Host genotype shapes the root rot resistance-associated microbiome of pea

Summary in the original language of the document

Soil-borne pathogens pose a major threat to legume cultivation, which is essential to sustainable plant-based protein production. In pea (Pisum sativum), for example, short crop rotations can result in soil fatigue, which is triggered by the enrichment of several pathogens forming the pea root rot complex (PRRC). The combined effect of the PRRC members hampers resistance breeding against root rot. Microbiome-mediated resistance poses a possible solution to mitigate yield losses caused by PRRCs. How the root microbial community interacts with the PRRC and if the pea genotype influences these interactions is, however, largely unknown. Here, 252 pea genotypes consisting of 173 landraces of the USDA pea core collection, 33 registered cultivars from Europe, and 46 advanced breeding lines from Switzerland were grown for 21 days in PRRC-infested soils in a walk-in climate chamber before roots were harvested for microbiome analysis. Root bacteria and fungi were characterized by 16S and ITS rRNA amplicon sequencing. Analyzing alpha diversity and microbial community composition showed associations with root rot resistance. Through network analysis, we identified (highly connected) hub taxa. Some of them were shown to be heritable. Based on differential abundance analysis, we further identified heritable bacterial and fungal taxa linked to root rot resistance. In a follow-up study, a subset of eight contrasting genotypes was grown in four different agricultural soils, revealing that some of the potentially beneficial microbes are associated with pea resistance in different infested soils. Further, the 252 pea lines were SNP genotyped allowing us to perform genome-wide association studies, which revealed several plant genomic regions significantly associated with relevant root microbial taxa and overall microbiota composition. The identified genetic markers will be used to select pea breeding material for field validation of microbiome-mediated resistance against PRRC. This work highlights the potential of microbiome-assisted breeding for more sustainable farming.