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

作者：Rui Zhang, Xiaohui Xi, Xinyi Chen, Yi Wang, Ming Zhou · 发表于：Frontiers in Plant Science · 年份：2024 · DOI：10.3389/fpls.2024.1451403 · 被引用次数：7 · 研究领域：Genetic Mapping and Diversity in Plants and Animals、GABA and Rice Research、Plant Gene Expression Analysis

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 TFs 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, five 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 r...