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.)

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. 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 revealed substantial Cd-responsive transcriptional reprogramming, with 3,784-4,167 differentially expressed genes (DEGs) detected across root control-versus-Cd comparisons and 2,216-3,532 DEGs detected across aboveground tissue comparisons. Overlap analysis showed 1,207 shared DEGs between root and aboveground DEG sets. GO classification and KEGG pathway annotation provided functional context for the Cd-responsive gene set, indicating the involvement of cellular regulation, metabolic responses, stress response, transport, detoxification, sulfur metabolism, glutathione-related metabolism, and protein degradation pathways. 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, a NAC-domain transcription factor, and two PLAC8-domain proteins annotated as Cd-resistance-related proteins. qRT-PCR analysis supported the expression patterns of the prioritized candidates. These results identify candidate genomic intervals and prioritized 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.