生物
染色质
基因组
结构变异
驯化
遗传学
基因
基因组学
染色体
计算生物学
拷贝数变化
染色体构象捕获
嘉雅宠物
进化生物学
选择(遗传算法)
DNA测序
数量性状位点
比较基因组学
顺序装配
表型
候选基因
蛋白质组学
否定选择
基因组进化
模式生物
作者
Zhen Zhou,Danfeng Cai,Changbin Zhao,S. L. Zhang,Jiahao Li,Z. Y. Zhang,Shaofen Kong,Xin Yang,Xiaoli Zhou,Farhad Bordbar,Fayi Chen,Yaohuan Xu,Zhe Zhang,Lihong Gu,Zhenhui Li,Xiquan Zhang,Wen Luo,Jingting Shu,Bolin Cai,Qinghua Nie
标识
DOI:10.1002/advs.202520068
摘要
As the first sequenced non-mammalian amniote, the chicken (Gallus gallus) has served as a major source of cost-effective and protein-enriched foods since domestication. However, how structural variations (SVs) affect 3D genome reorganization to influence domestication and production traits remains unclear in chickens. Here, fifteen de novo chromosome-level genome assemblies are newly generated, along with high-throughput chromosome conformation capture (Hi-C), ATAC and RNA sequencing data. By integrating 13 published assemblies, the first pan-3D genome resource is constructed, spanning genes, SVs, and chromatin architectures, to investigate the dynamic characteristics of the 3D genome at different levels and the roles of SVs in the conservation and reorganization of chromatin architectures. Furthermore, candidate SVs and their linked genes are identified for domestication and production traits based on 1,735 resequencing accessions. Notably, the 240-bp and 81-bp SVs in the TSHR and DIO2 genes are considered the key targets in artificial selection for seasonal reproduction, and a 266-bp deletion upstream of the KLF3 gene affects carcass performance by rewriting the chromatin loop interaction network. Finally, SVs significantly improve the predictive accuracy in genomic selection models. Collectively, this study presents a comprehensive pan-3D resource to advance functional genomic research and breeding practice for the community.
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