3D chromatin remodeling during domestication defines novel targets for crop improvement
Abstract
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.
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BibTeX
@article{huang2026chromatin,
title = {{3D chromatin remodeling during domestication defines novel targets for crop improvement}},
author = {Xianhui Huang and Yabin Peng and Xiubao Hu and Yuejin Wang and Zeyu Zhang and Xianzhe Huang and Xuanxuan Luo and Sainan Zhang and Zengyuan Zhao and Erin Farmer and Sheng-Kai Hsu and Corrinne Grover and Zhengyang Qi and Lu Li and Jinglei Yang and Yinfang He and Zhiwei Chen and Yuanhang Zhang and Ye Mei and Pengcheng Deng and Yang Meng and Yufei Wang and Mengyuan Ji and Junyuan Lv and Liuling Pei and Fang Liu and Xinhui Nie and Lili Tu and Keith Lindsey and Adnane Boualem and Abdelhafid Bendahmane and Jonathan Wendel and Michael Gore and Xianlong Zhang and Maojun Wang},
journal = {Cell},
year = {2026},
month = oct,
doi = {10.1016/j.cell.2026.08.038},
url = {https://hal.science/hal-05780798v1},
note = {CC BY-NC-ND},
}
RIS
TY - JOUR
TI - 3D chromatin remodeling during domestication defines novel targets for crop improvement
AU - Xianhui Huang
AU - Yabin Peng
AU - Xiubao Hu
AU - Yuejin Wang
AU - Zeyu Zhang
AU - Xianzhe Huang
AU - Xuanxuan Luo
AU - Sainan Zhang
AU - Zengyuan Zhao
AU - Erin Farmer
AU - Sheng-Kai Hsu
AU - Corrinne Grover
AU - Zhengyang Qi
AU - Lu Li
AU - Jinglei Yang
AU - Yinfang He
AU - Zhiwei Chen
AU - Yuanhang Zhang
AU - Ye Mei
AU - Pengcheng Deng
AU - Yang Meng
AU - Yufei Wang
AU - Mengyuan Ji
AU - Junyuan Lv
AU - Liuling Pei
AU - Fang Liu
AU - Xinhui Nie
AU - Lili Tu
AU - Keith Lindsey
AU - Adnane Boualem
AU - Abdelhafid Bendahmane
AU - Jonathan Wendel
AU - Michael Gore
AU - Xianlong Zhang
AU - Maojun Wang
PY - 2026
DA - 2026/10/06
JO - Cell
DO - 10.1016/j.cell.2026.08.038
UR - https://hal.science/hal-05780798v1
AB - 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.
SN - 0092-8674
SN - 1097-4172
ER -