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ORIGINAL RESEARCH article

Front. Plant Sci.
Sec. Plant Abiotic Stress
Volume 15 - 2024 | doi: 10.3389/fpls.2024.1451403
This article is part of the Research Topic Surviving and Thriving: How Crops Perceive and Respond to Temperature Stress View all 11 articles

Comparing time-series transcriptomes between chilling-resistant and -susceptible rice reveals potential transcription factors responding to chilling stress

Provisionally accepted
Rui Zhang Rui Zhang 1Xiaohui Xi Xiaohui Xi 1Xinyi Chen Xinyi Chen 1Yi Wang Yi Wang 1Ming Zhou Ming Zhou 1,2*
  • 1 State Key Laboratory of Plant Environmental Resilience, College of Life Sciences, Zhejiang University, Hangzhou, Jiangsu Province, China
  • 2 Institute of Nuclear-Agricultural Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Jiangsu Province, China

The final, formatted version of the article will be published soon.

    Low temperature is one of the most important environmental factors that inhibits rice growth and grain yield. Transcription factors (TFs) play crucial roles in chilling acclimation by regulating gene expression. However, transcriptional dynamics and key regulators responding to low temperature remain largely unclear in rice. In this study, a transcriptome-based comparative analysis was performed to explore genome-wide gene expression profiles between a chilling-resistant cultivar DC90 and a chilling-susceptible cultivar 9311 at a series of time points under low temperature treatment and recovery condition. A total of 3,590 differentially expressed genes (DEGs) between two cultivars were determined and divided into 12 co-expression modules. Meanwhile, several biological processes participating in the chilling response such as abscisic acid (ABA) responses, water deprivation, protein metabolic processes and transcription regulator activities were revealed. Through weighted gene co-expression network analysis (WGCNA), 15 hub transcription factors involved in chilling conditions were identified. Further, we used the gene regulatory network (GRN) to evaluate the top 50 TFs, which might have potential roles responding to chilling stress. Finally, 5 TFs, including a C-repeat binding factor (OsCBF3), a zinc finger-homeodomain protein (OsZHD8), a tandem zinc finger protein (OsTZF1), carbon starved anther (CSA) and indeterminate gametophyte1 (OsIG1) were identified as crucial candidates responsible for chilling resistance in rice. This study deepens our understanding in the gene regulation networks of chilling stress in rice, and offers potential gene resources for breeding climate-resilient crops.

    Keywords: comparative transcriptome, gene regulatory network, Transcription Factors, chilling stress, rice

    Received: 19 Jun 2024; Accepted: 17 Jul 2024.

    Copyright: © 2024 Zhang, Xi, Chen, Wang and Zhou. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

    * Correspondence: Ming Zhou, State Key Laboratory of Plant Environmental Resilience, College of Life Sciences, Zhejiang University, Hangzhou, 310058, Jiangsu Province, China

    Disclaimer: All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article or claim that may be made by its manufacturer is not guaranteed or endorsed by the publisher.