ArticleGenome biology2021
Homology-mediated inter-chromosomal interactions in hexaploid wheat lead to specific subgenome territories following polyploidization and introgression.
Article in Genome biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 43 papers.
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43 citing papers in PubMed, 88 citations in OpenAlex.
- Integration of the D-Genome Reshapes Gene Transcription, Chromatin Architecture, and Metabolome of Allohexaploid Wheat, Leading to Enhanced Environmental Adaptability.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Evolutionary characteristics of the GAPDH gene family and functional characterization of TaGAPDH5 in wheat.BMC plant biology · 2026Article
- Dynamic reorganization of three-dimensional genome architecture during Populus diversification.Nature ecology & evolution · 2026Article
- A high-resolution 3D genome map of kiwifruit provides insights into chromatin architecture and transcriptional activity.Horticulture research · 2026Article
- Profiling the transcriptional regulatory network reveals putative shared regulatory elements within homoeologs in polyploid Brassica napus.Genome biology · 2026Article
- Deciphering Complex Interactions Between LTR Retrotransposons and Three Papaver Species Using LTR_Stream.Genomics, proteomics & bioinformatics · 2025Article
- Molecular dissection of Xinong 511 spike rachis response to Fusarium head blight infection.Stress biology · 2025Article
- Transposable elements drive the subgenomic divergence of homoeologous genes to shape wheat domestication and improvement.Plant communications · 2025Article
- TAC-C uncovers open chromatin interaction in crops and SPL-mediated photosynthesis regulation.Science advances · 2025Article
- Topologically associating domains and the evolution of three-dimensional genome architecture in rice.The Plant journal : for cell and molecular biology · 2025Article
- Genome-Wide Identification ofPlants (Basel, Switzerland) · 2025Article
- Chromatin Topological Domains Associate With the Rapid Formation of Tandem Duplicates in Plants.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Epigenomic and 3D genomic mapping reveals developmental dynamics and subgenomic asymmetry of transcriptional regulatory architecture in allotetraploid cotton.Nature communications · 2024Article
- Chromatin loops gather targets of upstream regulators together for efficient gene transcription regulation during vernalization in wheat.Genome biology · 2024Article
- Unveiling RNA structure-mediated regulations of RNA stability in wheat.Nature communications · 2024Article
- An improved transcriptome annotation reveals asymmetric expression and distinct regulation patterns in allotetraploid common carp.Communications biology · 2024Article
- Genetic Regulatory Perturbation of Gene Expression Impacted by Genomic Introgression in Fiber Development of Allotetraploid Cotton.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- Variation in TaSPL6-D confers salinity tolerance in bread wheat by activating TaHKT1;5-D while preserving yield-related traits.Nature genetics · 2024Article
- A platform for whole-genome speed introgression from Aegilops tauschii to wheat for breeding future crops.Nature protocols · 2024Review
- Author Correction: Homology-mediated inter-chromosomal interactions in hexaploid wheat lead to specific subgenome territories following polyploidization and introgression.Genome biology · 2024Article
Corrections and comments
- Erratum issued
Authors and funding
16 authors at 8 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundPolyploidization and introgression are major events driving plant genome evolution and influencing crop breeding. However, the mechanisms underlying the higher-order chromatin organization of subgenomes and alien chromosomes are largely unknown.
resultsWe probe the three-dimensional chromatin architecture of Aikang 58 (AK58), a widely cultivated allohexaploid wheat variety in China carrying the 1RS/1BL translocation chromosome. The regions involved in inter-chromosomal interactions, both within and between subgenomes, have highly similar sequences. Subgenome-specific territories tend to be connected by subgenome-dominant homologous transposable elements (TEs). The alien 1RS chromosomal arm, which was introgressed from rye and differs from its wheat counterpart, has relatively few inter-chromosome interactions with wheat chromosomes. An analysis of local chromatin structures reveals topologically associating domain (TAD)-like regions covering 52% of the AK58 genome, the boundaries of which are enriched with active genes, zinc-finger factor-binding motifs, CHH methylation, and 24-nt small RNAs. The chromatin loops are mostly localized around TAD boundaries, and the number of gene loops is positively associated with gene activity.
conclusionsThe present study reveals the impact of the genetic sequence context on the higher-order chromatin structure and subgenome stability in hexaploid wheat. Specifically, we characterized the sequence homology-mediated inter-chromosome interactions and the non-canonical role of subgenome-biased TEs. Our findings may have profound implications for future investigations of the interplay between genetic sequences and higher-order structures and their consequences on polyploid genome evolution and introgression-based breeding of crop plants.
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