Transcriptomic Signatures of Nitrate Response in Rapeseed Genotypes With Distinct Root System Sizes

Nitrogen fertilization remains a cornerstone of modern agriculture, yet its excessive use contributes to environmental degradation. Rapeseed (Brassica napus L.) is notably inefficient in N uptake, highlighting the importance of root traits that enhance soil exploration and nutrient acquisition. This study investigated root transcriptomic responses to nitrate availability across rapeseed genetic diversity. A panel of 40 lines was screened on vertical agar plates, revealing substantial variation in root morphology, strong heritability, and genetic control. Low nitrate supply increased the root-to-shoot biomass ratio and stimulated lateral root proliferation. Transcriptomic profiling was then conducted on three genotype pairs selected to represent distinct root system sizes. Hydroponically grown plants were exposed to two divergent nitrate levels for 24 h, and root tissues were harvested for RNA sequencing. Differential expression analysis identified over a 1000 genes significantly induced or repressed by nitrate treatment, with only 10% shared across genotypes. Gene ontology enrichment analysis revealed a central nitrate-responsive transcriptional program, accompanied by distinct molecular signatures associated with root size. Co-expression network analysis identified regulatory modules that integrate nitrate transporters with auxin signaling and energy metabolism. These modules also uncovered roles for glucosinolate biosynthesis and aquaporin-mediated water transport. This study provides a set of candidate genes and regulatory networks that represent promising targets for breeding rapeseed varieties with optimized root traits for sustainable agriculture.