Identifying plant genes shaping microbiota composition in the barley rhizosphere

Carmen Escudero-Martinez, Max Coulter, Rodrigo Alegria Terrazas, Alexandre Foito, Rumana Kapadia, Laura Pietrangelo, Mauro Maver, Rajiv Sharma, Alessio Aprile, Jenny Morris, Pete E. Hedley, Andreas Maurer, Klaus Pillen, Gino Naclerio, Tanja Mimmo, Geoffrey J. Barton, Robbie Waugh, James Abbott and Davide Bulgarelli ()
Additional contact information
Carmen Escudero-Martinez: University of Dundee, Plant Sciences, School of Life Sciences
Max Coulter: University of Dundee, Plant Sciences, School of Life Sciences
Rodrigo Alegria Terrazas: University of Dundee, Plant Sciences, School of Life Sciences
Alexandre Foito: The James Hutton Institute
Rumana Kapadia: University of Dundee, Plant Sciences, School of Life Sciences
Laura Pietrangelo: University of Dundee, Plant Sciences, School of Life Sciences
Mauro Maver: University of Dundee, Plant Sciences, School of Life Sciences
Rajiv Sharma: Scotland’s Rural College
Alessio Aprile: University of Dundee, Plant Sciences, School of Life Sciences
Jenny Morris: The James Hutton Institute
Pete E. Hedley: The James Hutton Institute
Andreas Maurer: Martin-Luther-University
Klaus Pillen: Martin-Luther-University
Gino Naclerio: University of Molise
Tanja Mimmo: Free University of Bozen-Bolzano
Geoffrey J. Barton: University of Dundee, Computational Biology, School of Life Sciences
Robbie Waugh: University of Dundee, Plant Sciences, School of Life Sciences
James Abbott: University of Dundee, Computational Biology, School of Life Sciences
Davide Bulgarelli: University of Dundee, Plant Sciences, School of Life Sciences

Nature Communications, 2022, vol. 13, issue 1, 1-14

Abstract: 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 use 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 identify a small number of loci with a major effect on the composition of rhizosphere communities. One of those, designated the QRMC-3HS, emerges as a major determinant of microbiota composition. We subject soil-grown sibling lines harbouring contrasting alleles at QRMC-3HS and hosting contrasting microbiotas to comparative root RNA-seq profiling. This allows 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 insights into the footprint of crop improvement on the plant’s capacity of shaping rhizosphere microbes.

Date: 2022
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DOI: 10.1038/s41467-022-31022-y

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