Genetic Control of Root Morphology in Rapeseed Recombinant Inbred Lines Grown Under Contrasting Nitrogen Levels

Nitrogen fertilization is critically important for the growth of oleaginous rapeseed (Brassica napus L.). Optimizing root morphology for improved soil nitrogen uptake can reduce the fertilizer need, leading to more cost-effective and sustainable agricultural practices. This study investigated the genetic basis of root traits using two connected populations of recombinant inbred lines, grown hydroponically with 0.2 or 5 mM nitrate levels. Low nitrate increased the root-to-shoot biomass ratio and promoted primary root growth in both populations, while lateral root responses varied depending on the population. Significant genotype × nitrate interactions were observed, explaining a larger proportion of phenotypic variance than genotype alone. Heritability estimates ranged from moderate to high under both nitrate levels. QTL mapping was conducted using both population-specific and multi-parental models, applied separately under each nitrate level, as well as for nitrate response. A total of 36 QTLs were identified. Notably, five chromosomal regions were shared between populations, and one region remained stable across both nitrate levels and mapping strategies. These regions contained candidate genes like A03p54730 (CYTOKININ RESPONSE FACTOR 2), A03p54920 (NIN LIKE PROTEIN 7) and A06p12530 (LOB DOMAIN-CONTAINING PROTEIN 3), making them promising selection targets for optimizing root morphology in rapeseed crops.