Field site-specific proteome remodeling under contrasting environmental conditions in Brassica rapa

Abstract Background Plant plasticity enables adaptation to heterogeneous environments, yet the molecular mechanisms underlying long-term climatic acclimation in crops remain insufficiently understood. Here, we investigated the proteome plasticity of Brassica rapa across three contrasting field sites representing subarctic (68°N), temperate (59°N), and subtropical (44°N) climate-associated conditions. Twelve accessions spanning three crop types were cultivated, and subjected to proteome analysis and protein-metabolite correlation analysis. Results Principal component and clustering analyses revealed a strong imprint of the field sites on proteome patterns. Functional enrichment analysis identified site-specific protein networks: subarctic conditions favored enrichment of proteins involved in photosynthesis, carbohydrate metabolism, and glycolysis, supporting energy capture and cold acclimation; temperate conditions induced proteins related to respiration and redox homeostasis; and subtropical conditions induced proteins involved in clade-specific metabolism, particularly glucosinolate biosynthesis, alongside amino acid and redox pathways. Based on proteome data, key adaptive responses to the three field sites included modulation of cellular respiration proteins, such as NADH dehydrogenase subunits, and shifts in phytohormone regulation, with cytokinins enriched under subarctic, gibberellin-regulated proteins under temperate, and auxin-associated proteins under subtropical conditions. Chinese cabbage accession A247 demonstrated the highest proteome plasticity, whereas root turnip accessions showed lower plasticity. Reaction-norm analyses across the latitudinal climate gradient revealed genotype and crop type dependent trajectories in mean protein Z-scores, which shows contrasting adaptive strategies across cultivars. Conclusions B. rapa shows strong proteomic flexibility across different field sites, indicating distinct metabolic adjustments. These findings suggest that proteomic profiling aids in identifying adaptive traits and could guide crop breeding strategies to improve resilience under future climate change.