Screening of transcription factors of apple cold resistant dwarfing rootstock in response to cold stress

Transcription factors (TF) play a crucial role in the plant's response to stress. Young in vitro plantlets of the cold -resistant apple dwarf rootstock '71-3-150' were exposed to time -course cold stress (4 C) of 0, 2, 6, 12, and 24 h, and their transcriptome was examined by RNA sequencing. In four comparison groups (0 vs. 2 h, 0 vs. 6 h, 0 vs. 12 h, 0 vs. 24 h), 83, 98, 115, and 136 differentially expressed TF genes were identified, respectively, totaling 226 unique genes. These genes included eight new individuals without annotations in the apple reference genome v1.0 and belonged to 32 TF families in which most were members of WRKY, AP2/ERF, bHLH, MYB, NAC, HSF, and CO -like. All TF genes identified showed four expression patterns on the whole. Eighty-seven and 84 genes were classified as continuously downregulated and upregulated patterns, respectively. Fifteen genes were repressed during 0-6 h and then upregulated with a peak at 12 h. The rest of the 40 genes indicated an upregulated trend before 6 h of cold treatment and then a downregulated trend after 6 h. Only ten and nine common genes were found in the four comparison groups with continuously up- or downregulating patterns, respectively. However, no common gene showing a fluctuant expression was found among the four comparison groups. This suggested that members of the same TF family express in various patterns. The observed dynamic changes of expression levels of various TF genes under time -course cold stress implied multiple and intricate transcription regulation processes of the rootstock that could be related to important responsive mechanisms to adapt to cold stress. Additionally, we used qRT-PCR to validate that the transcriptome data was reliable and repeatable.