Integrated transcriptome and metabolome analysis reveals the mechanisms underlying yield trends and alterations in seed oil composition of winter oilseed rape (Brassica napus L.) under paddy-upland rotation systems

Crop rotation systems exert a significant influence on soil physicochemical properties and crop growth. However, the mechanisms by which winter oilseed rape coordinates growth and environmental adaptation under paddy-upland rotation systems remain unclear. This study integrated analyses of agronomic traits, yield and quality, transcriptomics, and metabolomics to compare the effects of two consecutive years of either rice-oilseed rape (OsBn) or tobacco-oilseed rape (NtBn) rotations. Results demonstrated that under identical fertilization regimes, the OsBn system was associated with a numerical decreasing trend in yield (259 kg ha -1 , approximately 3.67%) and alterations in seed oil composition (e.g., a significant increase in C15:0 and decrease in C18:3n3) relative to NtBn system. These changes were correlated with diminished soil nitrogen availability and the efficiency of NH 4 + uptake. Integrated transcriptomic and metabolomic analyses revealed that the observed trends and alterations in OsBn were likely driven by a pervasive down-regulation of carbon allocation towards sugars and lipids, coupled with an up-regulation of secondary metabolism. This metabolic reprogramming was potentially mediated through the activation of the MAPK signaling cascade, suggesting its role as a central regulator coordinating resource allocation in response to the paddy-upland rotation stress. Consequently, nitrogen management, particularly the timing of topdressing requires particular attention in oilseed rape paddy-upland rotation systems to optimize sustainable practices. • Nitrogen loss in rice season reduces yield and oil content of subsequent rapeseed. • NH 4 + uptake underpins key N-use differences in paddy-upland vs. upland of rapeseed. • MAPK cascade mediates winter rapeseed adaptation to paddy-upland rotation. • MAPK cascade primarily regulates sugar and secondary metabolism in rapeseed.