Identification of plant genotype dependent microbiome recruitment associated with disease resistance against root rot in peas

Summary

The cultivation of pea (Pisum sativum) is highly constrained by various soil-borne pathogens. Together these pathogens form a pea root rot complex (PRRC) and trigger soil fatigue. Microbiome-mediated disease resistance poses a possible mechanism to mitigate yield loss through PRRC. It is however largely unknown how the PRRC interacts with other members of the root microbiome and how this affects plant resistance. Here, we compared the root microbiome of 252 pea lines in a controlled soil-based phenotyping assay that was previously shown to predict field-relevant resistance against PRRC. Root bacteria and fungi were characterized by 16S rRNA and ITS amplicon sequencing. We analyzed alpha diversity and microbial community composition, and identified heritable hub OTUs. Based on differential abundance analysis we further identified heritable bacterial and fungal hub taxa that are associated with root rot resistance. Subsequent genome-wide association studies revealed plant genomic regions that are significantly correlated with beneficial hub taxa and overall microbial community composition. In a next step, the identified genetic markers will be used to select pea breeding material for field validation of microbiome-mediated resistance against PRRC. This work demonstrates the potential of microbiome-assisted breeding to promote sustainable farming practices.