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, Davide Bulgarelli*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

46 Citations (Scopus)
61 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 plant's capacity of shaping rhizosphere microbes.

Original languageEnglish
Article number3443
Pages (from-to)3443
JournalNature Communications
Issue number1
Early online date16 Jun 2022
Publication statusFirst published - 16 Jun 2022

Bibliographical note

© 2022. The Author(s).


  • Bacteria/genetics
  • Genes, Plant/genetics
  • Hordeum/genetics
  • Microbiota/genetics
  • Plant Roots/genetics
  • Rhizosphere
  • Soil/chemistry
  • Soil Microbiology


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