The identification of novel and differentially expressed apple-tree genes under low-temperature stress using high-throughput Illumina sequencing.

Low temperature is a major environmental constraint on the production of apples worldwide. An apple rootstock with high cold tolerance was selected to identify genes related to stress tolerance. The transcriptional profiles of the genes in the leaves were examined after various intervals of exposure to cold stress. We obtained three libraries of 14,219, 11,176 and 16,116 tag-mapped predicted coding sequences at three time points (0, 1 and 6 h) during cold stress. In the two time periods, which were from 0 to 1 h and from 1 to 6 h, 139 and 1,085 genes were upregulated, and 1,499 and 381 genes were downregulated, respectively. These groups included a large number of unknown genes. The distribution of genes indicated cold adaptation in the plant. Most of the differential expression genes (DEGs) had temporal specificity and significantly different expression changes at different time points. The classification of DEGs by GO category and KEGG pathway analysis revealed that the DEGs are involved in numerous biological pathways, including metabolism, plant-pathogen interaction and signal transduction. Eleven randomly selected tag-mapped genes were examined by qRT-PCR. The results of the qRT-PCR were in accordance with the transcriptional profiles. The most upregulated gene (MDP0000198054) from 0 to 1 h encodes a dehydration-responsive element-binding protein/C-repeat factor (DREB/CBF). In this study, MDP0000198054 and related genes involved in the cold stress response were discussed. These results could provide new insights into the stress tolerance mechanisms of apple rootstocks.