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 A. Morris, Pete E. Hedley, Andreas Maurer, Klaus Pillen, Gino Naclerio, Tanja Mimmo, Geoffrey J. Barton, Robbie Waugh, James Abbott, Davide Bulgarelli (Lead / Corresponding author)

Research output: Contribution to journalArticlepeer-review

24 Citations (Scopus)
43 Downloads (Pure)


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 plants capacity of shaping rhizosphere microbes.
Original languageEnglish
Article number3443
Number of pages14
JournalNature Communications
Publication statusPublished - 16 Jun 2022


  • Agricultural genetics
  • Microbiome
  • Plant domestication

ASJC Scopus subject areas

  • Physics and Astronomy(all)
  • Chemistry(all)
  • Biochemistry, Genetics and Molecular Biology(all)


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