Constraint of accessible chromatins maps regulatory loci involved in maize speciation and domestication
Abstract Comparative genomic studies can identify genes under evolutionary constraint or specialized for trait innovation. Growing evidence suggests that evolutionary constraint also acts on non-coding regulatory sequences, exerting significant impacts on fitness-related traits, although it has yet...
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Nature Portfolio
2025-03-01
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| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-025-57932-1 |
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| author | Yuting Liu Xiang Gao Hongjun Liu Xuerong Yang Xiao Liu Fang Xu Yuzhi Zhu Qingyun Li Liangliang Huang Fang Yang Jinsheng Lai Junpeng Shi |
| author_facet | Yuting Liu Xiang Gao Hongjun Liu Xuerong Yang Xiao Liu Fang Xu Yuzhi Zhu Qingyun Li Liangliang Huang Fang Yang Jinsheng Lai Junpeng Shi |
| author_sort | Yuting Liu |
| collection | DOAJ |
| description | Abstract Comparative genomic studies can identify genes under evolutionary constraint or specialized for trait innovation. Growing evidence suggests that evolutionary constraint also acts on non-coding regulatory sequences, exerting significant impacts on fitness-related traits, although it has yet to be thoroughly explored in plants. Using the assay for transposase-accessible chromatin by sequencing (ATAC-seq), we profile over 80,000 maize accessible chromatin regions (ACRs), revealing that ACRs evolve faster than coding genes, with about one-third being maize-specific and regulating genes associated with speciation. We highlight the role of transposable elements (TEs) in driving intraspecific innovation of ACRs and identify hundreds of candidate ACRs potentially involved in transcriptional rewiring during maize domestication. Additionally, we demonstrate the importance of accessible chromatin in maintaining subgenome dominance and controlling complex trait variations. This study establishes a framework for analyzing the evolutionary trajectory of plant regulatory sequences and offers candidate loci for downstream exploration and application in maize breeding. |
| format | Article |
| id | doaj-art-c36feaf0d1694663bb0bb99c38d3362a |
| institution | DOAJ |
| issn | 2041-1723 |
| language | English |
| publishDate | 2025-03-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj-art-c36feaf0d1694663bb0bb99c38d3362a2025-08-20T03:01:41ZengNature PortfolioNature Communications2041-17232025-03-0116111410.1038/s41467-025-57932-1Constraint of accessible chromatins maps regulatory loci involved in maize speciation and domesticationYuting Liu0Xiang Gao1Hongjun Liu2Xuerong Yang3Xiao Liu4Fang Xu5Yuzhi Zhu6Qingyun Li7Liangliang Huang8Fang Yang9Jinsheng Lai10Junpeng Shi11State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology, School of Agriculture and Biotechnology, The Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen UniversityState Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology, School of Agriculture and Biotechnology, The Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen UniversityState Key Laboratory of Wheat Improvement, College of Life Science, Shandong Agricultural UniversityState Key Laboratory of Wheat Improvement, College of Life Science, Shandong Agricultural UniversityThe Key Laboratory of Plant Development and Environmental Adaption Biology, Ministry of Education, School of Life Sciences, Shandong UniversityThe Key Laboratory of Plant Development and Environmental Adaption Biology, Ministry of Education, School of Life Sciences, Shandong UniversityState Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology, School of Agriculture and Biotechnology, The Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen UniversityState Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology, School of Agriculture and Biotechnology, The Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen UniversityCollege of Biotechnology and Agronomy, China Agricultural UniversityState Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology, School of Agriculture and Biotechnology, The Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen UniversityCollege of Biotechnology and Agronomy, China Agricultural UniversityState Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology, School of Agriculture and Biotechnology, The Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen UniversityAbstract Comparative genomic studies can identify genes under evolutionary constraint or specialized for trait innovation. Growing evidence suggests that evolutionary constraint also acts on non-coding regulatory sequences, exerting significant impacts on fitness-related traits, although it has yet to be thoroughly explored in plants. Using the assay for transposase-accessible chromatin by sequencing (ATAC-seq), we profile over 80,000 maize accessible chromatin regions (ACRs), revealing that ACRs evolve faster than coding genes, with about one-third being maize-specific and regulating genes associated with speciation. We highlight the role of transposable elements (TEs) in driving intraspecific innovation of ACRs and identify hundreds of candidate ACRs potentially involved in transcriptional rewiring during maize domestication. Additionally, we demonstrate the importance of accessible chromatin in maintaining subgenome dominance and controlling complex trait variations. This study establishes a framework for analyzing the evolutionary trajectory of plant regulatory sequences and offers candidate loci for downstream exploration and application in maize breeding.https://doi.org/10.1038/s41467-025-57932-1 |
| spellingShingle | Yuting Liu Xiang Gao Hongjun Liu Xuerong Yang Xiao Liu Fang Xu Yuzhi Zhu Qingyun Li Liangliang Huang Fang Yang Jinsheng Lai Junpeng Shi Constraint of accessible chromatins maps regulatory loci involved in maize speciation and domestication Nature Communications |
| title | Constraint of accessible chromatins maps regulatory loci involved in maize speciation and domestication |
| title_full | Constraint of accessible chromatins maps regulatory loci involved in maize speciation and domestication |
| title_fullStr | Constraint of accessible chromatins maps regulatory loci involved in maize speciation and domestication |
| title_full_unstemmed | Constraint of accessible chromatins maps regulatory loci involved in maize speciation and domestication |
| title_short | Constraint of accessible chromatins maps regulatory loci involved in maize speciation and domestication |
| title_sort | constraint of accessible chromatins maps regulatory loci involved in maize speciation and domestication |
| url | https://doi.org/10.1038/s41467-025-57932-1 |
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