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When rice gets the chills: Comparative transcriptome profiling at germination shows WRKY transcription factors responses.

Rice is vital for food security. Due to its tropical origin, rice suffers from cold that affects the entire plant lifecycle. Key genes have been identified involved in cold tolerance. WRKY transcription factors have been reported downstream of cold signaling cascade and regulate cold responsive genes. WRKYs generally are downstream of MAPK cascade and can act together with VQ proteins to regulate stress-responsive genes. Chilling treatment was applied at germination in two rice genotypes (tolerant and sensitive). Shoots at S3 stage were collected for RNA-seq to identify OsWRKY, OsMAPKs and OsVQs expression. Relationships among MAPKs, WRKYs and VQs were predicted through correlation analysis. OsWRKY transcriptional regulation was predicted by in silico analysis of cis-regulatory elements. 39 OsWRKYs were differentially expressed. OsWRKY21, OsWRK24 and OsWRKY69 are potential positive while OsWRKY10, OsWRK47, OsWRKY62, OsWRKY72 and OsWRKY77 are potential negative regulators of chilling tolerance. 12 OsMAPKs were differentially expressed. OsMAPKs were downregulated and negatively correlated with the upregulated OsWRKYs in the tolerant genotype. 19 OsVQs were differentially expressed, 3 and 6 OsVQs were positively correlated with OsWRKYs in the tolerant and sensitive genotype, respectively. Seven differentially expressed OsWRKYs presented cold responsive elements in its promoters and five upregulated OsWRKYs in the tolerant genotype showed W-box motif. Chilling causes changes in OsWRKY, OsMAPK and OsVQ gene expression at germination. OsWRKYs may not act downstream of MAPK cascade to coordinate chilling tolerance. OsWRKYs may act with VQs to regulate chilling tolerance. Candidate OsWRKY are correlated and present W-box in its promoter suggesting an auto-regulation mechanism.