IDENTIFYING PLANT GENES SHAPING MICROBIOTA COMPOSITION IN THE BARLEY RHIZOSPHERE

Abstract

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

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

* In this revision, we addressed each one of the individual questions and concerns raised by the reviewers. In particular, we conducted additional experiments in silico to provide further support to some of the analytical choices we made as well as to our conclusions. In addition, we integrated in the discussion additional examples from the literature to provide readers with a more balanced vision of our interpretations. Finally, we rephrased sections that Reviewers deemed unclear and rectified typographical errors throughout the documents. The names of three authors were re-ordered to better reflect their contribution in the revision of the manuscript. Crucially, the revision did not alter original findings and conclusions of the manuscript

* https://github.com/BulgarelliD-Lab/Microbiota_mapping