When rice gets the chills: comparative transcriptome profiling at germination shows WRKY transcription factor...

Area of Science:

• Plant Science
• Molecular Biology
• Genetics

Background:

• Rice, crucial for global food security, is highly susceptible to cold stress due to its tropical origins.
• Cold temperatures significantly impair rice growth and development throughout its life cycle.
• Understanding the genetic basis of cold tolerance is essential for developing resilient rice varieties.

Purpose of the Study:

• To identify key rice WRKY, MAPK, and VQ genes involved in chilling tolerance at the germination stage.
• To elucidate the regulatory relationships among these gene families under cold stress.
• To predict potential auto-regulatory mechanisms of OsWRKY genes in chilling response.

Main Methods:

• Differential gene expression analysis using RNA-sequencing (RNA-seq) on two rice genotypes (tolerant and sensitive) subjected to chilling treatment.
• Correlation analysis to predict relationships between OsWRKY, OsMAPK, and OsVQ gene expression.
• In silico analysis of cis-regulatory elements in OsWRKY promoters to predict transcriptional regulation.

Main Results:

• 39 OsWRKY genes were differentially expressed, with specific candidates identified as potential positive (e.g., OsWRKY21) or negative (e.g., OsWRKY10) regulators of chilling tolerance.
• 12 OsMAPK genes were differentially expressed, showing downregulation and negative correlation with upregulated OsWRKYs in the tolerant genotype.
• 19 OsVQ genes were differentially expressed, with varying correlations with OsWRKYs across genotypes. Seven OsWRKYs possessed cold-responsive elements, and five upregulated OsWRKYs in the tolerant genotype contained W-box motifs.

Conclusions:

• Chilling stress significantly alters the expression of OsWRKY, OsMAPK, and OsVQ genes during rice germination.
• OsWRKYs may not function downstream of the MAPK cascade but could collaborate with VQ proteins to regulate chilling tolerance.
• The presence of W-box motifs in upregulated OsWRKY promoters suggests a potential auto-regulation mechanism contributing to chilling tolerance in rice.