Xianhui Huang#, Yabin Peng#, Xiubao Hu#, Yuejin Wang#, Zeyu Zhang#, Xianzhe Huang, Xuanxuan Luo, Sainan Zhang, Zengyuan Zhao, Erin Farmer, Sheng-Kai Hsu, Corrinne E. Grover, Zhengyang Qi, Lu Li, Jinglei Yang, Yinfang He, Zhiwei Chen, Yuanhang Zhang, Ye Mei, Pengcheng Deng, Yang Meng, Yufei Wang, Mengyuan Ji, Junyuan Lv, Liuling Pei, Fang Liu, Xinhui Nie, Lili Tu, Keith Lindsey, Adnane Boualem, Abdelhafid Bendahmane, Jonathan F. Wendel, Michael A. Gore, Xianlong Zhang*, Maojun Wang*

Cell, September 16, 2026

Highlights

Summary

Three-dimensional (3D) genome folding shapes gene regulation, yet the genetic underpinnings linking 3D genome evolution to phenotypic innovation during domestication remain elusive. Using population-scale Hi-C profiling of 34 semi-wild and 267 cultivated allotetraploid cottons, we generated a pan-3D genome atlas capturing extensive diversity in topologically associating domains (TADs) and chromatin loops. Chromatin interactome-wide association studies identified 105 TAD reconfigurations and 58 loop rewirings that were established as the 3D chromatin basis of fiber quality, boosting heritability estimates for fiber strength by 16% and fiber length by 20%. We reveal that domestication selection within sequence-defined sweeps fixed 57% of 3D conformation signatures, thereby decoupling sequence-level from chromatin-level selection and shifting the subgenome expression balance of 39 homoeologs in cultivated cotton. Sequence-based modeling and mutational analyses identified the C2H2 zinc-finger protein YY1 as a conserved mediator of 3D genome organization. This study provides a resource for redefining precision-breeding paradigms by harnessing cryptic 3D chromatin targets.

Graphical abstract

Keywords

3D genome; cotton fiber; domestication; polyploidy

论文链接：https://www.cell.com/cell/fulltext/S0092-8674(26)01011-1