Population-wide DNA methylation polymorphisms at single-nucleotide resolution in 207 cotton accessions reveal epigenomic contributions to complex traits

作者：Ting Zhao, Xueying Guan, Yan Hu, Ziqian Zhang, Han Yang, Xiaowen Shi, Jin Han, Huan Mei, Luyao Wang, Lei Shao, Hongyu Wu, Qianqian Chen, Yongyan Zhao, Jiaying Pan, Yupeng Hao, Zeyu Dong, Xuan Long, Qian Deng, Shengjun Zhao, Mengke Zhang, Yumeng Zhu, Xiaowei Ma, Zequan Chen, Yayuan Deng, Zhanfeng Si, Xin Li, Tianzhen Zhang, Fei Gu, Xiaofeng Gu, Lei Fang · 发表于：Cell Research · 年份：2024 · DOI：10.1038/s41422-024-01027-x · 被引用次数：36 · 研究领域：Research in Cotton Cultivation、Plant Molecular Biology Research、Cocoa and Sweet Potato Agronomy

DNA methylation plays multiple regulatory roles in crop development. However, the relationships of methylation polymorphisms with genetic polymorphisms, gene expression, and phenotypic variation in natural crop populations remain largely unknown. Here, we surveyed high-quality methylomes, transcriptomes, and genomes obtained from the 20-days-post-anthesis (DPA) cotton fibers of 207 accessions and extended the classical framework of population genetics to epigenetics. Over 287 million single methylation polymorphisms (SMPs) were identified, 100 times more than the number of single nucleotide polymorphisms (SNPs). These SMPs were significantly enriched in intragenic regions while depleted in transposable elements. Association analysis further identified a total of 5,426,782 cis-methylation quantitative trait loci (cis-meQTLs), 5078 cis-expression quantitative trait methylation (cis-eQTMs), and 9157 expression quantitative trait loci (eQTLs). Notably, 36.39% of cis-eQTM genes were not associated with genetic variation, indicating that a large number of SMPs associated with gene expression variation are independent of SNPs. In addition, out of the 1715 epigenetic loci associated with yield and fiber quality traits, only 36 (2.10%) were shared with genome-wide association study (GWAS) loci. The construction of multi-omics regulatory networks revealed 43 cis-eQTM genes potentially involved in fiber development, which cannot be identified by GWAS alone. Among these genes, the role o...