Integrative BSA-seq and time-course RNA-seq prioritize candidate loci and genes associated with whole-plant cadmium (Cd) accumulation and tolerance in dark jute (Corchorus olitorius L.)

Background: Dark jute ( Corchorus olitorius L.) is a high-biomass fiber crop with potential value for phytoremediation, but the genetic basis of whole-plant cadmium (Cd) accumulation and tolerance remains poorly understood. Identifying loci and candidate genes associated with Cd-related traits can support molecular improvement of dark jute for cultivation in Cd-affected environments. Results: In this study, we integrated bulked segregant analysis sequencing (BSA-seq) with time-course RNA sequencing (RNA-seq), Cd phenotyping, and qRT-PCR validation to investigate Cd accumulation and tolerance in dark jute. A Cd-tolerant, low-accumulating accession (CO57) and a Cd-sensitive, high-accumulating accession (CO83) were used to generate an F₂ population for extreme-phenotype bulking. Time-course RNA-seq of the tolerant parent identified 2,830 and 4,525 Cd-responsive differentially expressed genes in roots and aboveground tissues, respectively, with 1,207 shared genes. Functional enrichment showed that aboveground responses were mainly associated with plastid and photosynthesis-related processes, whereas root responses involved redox regulation, cell wall and cytoskeleton remodeling, and metal-stress-related functions. For BSA-seq, 50 extremely low-accumulating and 50 extremely high-accumulating F₂ individuals were pooled, yielding 625,354 high-quality SNPs. ΔSNP-index analysis detected five candidate intervals spanning 7.13 Mb and containing 662 annotated genes. By integrating positional evidence, Cd-responsive expression patterns, and functional annotations, seven candidate genes were prioritized, including genes encoding ABC transporter-like proteins, NAC-domain regulators, and two PLAC8-domain proteins annotated as Cd-resistance-related proteins. qRT-PCR analysis supported the RNA-seq expression patterns of the prioritized candidates. Conclusions: These results define candidate genomic intervals and Cd-responsive genes associated with whole-plant Cd accumulation and tolerance in dark jute. The study provides a genetic and transcriptomic framework for future functional validation, marker development, and phytoremediation-oriented improvement of dark jute.