Tissue-Specific Metabolic Reprogramming, Not Anthocyanins, Drives Chromium Tolerance in <i>Brassica rapa</i>

Chromium (Cr) contamination affects over 20 million hectares globally, threatening agricultural productivity and food safety. Current phytoremediation efforts face challenges due to a limited understanding of Cr-tolerance mechanisms and the unclear role of anthocyanins in metal detoxification. This study investigates Cr-tolerance responses in two <i>Brassica rapa</i> varieties: the tolerant <i>chinensis</i> (BRC) and the sensitive <i>purpuraria</i> (BRP), using an integrated multiomics framework. BRC showed 30% less biomass reduction than BRP under Cr stress. Genomic analysis identified gene clusters specific to BRC associated with metabolic flexibility. Transcriptomic and metabolomic profiling revealed regulatory networks driven by transcription factors that support tolerance. Mechanisms contributing to Cr-tolerance included improved root glutathione metabolism for Cr sequestration, suppressed glyoxylate pathways in the stem to reduce oxidative stress, and increased leaf cysteine and methionine metabolism to support antioxidant production. Notably, anthocyanin accumulation did not correlate with Cr-tolerance; BRP accumulated 15% more anthocyanins than BRC under stress. The findings indicate that Cr-tolerance in <i>B. rapa</i> relies on metabolic changes and transcriptional control of detoxification pathways, not anthocyanins. Identifying key targets in specific tissues, such as root glutathione synthase and leaf sulfur metabolism pathways, offers potential avenues for developing Cr-resistant crop varieties and enhancing agricultural sustainability in metal-contaminated soils.