Computational identification of cold-specific regulatory genes using a Chinese cabbage microarray

Abstract

We identified 1,915 candidate genes in Chinese cabbage (<em>Brassica rapa</em>) that are related to cold biosynthesis by comparison of gene expression in spring and winter cultivars of Chinese cabbage during four cold treatment stages by 300K microarray analysis. Using this method, we screened 835 ortholog genes, 87 transcription factors, and 29 pathway genes associated with cold-related biosynthesis. The transcription factor genes were classified into nine groups and genes associated with cold-related pathways were characterized by gene mapping and phylogenetic analysis. Finally, by comparison of pathway network transcription factor, and ortholog genes we identified seven cold-related genes and verified their differential expression using reverse transcription-polymerase chain reaction. These genes may play regulatory roles in cold resistance or metabolism during cold biosynthesis. Although further validation and characterization of these genes is required, our results illustrate the potential usefulness of this screening method using Chinese cabbage microarrays.