驯化过程中的三维染色质重塑定义了作物改良的新目标，这一成果由华中农业大学王茂军研究小组经过不懈努力而取得。相关论文于近日发表在《细胞》杂志上。

三维（3D）基因组折叠塑造基因调控，然而将3D基因组演化与驯化过程中表型创新联系起来的遗传基础仍不清楚。研究人员利用对34份半野生和267份栽培异源四倍体棉花的群体规模Hi-C分析，构建了一个泛3D基因组图谱，捕获了拓扑关联结构域（TAD）和染色质环的广泛多样性。染色质相互作用组全关联研究鉴定出105个TAD重构和58个环重连，这些被确立为纤维品质的3D染色质基础，将纤维强度的遗传力估计提高了16%，纤维长度提高了20%。研究人员揭示，序列定义的选择性清除内的驯化选择固定了57%的3D构象特征，从而将序列水平选择与染色质水平选择解耦，并改变了栽培棉中39个同源基因的亚基因组表达平衡。基于序列的建模和突变分析鉴定出C2H2锌指蛋白YY1是3D基因组组织的保守介导因子。这项研究提供了一个资源，通过利用隐藏的3D染色质靶点来重新定义精准育种范式。

附：英文原文

Title: 3D chromatin remodeling during domestication defines novel targets for crop improvement

Author: 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

Issue&Volume:

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.

DOI: 10.1016/j.cell.2026.08.038

Source: https://www.cell.com/cell/abstract/S0092-8674(26)01011-1