Comparative transcriptome profiling of freezing stress responsiveness in two contrasting Chinese cabbage genotypes, Chiifu and Kenshin

Freezing stress is a major factor affecting plant growth, crop productivity, and the geographical distribution of plants. To identify freezing-responsive genes in Brassica rapa, we analyzed transcriptome profiles of two contrasting inbred lines with different geographic origins, Chiifu and Kenshin, in control and -4 A degrees C-treated leaves. A total of 3,301 genes were differentially expressed between Chiifu and Kenshin upon freezing treatment. Among these, 67 and 1,633 genes were specifically expressed in Chiifu and Kenshin, respectively. An ortholog (BrTPP1) of Arabidopsis trehalose-6-phosphate phosphatase 1 (TPP1) was specifically and highly induced in Chiifu by freezing treatment. However, most cold-responsive genes, including CBF pathway-related genes, showed similar patterns of expression between Chiifu and Kenshin. Many genes involved in stress responses (i.e., to freezing temperatures) were intrinsically and specifically expressed in Chiifu, which is tolerant of freezing temperatures. The results suggest that the CBF pathway is not the main factor conferring freezing tolerance to Chiifu, but genes that are expressed prior to cold acclimation, along with other regulatory genes, may play important roles in freezing tolerance.