Loss of cold tolerance is conferred by absence of the WRKY34 promoter fragment during tomato evolution

Mingyue Guo, Fengjun Yang, Lijuan Zhu, Leilei Wang, Zhichao Li, Zhenyu Qi, Vasileios Fotopoulos, Jingquan Yu and Jie Zhou ()
Additional contact information
Mingyue Guo: Zhejiang University
Fengjun Yang: Zhejiang University
Lijuan Zhu: Zhejiang University
Leilei Wang: Zhejiang University
Zhichao Li: Zhejiang University
Zhenyu Qi: Zhejiang University
Vasileios Fotopoulos: Biotechnology and Food Science
Jingquan Yu: Zhejiang University
Jie Zhou: Zhejiang University

Nature Communications, 2024, vol. 15, issue 1, 1-20

Abstract: Abstract Natural evolution has resulted in reduced cold tolerance in cultivated tomato (Solanum lycopersicum). Herein, we perform a combined analysis of ATAC-Seq and RNA-Seq in cold-sensitive cultivated tomato and cold-tolerant wild tomato (S. habrochaites). We identify that WRKY34 has the most significant association with differential chromatin accessibility and expression patterns under cold stress. We find that a 60 bp InDel in the WRKY34 promoter causes differences in its transcription and cold tolerance among 376 tomato accessions. This 60 bp fragment contains a GATA cis-regulatory element that binds to SWIBs and GATA29, which synergistically suppress WRKY34 expression under cold stress. Moreover, WRKY34 interferes with the CBF cold response pathway through regulating transcription and protein levels. Our findings emphasize the importance of polymorphisms in cis-regulatory regions and their effects on chromatin structure and gene expression during crop evolution.

Date: 2024
References: View references in EconPapers View complete reference list from CitEc
Citations:

Downloads: (external link)
https://www.nature.com/articles/s41467-024-51036-y 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:15:y:2024:i:1:d:10.1038_s41467-024-51036-y

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

DOI: 10.1038/s41467-024-51036-y

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 ().