Constraint of accessible chromatins maps regulatory loci involved in maize speciation and domestication

Yuting Liu, Xiang Gao, Hongjun Liu, Xuerong Yang, Xiao Liu, Fang Xu, Yuzhi Zhu, Qingyun Li, Liangliang Huang, Fang Yang, Jinsheng Lai and Junpeng Shi ()
Additional contact information
Yuting Liu: Sun Yat-sen University
Xiang Gao: Sun Yat-sen University
Hongjun Liu: Shandong Agricultural University
Xuerong Yang: Shandong Agricultural University
Xiao Liu: Shandong University
Fang Xu: Shandong University
Yuzhi Zhu: Sun Yat-sen University
Qingyun Li: Sun Yat-sen University
Liangliang Huang: China Agricultural University
Fang Yang: Sun Yat-sen University
Jinsheng Lai: China Agricultural University
Junpeng Shi: Sun Yat-sen University

Nature Communications, 2025, vol. 16, issue 1, 1-14

Abstract: 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.

Date: 2025
References: Add references at CitEc
Citations:

Downloads: (external link)
https://www.nature.com/articles/s41467-025-57932-1 Abstract (text/html)

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-57932-1

Ordering information: This journal article can be ordered from
https://www.nature.com/ncomms/

DOI: 10.1038/s41467-025-57932-1

Access Statistics for this article

Nature Communications is currently edited by Nathalie Le Bot, Enda Bergin and Fiona Gillespie

More articles in Nature Communications from Nature
Bibliographic data for series maintained by Sonal Shukla () and Springer Nature Abstracting and Indexing ().