Department of Horticulture, Zhejiang Provincial Key Laboratory of Horticultural Crop Quality Regulation, Zhejiang University, Yuhangtang Road 866, Hangzhou, 310058, China.
Hainan Institute, Zhejiang University, Sanya, 572000, China.
Nat Commun. 2024 Aug 6;15(1):6667. doi: 10.1038/s41467-024-51036-y.
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.
自然进化导致栽培番茄（Solanum lycopersicum）的耐寒性降低。在此，我们对耐寒野生番茄（S. habrochaites）和敏感栽培番茄进行了 ATAC-Seq 和 RNA-Seq 的联合分析。我们发现 WRKY34 与低温胁迫下的差异染色质可及性和表达模式具有最显著的关联。我们发现 WRKY34 启动子中的 60bp 缺失导致 376 个番茄品种间转录和耐寒性的差异。该 60bp 片段包含一个 GATA 顺式调控元件，与 SWIBs 和 GATA29 结合，在低温胁迫下协同抑制 WRKY34 的表达。此外，WRKY34 通过调控转录和蛋白水平干扰 CBF 冷响应途径。我们的研究结果强调了顺式调控区域多态性及其对作物进化过程中染色质结构和基因表达的影响的重要性。
