Identification of novel C-repeat binding factor (CBF) genes in rye (Secale cereale L.) and expression studies

Although rye is one of the most cold-tolerant species among temperate cereals, its huge and complex genome has prevented us from identifying agronomically useful genes. However, advances in high-throughput sequencing technology are making it increasingly possible to investigate its genome. The C-repeat binding factor (CBF) gene family controls cold tolerance in plants and its members are well conserved among eudicots and monocots, among which there are diverse homologs. Despite its large genome, only a small number of CBF genes have been identified in rye. In this study, we explored high-throughput sequencing data of the rye genome and identified 12 novel CBF genes. Sequence analyses revealed that these genes contain signature sequences of the CBF family. Chromosomal localization of the genes by PCR using wheat–rye addition lines showed that most of these are located on the long arm of chromosome 5, but also on the long arm of chromosomes 2 and 6. On the basis of comparative analyses of CBF family members in the Triticeae, CBF proteins were divided into several groups according to phylogenetic relationship and conserved motifs. Light is essential to fully induce CBF gene expression and there is specificity in the response to different types of abiotic stresses in ScCBF genes. The results of our study will assist investigations of CBF genes in the Triticeae and the mechanism of cold tolerance through the CBF-dependent pathway in plants.