IDENTIFYING PLANT GENES SHAPING MICROBIOTA COMPOSITION IN THE BARLEY RHIZOSPHERE. Microbiota mapping

Identifying plant genes underpinning microbiota composition in the rhizosphere, the interface between roots and soil, is a pre-requisite to exploit the potential of soil microbes for sustainable crop production. Here we used metagenomics information as an external quantitative phenotype to map the genetic determinants of the rhizosphere microbiota in wild and domesticated genotypes of barley, the fourth most cultivated cereal globally. We identified a few loci with a major effect on the composition of rhizosphere communities. One of those, designated locus 3H, emerged as a major regulator of microbiota composition. We then subjected soil-grown introgression lines harbouring contrasting alleles at locus 3H and hosting contrasting microbiotas to a comparative root RNA-seq profiling. This allowed us to identify three primary candidate genes, including an individual Nucleotide-Binding-Leucine-Rich-Repeat (NLR) gene in a region of structural variation of the barley genome. Taken together, our results provide novel insights into the footprint of crop improvement on the plant’s capacity of shaping rhizosphere microbes.