
Structural variants impact 3D genome architecture. [Photo/news.hzau.edu.cn]
Three-dimensional chromatin architecture plays a vital role in plant evolution, yet its population-level dynamics during crop domestication remain poorly understood. By generating a high-resolution pan-3D genome atlas of 34 semi-wild and 267 cultivated allotetraploid cottons, researchers from Wang Maojun's team at Huazhong Agricultural University uncovered extensive topological variations that shape agronomic traits.
Integrative analyses revealed that structural variations and epigenetic dynamics drive significant chromatin reorganization, influencing gene expression and subgenome-biased regulation. Chromatin interactome-wide association studies successfully connected 3D structural reconfigurations with enhanced fiber quality, substantially outperforming traditional association models in explaining phenotypic variance.
Furthermore, sequence-based modeling and mutational profiling identified the C2H2 zinc-finger protein YY1 as a conserved architectural regulator stabilizing topologically associating domains across plants. These findings highlight 3D genome topology as a critical regulatory layer and provide novel targets for precision crop breeding.