Identifying plant genes shaping microbiota

20 21 A prerequisite to exploiting soil microbes for sustainable crop production is the 22 identification of the plant genes shaping microbiota composition in the rhizosphere, 23 the interface between roots and soil. Here we used metagenomics information as an 24 external quantitative phenotype to map the host genetic determinants of the 25 rhizosphere microbiota in wild and domesticated genotypes of barley, the fourth most 26 cultivated cereal globally. We identified a small number of loci with a major effect on 27 the composition of rhizosphere communities. One of those, designated the QRMC28 3HS locus, emerged as a major determinant of microbiota composition. We then 29 subjected soil-grown sibling lines harbouring contrasting alleles at QRMC-3HS and 30 hosting contrasting microbiotas to comparative root RNA-seq profiling. This allowed 31 us to identify three primary candidate genes, including a Nucleotide-Binding-Leucine32 Rich-Repeat (NLR) gene in a region of structural variation of the barley genome. Our 33 results provide novel insights into the footprint of crop improvement on the plant’s 34 capacity of shaping rhizosphere microbes. 35