Genetic diversity, population structure, and candidate regions of differentiation in Corchorus capsularis L. germplasm collection

Background The discovery and effective use of important traits in white jute ( Corchorus capsularis L.) depend on a clear understanding of how genetic diversity is structured and shaped within germplasm collections. This study assessed genetic diversity, population structure, linkage disequilibrium (LD), and candidate regions of genetic differentiation in a World Vegetable Center germplasm collection using DArTseq-derived SNP markers. Results Following stringent marker- and accession-level quality control, 6,829 chromosome-anchored SNPs across 94 accessions were retained, with an overall genotype call rate of 96.65%. Principal component and ancestry analyses identified two highly divergent accessions, VI048152 and VI050629. After their exclusion, 2,026 SNPs remained polymorphic among 92 accessions, and independent clustering resolved two genetic groups, G 1 ( n = 31) and G 2 ( n = 61), which were clearly differentiated by discriminant analysis of principal components. Overall expected heterozygosity was low ( H e = 0.0215). AMOVA attributed 18.44% of molecular variation to differences between groups and 81.56% to within-group variation (Φ = 0.1844, p < 0.001), while pairwise F ST was 0.1421. LD was highly variable and lacked a consistent distance-dependent decay pattern, precluding robust estimation of genome-wide LD half-decay. Among 180 eligible 100-kb windows, two exceeded the empirical 99th-percentile F ST threshold: Chr6 at 35.4–35.5 Mb ( F ST = 0.907) and Chr2 at 44.1–44.2 Mb ( F ST = 0.301). Neither exceeded the empirical nucleotide-diversity-ratio thresholds and were therefore interpreted as regions of elevated differentiation rather than confirmed selective sweeps. The regions contained 28 annotated genes and seven candidate SNPs (five intronic and two coding), directly intersecting five priority positional genes encoding pTAC5-like, GBA2-type β-glucosidase, UPL5-like E3 ubiquitin-protein ligase, NTF2-like, and SWIB/BAF60 domain-containing proteins. Conclusions These findings reveal a relatively narrow genetic base but substantial differentiation among accessions and genetic groups. The highly divergent accessions represent genetically distinctive germplasm that can be prioritized for further evaluation, while the two differentiated genomic regions and five priority positional genes provide testable targets for subsequent genomic and functional investigation. Denser genomic data, phenotypic evaluation and functional validation will be required to establish their evolutionary and breeding significance.