ArticleThe Plant cell2021
Altered chromatin architecture and gene expression during polyploidization and domestication of soybean.
Article in The Plant cell, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 76 papers.
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76 citing papers in PubMed, 127 citations in OpenAlex.
- Coolsecture: an easy-to-use and improved framework for cross-species Hi-C contact map comparison.Bioinformatics (Oxford, England) · 2026Article
- Structural Variation and Its Roles in Plant Genomes.Plants (Basel, Switzerland) · 2026Review
- Integrated Comparative Genomics and Population Genomics Reveal the Genomic and Epigenomic Basis of Barley (Plants (Basel, Switzerland) · 2026Article
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- 3D Chromatin Architecture Provides Insights Into Leaf Trait Variation Among Pear Species.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Haplotype-Resolved 3D Genomic Landscapes and Their Impacts on Agronomic Traits in Grapevine.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- A fourth subgenome of the Camelina genus reveals gene dominance is influenced by chromosomal proximity.Nature communications · 2026Article
- Post-polyploid chromosomal diploidization in plants is affected by clade divergence and constrained by shared genomic features.Nature communications · 2026Article
- Power-law penalties correct distance bias in single-cell co-accessibility and deep-learning chromatin interaction predictions.NAR genomics and bioinformatics · 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
- Circadian oscillations in chromatin accessibility systematically orchestrate rhythmic gene transcription in soybean.The Plant cell · 2026Article
- The GATA8-GRF5-XTH9 feed-forward loop regulates cell size in poplar.Horticulture research · 2026Article
- Autopolyploidization-Induced Chromatin Remodeling Regulates Leaf Size Variation in Brassica rapa.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Spilling the beans on duplicated genes: unraveling the mechanisms underlying transcriptional divergence in soybean.The Plant cell · 2026Article
- From duplication to divergence: Single-cell insights into transcriptional and cis-regulatory landscapes in soybean.The Plant cell · 2025Article
- Epigenomics and Non-Coding RNAs in Soybean Adaptation to Abiotic Stresses.International journal of molecular sciences · 2025Review
- Domestication shaped the chromatin landscape of grain amaranth.Nature communications · 2025Article
- UV-B Responsive Flavonoid Synthesis Contributes to Tartary Buckwheat High-Altitude Adaption.Plant biotechnology journal · 2025Article
- Dynamic 3D chromatin organization and epigenetic regulation of gene expression in peanut nodules.Journal of integrative plant biology · 2025Article
16 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Polyploidy or whole-genome duplication (WGD) is widespread in plants and is a key driver of evolution and speciation, accompanied by rapid and dynamic changes in genomic structure and gene expression. The 3D structure of the genome is intricately linked to gene expression, but its role in transcription regulation following polyploidy and domestication remains unclear. Here, we generated high-resolution (∼2 kb) Hi-C maps for cultivated soybean (Glycine max), wild soybean (Glycine soja), and common bean (Phaseolus vulgaris). We found polyploidization in soybean may induce architecture changes of topologically associating domains and subsequent diploidization led to chromatin topology alteration around chromosome-rearrangement sites. Compared with single-copy and small-scale duplicated genes, WGD genes displayed more long-range chromosomal interactions and were coupled with higher levels of gene expression and chromatin accessibilities but void of DNA methylation. Interestingly, chromatin loop reorganization was involved in expression divergence of the genes during soybean domestication. Genes with chromatin loops were under stronger artificial selection than genes without loops. These findings provide insights into the roles of dynamic chromatin structures on gene expression during polyploidization, diploidization, and domestication of soybean.
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