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 

机构地区：[1]Zhejiang Provincial Key Laboratory of Crop Genetic Resources,the Advance Seed Institute,Key Laboratory of Plant FactoryGeneration-adding Breeding,Ministry of Agriculture and Rural Affairs,College of Agriculture and Biotechnology,Zhejiang University,Hangzhou,Zhejiang,China [2]Damo Academy,Alibaba Group,Hangzhou,Zhejiang,China [3]Hainan Institute of Zhejiang University,Yazhou Bay Science and Technology City,Yazhou District,Sanya,Hainan,China [4]Hupan Lab,Hangzhou,Zhejiang,China [5]Biotechnology Research Institute,Chinese Academy of Agricultural Sciences,Beijing,China

出　　处：《Cell Research》2024年第12期859-872,共14页细胞研究（英文版）

基　　金：This work was financially supported in part by grants from the Biological Breeding-Major Projects(2023ZD04076);the National Natural Science Foundation of China(32341024);Fundamental Research Funds for the Central Universities(226-2022-00100;226-2024-00205);the Alibaba-Zhejiang University Joint Research Institute of Frontier Technologies.

摘　　要：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 of one encoding CBL-interacting protein kinase 10 in fiber length regulation was successfully validated through gene editing.Taken together,our findings prove that DNA methylation data can serve as an additional resource for breeding purposes and can offer opportunities to enhance and expedite the crop improvement process.

关 键 词：breeding alone COTTON 

分 类 号：Q37[生物学—遗传学]