Integrative multi-omics identifies BnaBAHD3 as a regulator of arsenic and cadmium tolerance linked to phenylpropanoid metabolism in Brassica napus

Brassica napus L. is a major allotetraploid oilseed crop in China with potential for the phytoremediation of arsenic (As)- and cadmium (Cd)-contaminated agricultural soils. However, the genetic determinants underlying As and Cd tolerance in B. napus remain incompletely understood, limiting the development of heavy-metal-tolerant germplasm for the sustainable use of contaminated farmland. Here, we integrated genome-wide association analysis, transcriptomics and metabolomics in a panel of 140 B. napus accessions exposed to As and Cd stress. Genome-wide association study (GWAS) identified 27 significant single-nucleotide polymorphisms shared between the As and Cd stress analyses across seven chromosomes, including a major locus on chromosome C01 within which BnaBAHD3 , encoding a BAHD acyltransferase, was prioritized as the leading candidate. Transcriptome and metabolome analyses further linked BnaBAHD3 to phenylpropanoid-related responses under heavy metal stress. Heterologous functional assays in Arabidopsis thaliana supported a positive role for BnaBAHD3 in As/Cd tolerance: at 16 days post-treatment, root length in 35S:: BnaBAHD3 lines was 1.2–1.5-fold that of wild type (WT), whereas the Atbahd mutant showed 90% and 50% reductions in root length relative to WT under As and Cd stress, respectively. In contrasting B. napus accessions, higher BnaBAHD3 transcript abundance was associated with greater stress tolerance. Together, these results support a model in which BnaBAHD3 -associated tolerance is accompanied by phenylpropanoid-related transcriptional and metabolic changes that may contribute to cell-wall reinforcement and antioxidant protection. These findings identify BnaBAHD3 as a promising target for improving heavy-metal tolerance in rapeseed.