Multi-omics analysis to uncover constitutive priming and dynamic metabolic reprogramming conferring white rust resistance in Brassica juncea.

White rust, caused by Albugo candida, is one of the most devastating diseases of Indian mustard (Brassica juncea), causing yield losses of up to 90%. Durable resistance sources within cultivated Brassica germplasm remain limited. In this study, near-isogenic lines (NILs) of B. juncea cv. Varuna harbouring resistance from an East European source (Donskaja-IV, possessing a single CC-NB-LRR protein-coding R gene) was used to investigate the molecular basis of resistance through integrated transcriptomic and metabolomic analyses at 48 and 96 hours post-inoculation (hpi). Transcriptomic profiling revealed that the resistant Varuna_WRR line exhibited significantly higher unique transcript expression (18.76%) compared to the susceptible parent (8.41%) during the progression of infection. Principal component analysis showed clear separation between genotypes based on infection status, time, and genetic background. In the resistant line, upregulated genes were enriched in ethylene-activated signaling, protein phosphorylation, endoplasmic reticulum stress response, pectin biosynthesis, and hypersensitive response at 48 hpi, shifting toward programmed cell death, protein ubiquitination, abscisic acid metabolism, and starch biosynthesis at 96 hpi. Conversely, the susceptible line displayed broad downregulation of primary metabolic processes, indicating metabolic exhaustion. Metabolomic analysis demonstrated that the resistant genotype accumulated higher levels of defense-related amino acids (proline, glutamine, glutamic acid, serine, threonine, glycine), carbohydrates, organic acids, and polyamines, supporting enhanced nitrogen assimilation, energy reserves, membrane stability, and signaling. Together, these findings indicate that constitutive priming and dynamic activation of defense signaling, protein turnover, and osmoprotectant accumulation underpin the enhanced resistance in Varuna_WRR against Albugo candida. This integrated multi-omics approach provides valuable insights for breeding durable white rust resistance in Brassica juncea.