Abiotic stress-responsive transcription factor derived-SSR markers reveal conserved regulatory genes and genetic structure in two cultivated jute species

BACKGROUND: Jute (Corchorus spp.) is an important natural bast-fibre crop, but its productivity is severely affected by abiotic stresses such as drought, salinity, and waterlogging. Improvement of stress resilience in jute requires functional molecular markers directly linked to regulatory genes governing stress responses. The present study aimed to develop such resources through an integrated transcriptome-driven approach in the two cultivated species, Corchorus capsularis and C. olitorius. RESULTS: Analysis of publicly available RNA sequencing datasets identified 1889-6376 and 808-6259 stress-responsive differentially expressed genes under various abiotic stress conditions in C. capsularis and C. olitorius, respectively. From these datasets, 370 differentially expressed transcription factor genes harboring microsatellite motifs were identified in C. capsularis, while 348 such genes were identified in C. olitorius. A total of 728 and 702 simple sequence repeat markers were developed from these transcription factor genes in C. capsularis and C. olitorius, respectively. The majority of markers (77% in C. capsularis and 74% in C. olitorius) were located in regulatory untranslated regions, predominantly enriched with A/T-rich di- and tri-nucleotide motifs. Major stress-responsive transcription factor families, including MYB, basic helix-loop-helix, NAC, WRKY, AP2/ethylene-responsive factor, and homeobox, were highly represented. Synteny analysis revealed 173 conserved syntenic transcription factor-simple sequence repeats gene pairs within collinear chromosomal regions, indicating strong evolutionary conservation of regulatory frameworks between the two species. Population structure analysis revealed three genetic clusters (K = 3) broadly corresponding to species identity, with some admixture in C. olitorius, which may reflect shared ancestry or limited marker resolution rather than definitive gene flow. Pairwise genetic distance values ranged from 0.091(CIN-540 and CEX-39) to 0.773 (CIN-534 and OIN-578), reflecting substantial intraspecific diversity. CONCLUSIONS: This study provides a comprehensive set of transcription factor-derived simple sequence repeat markers tightly associated with stress-responsive regulatory genes in jute. They offer potential advantages over anonymous genomic markers and represent valuable genomic resources for marker-assisted breeding, genomic selection, and the development of climate-resilient jute cultivars.