Holobiont genetic basis of pea root rot resistance

Summary in the original language of the document

Pea (Pisum sativum) cultivation is an important source of sustainable plant proteins. The production is, however, highly compromised by various soil-borne pathogens that can synergistically attack the roots and trigger soil fatigue. While resistant cultivars to individual pathogens exist, the combination of pathogens found in the pea root rot complex (PRRC) can still provoke root infections. Microbiome-mediated disease resistance poses a possible mechanism to mitigate yield loss through PRRCs. So far, it is largely unknown how the PRRC interacts with other members of the root microbial community and whether the pea genotype affects these interactions. To shed light on this, we sequenced amplicons of the root microbiota (fungi and bacteria) of 252 diverse pea lines grown under controlled conditions in a naturally-infested soil, and plants from the same batch of seeds were sequenced by genotyping-by-sequencing. We found that pea lines grown under root rot stress harbor a genotype-specific root microbial community and that the composition of the microbial community is associated with disease resistance. Further analyses enabled us to identify heritable microbial (highly connected) hub taxa that are associated with root rot resistance. Subsequent genome-wide association studies revealed plant genomic regions correlated with the microbiota abundance and overall community composition. Genomic predictions showed that the holobiont (plant and microbial markers together) significantly determines the resistance of the plant. The prediction ability was improved compared to standard plant genomic predictions. Some of the microbial markers for disease resistance were validated in three additional soils. Building on these findings, the breeding company KWS developed a marker assay for putative microbiome-mediated and direct root rot resistance and screened their breeding material. This will be instrumental in selecting pea breeding material for field validation of microbiome-mediated resistance against PRRCs. Overall, this research highlights the potential of microbiome-assisted breeding to promote sustainable farming practices.