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Wheat lines carrying the 1B/1R translocation have been widely utilized in breeding due to their enhanced disease resistance and yield stability. However, its impact on the three-dimensional (3D) chromatin architecture and transcriptional regulation of non-translocated subgenomes remains largely unexplored. Here, we used a 1B/1R translocation line, Wanmai 270, and its corresponding near-isogenic line lacking the 1B/1R segment to investigate chromatin spatial remodeling in the wheat A subgenome and its relationship with gene expression. By integrating Hi-C, RNA-seq, and qRT-PCR, we systematically characterized the effects of the 1B/1R translocation on 3D genome organization. A substantial number of A/B compartment switching regions were identified in the A subgenome, with a predominance of B-to-A transitions. Notably, compartment reorganization exhibited pronounced heterogeneity across chromosomes. To assess the association between compartment switching and transcriptional changes, 20 differentially expressed genes located within translocation regions were selected for qRT-PCR. Genes in A-to-B regions showed reduced expression in Wanmai 270 relative to those in the near-isogenic line, whereas genes in B-to-A regions exhibited increased expression, consistent with the direction of compartment transitions. Subcompartment analysis revealed a genome-wide decrease in A1/A2 proportions and an increase in B1/B2 proportions in the A subgenome of Wanmai 270, with the most prominent reorganization observed on chromosomes 1A and 3A. Topologically associating domains (TAD) analysis showed that the overall TAD framework was largely conserved between the two lines, although local TAD merging and boundary reorganization occurred in specific regions of Wanmai 270. Integration with transcriptome data further indicated that compartment-translocation regions were enriched for differentially expressed genes involved in chromatin organization, DNA replication, carbohydrate metabolism, and amino acid metabolism. GO, KEGG, and GSEA analyses revealed that transcriptional differences in Wanmai 270 were not characterized by global activation of basal metabolic pathways, but rather by fine-tuned regulation within specific pathways. In summary, the 1B/1R translocation preserves the overall 3D chromatin framework of the A subgenome while inducing multiscale spatial remodeling at the levels of compartments, subcompartments, and local TADs, thereby modulating transcriptional responses through changes in the chromatin regulatory landscape.
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| 科 Family | 属数 Number of genus | 种数 Number of species | 占总种数比例 Percentage of total species (%) | 属 Genus | 种数 Number of species | 占总种数比例 Percentage of total species (%) |
|---|---|---|---|---|---|---|
| 鹅膏菌科Amanitaceae | 2 | 11 | 5.26 | 鹅膏菌属 Amanita | 10 | 4.78 |
| 小菇科 Mycenaceae | 2 | 12 | 5.74 | 丝盖伞属 Inocybe | 5 | 2.39 |
| 多孔菌科 Polyporaceae | 8 | 14 | 6.70 | 蜡蘑属 Laccaria | 5 | 2.39 |
| 红菇科 Russulaceae | 3 | 23 | 11.00 | 小皮伞属 Marasmius | 6 | 2.87 |
| 小菇属 Mycena | 11 | 5.26 | ||||
| 光柄菇属 Pluteus | 5 | 2.39 | ||||
| 红菇属 Russula | 17 | 8.13 | ||||
| 栓菌属 Trametes | 5 | 2.39 |
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