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.).
7 affiliations
- 1Key Laboratory of Genetics, Breeding and Multiple Utilization of Bast Fiber Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, 350002, China. [email protected].
- 2Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China. [email protected].
- 3Key Laboratory of Biological Breeding for Fujian and Taiwan Crops, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou, 350002, China. [email protected].
- 4Key Laboratory of Genetics, Breeding and Multiple Utilization of Bast Fiber Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
- 5Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.
- 6Key Laboratory of Biological Breeding for Fujian and Taiwan Crops, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
- 7Experiment Station of Ministry of Agriculture and Rural Affairs for Jute and Kenaf in Southeast China, Fujian Public Platform for Germplasm Resources of Bast Fiber Crops, Fujian International Science and Technology Cooperation Base for Genetics, Breeding and Multiple Utilization Development of Southern Economic Crops, Fujian Agriculture and Forestry University, Fuzhou, China.
Abstract
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 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.Conclusions
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.
Related
- Integrative Genomic Analyses Identify and Prioritize Candidate Loci for Metatarsal Length and Circumference in Broilers.
- Integrative GWAS and Transcriptome Analysis Reveal Genetic Architecture and Candidate Genes for Drought Tolerance During Soybean Germination
- Genome-wide association analysis identifies candidate loci associated with hydroxycinnamic acid accumulation in sweetpotato
- Genome-Wide Association Mapping of Low-Nitrogen Tolerance in Hexaploid Oat Identifies a Suggestive Candidate Locus near P5CDH Associated with Root Dry Weight.
- Integrative transcriptomics and reverse network pharmacology prioritize DPP4 and Achyranthes bidentata in Barrett’s esophagus
BibTeX
@article{jiantang2026integrative,
title = {{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.).}},
author = {Xu Jian-Tang and Zhu Shixin and Victoria Oluwapelumi Akintayo and Zhao Yaqi and Li Lijun and Li Han and Zhang Wei-Qun and Tao Aifen and Fang Pingping and Qi Jianmin and Zhang Shu-Biao},
journal = {BMC plant biology},
year = {2026},
month = jul,
doi = {10.1186/s12870-026-09553-z},
url = {https://europepmc.org/article/MED/42894123},
note = {CC BY-NC-ND},
}
RIS
TY - JOUR
TI - 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.).
AU - Xu Jian-Tang
AU - Zhu Shixin
AU - Victoria Oluwapelumi Akintayo
AU - Zhao Yaqi
AU - Li Lijun
AU - Li Han
AU - Zhang Wei-Qun
AU - Tao Aifen
AU - Fang Pingping
AU - Qi Jianmin
AU - Zhang Shu-Biao
PY - 2026
DA - 2026/07/01
JO - BMC plant biology
DO - 10.1186/s12870-026-09553-z
UR - https://europepmc.org/article/MED/42894123
AB - 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 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.Conclusions 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.
SN - 1471-2229
ER -