosphere (Horton et al 2014;Whipps et al 2008).…”

Assembly of seed-associated microbial communities within and across successive plant generations

“…plant genotype) influence the variation of bacterial root microbiota profiles (Bulgarelli et al 2012;Lundberg et al 2012;Peiffer et al 2013;Edwards et al 2015;Dombrowski et al 2017). Selection by the environment and the host are also important drivers of leaf-associated microbiota composition Horton et al 2014;Wagner et al 2016). In comparison to selection, the relative importance of dispersal, diversification and ecological drift in driving assembly of plant-associated microbiota has not been well investigated.…”

Forest tree genomics: 10 achievements from the past 10 years and future prospects

“…Significant advances have been made recently on this latter topic on the model plant A. thaliana. The use of mutant lines and genome-wide association mapping revealed that plant loci responsible for defense, cell wall integrity, and cuticular wax composition influence the foliar microbiota (Riesberg et al 2013;Horton et al 2014). Another challenge is to go beyond the identification of the genes and environmental factors structuring microbial communities, by elucidating the effects of these hyperdiverse communities on tree growth, health, and reproduction.…”