Mapping and identifying candidate genes enabling lead (Pb) accumulation and tolerance in dark jute (Corchorus olitorius L.) using BSA-seq and RNA-seq

Dark jute ( Corchorus olitorius L.) can absorb lead (Pb) in the roots and translocate it to the shoots, making it a potential candidate for phytoremediation of Pb-contaminated soils. However, the genetic and molecular mechanisms regulating this process remain unclear. In this study, VA-50, a dwarf dark jute accession that accumulates Pb only in roots, and 18BS-81, a tall, late-flowering accession capable of transferring Pb to its shoots, were selected as parents. An F₂ population from their cross was used to map QTL intervals and identify candidate genes related to Pb accumulation and tolerance. Thirty extreme sensitive and resistant F₂ individuals were subjected to Bulk Segregant Analysis (BSA) under 400 μmol/L Pb stress, together with transcriptome analysis of the parents. BSA-seq identified 668,436 high-quality SNPs and overlapping SNP and InDel signals revealed six candidate regions on chromosome 5 spanning 0.46 Mb. Transcriptome data were also used to screen 142 genes within this region, from which six candidate genes were selected. COS05g_00848 and COS05g_00849 encode lipoxygenases (LOX), COS05g_00890 encodes a mitochondrial ADP/ATP carrier protein, COS05g_00801 encodes PTZ00169 protein, while COS05g_01275 and COS05g_01276 lack predicted protein families, suggesting novel functions. These genes are associated with lipid oxidation pathways linked to glycerolipid and glycerophospholipid metabolism, which support membrane stability and mitigate Pb toxicity in sensitive cellular components. This study integrates BSA-seq and RNA-seq to identify candidate genes regulating Pb accumulation and tolerance in dark jute, providing a foundation for genetic improvement of dark jute for phytoremediation applications. • Hydroponic screening of a dark jute F₂ population exposed to 400 μmol/L Pb stress. • BSA-seq mapped a major Pb response QTL on chromosome 5 within 0.46 Mb interval. • Integration of QTL mapping and RNA-seq narrowed down 142 genes to six key candidates. • Identified candidate genes include two lipoxygenases (LOXs), a mitochondrial ADP/ATP carrier, and PTZ00169. • qRT-PCR validation showed that COS05g_00801 (PTZ00169) and COS05g_00848 (LOX) are significantly upregulated under Pb stress.