Natural variation of WRKY33 promoter causes cold sensitivity in cultivated tomato

Natural variations in cis-regulatory regions often affect crop phenotypes by altering gene expression. However, the mechanism of how promoter mutations affect gene expression and crop stress tolerance is still poorly understood. Here, we found that the transcripts of WRKY33 are almost unchanged in cold-sensitive cultivated tomato Solanum lycopersicum L. cv Ailsa Craig (AC), but are significantly induced in cold-tolerant wild tomato relatives S. habrochaites LA1777 and S. pennellii LA0716 under cold stress. We identified that mutation of the critical W-box in SlWRKY33 promoter results in the loss of self-transcription function of SlWRKY33 under cold stress. Furthermore, overexpressing SlWRKY33 confers cold tolerance through activation of various signaling pathways in cultivated tomato. In addition, heat- and Botrytis-induced WRKY33s expression in both wild and cultivated tomatoes are independent of the critical W-box variation. Our findings suggest natural variation in cis-regulatory regions is a crucial reason for resistance loss during tomato domestication.