Root Microbial Functions and Robust Network Drive High-Yielding Canola Genotype

Plants and their root microbiomes have co-evolved complex relationships that influence growth and development. While plant genotype is known to shape root microbiomes, a detailed understanding of this interplay remains limited. We used shotgun metagenomic sequencing to examine the composition, function, and microbial association networks of root bacterial communities in two Brassica napus (canola) genotypes with contrasting yields: NAM-23 and NAM-30. Root samples were collected at three developmental stages (vegetative, flowering, and maturation) across three field sites. Growth stage significantly influenced alpha diversity and beta diversity, but not KEGG pathway functions. Genotype had minimal effect on overall diversity and function, but specifically influenced the recruitment of certain bacterial taxa and the topology of microbial association networks. NAM-23, the high-yielding genotype, was enriched in plant growth-promoting bacteria (Rahnella) and genes related to carbohydrate and phosphorus metabolism. Additionally, NAM-23 exhibited a more robust and connected microbial network, with higher degree, betweenness, clustering coefficient, and more genotype-specific hub taxa, traits often associated with enhanced resistance to abiotic and biotic stresses and potentially contributing to its higher yield. Our findings provide a high-resolution view of genotype-specific interactions with the root microbiome, highlighting key microbial features associated with high yield. These insights support microbiome-informed strategies for crop improvement in sustainable agriculture.