Transcriptome Analysis of a cbf3 Mutant By RNA-Seq in Brachypodium distachyon

C-repeat binding factors (CBFs) are transcription factors that play key regulatory roles in plant cold acclimation process. Silencing of the putative Brachypodium distachyon BdCBF3 gene in RNAi mutant cbf3 plants results in significant reduction in plant survival rates after exposure to freezing temperatures. RNA-seq transcriptomic analysis was conducted using the wild type and cbf3 mutant plants under both normal (23°C) and cold conditions (4°C). Differential gene expression analysis identified 460, 3213, 2839 and 1871 genes exhibiting different expression levels by pairwise comparisons of cbf3 (23°C) versus WT (23°C), WT (23°C) versus WT (4°C), cbf3 (23°C) versus cbf3 (4°C), and cbf3 (4°C) versus WT (4°C), respectively. Combined analyses of differentially expressed genes detected in the cbf3 (23°C) vs. cbf3 (4°C) and the WT (23°C) vs. WT (4°C) were compared together and three gene categories were classified as BdCBF3-dependent, -independent or -compensatory cold-responsive genes. These differentially expressed genes were enriched in several biological pathways and will be targets for further investigations.