Homology-mediated inter-chromosomal interactions in hexaploid wheat lead to specific subgenome territories following polyploidization and introgression

文献类型： 外文期刊

第一作者： Jia, Jizeng

作者： Jia, Jizeng;Li, Guangwei;Cui, Dangqun;Wang, Daowen;Jia, Jizeng;Kong, Chuizheng;Gao, Lifeng;Zhao, Guangyao;Xie, Yilin;Cheng, Jingfei;Wang, Meiyue;Zhao, Fei;Guo, Jingyu;Zhang, Yijing;Xie, Yilin;Cheng, Jingfei;Wang, Meiyue;Zhao, Fei;Zhang, Yijing;Guo, Jingyu;Hu, Tiezhu;Ru, Zhengang;Wang, Kai

作者机构：

关键词： Wheat; Polyploidization; Introgression; 1RS/1BL translocation; 3D genome; Hi-C; Homology-mediated chromatin interaction; Subgenome-biased TE

期刊名称：GENOME BIOLOGY （ 影响因子：13.583； 五年影响因子：17.433 ）

ISSN： 1474-760X

年卷期： 2021 年 22 卷 1 期

页码：

收录情况： SCI

摘要： Background: Polyploidization and introgression are major events driving plant genome evolution and influencing crop breeding. However, the mechanisms underlying the higher-order chromatin organization of subgenomes and alien chromosomes are largely unknown. Results: We probe the three-dimensional chromatin architecture of Aikang 58 (AK58), a widely cultivated allohexaploid wheat variety in China carrying the 1RS/1BL translocation chromosome. The regions involved in inter-chromosomal interactions, both within and between subgenomes, have highly similar sequences. Subgenome-specific territories tend to be connected by subgenome-dominant homologous transposable elements (TEs). The alien 1RS chromosomal arm, which was introgressed from rye and differs from its wheat counterpart, has relatively few inter-chromosome interactions with wheat chromosomes. An analysis of local chromatin structures reveals topologically associating domain (TAD)-like regions covering 52% of the AK58 genome, the boundaries of which are enriched with active genes, zinc-finger factor-binding motifs, CHH methylation, and 24-nt small RNAs. The chromatin loops are mostly localized around TAD boundaries, and the number of gene loops is positively associated with gene activity. Conclusions: The present study reveals the impact of the genetic sequence context on the higher-order chromatin structure and subgenome stability in hexaploid wheat. Specifically, we characterized the sequence homology-mediated inter-chromosome interactions and the non-canonical role of subgenome-biased TEs. Our findings may have profound implications for future investigations of the interplay between genetic sequences and higher-order structures and their consequences on polyploid genome evolution and introgression-based breeding of crop plants.

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