Plant-associated microbes play a crucial role in plant growth, enhancing nutrient uptake and disease resistance. However, modern crop varieties, bred for high-input agriculture, often show reduced root colonization by beneficial soil microbes. The international research consortium Wheat Alliance seeks to identify genetic factors in wheat that influence the recruitment of these beneficial microbes. With up to 1100 wheat-related genotypes available, we screen plant growth under nitrogen- and phosphate-limited conditions. Our approach integrates high-throughput phenotyping of shoot traits with root metagenome sequencing. Initial screening of 11 wheat genotypes revealed clearly distinguishable bacterial root communities (PERMANOVA: R2 = 0.44, adjusted p = 0.001). LASSO with five-fold cross-validation identified 17 bacterial genera that robustly discriminate wheat genotype, achieving a mean classification accuracy of 84.5 ± 3.9% (mean ± SE across folds). These are promising taxa to trace in larger screenings investigating plant growth-associated microbiota. One-hundred wheat genotypes have been screened in greenhouses, and root samples are currently being processed for sequencing. The plant microbiome and shoot phenotyping data will be used to train machine learning models, enabling us to uncover complex interactions between plant traits, microbial composition, and nutrient acquisition. A genome-wide association study (GWAS) will then pinpoint genetic drivers shaping the root microbiome, providing new avenues for microbiome-based breeding and more sustainable wheat cultivation.

Co-authors: Caitlan Smart, Simona Radutoiu, Ronnie de Jonge