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Background  In order to identify genes that might confer and maintain freeze resistance of winter wheat, a comparative transcriptome analysis was performed between control and 4 wk cold-acclimated crown tissue of two winter wheat lines that differ in field freeze survival. The lines, generated by azide mutagenesis of the winter wheat cultivar 'Winoka' were designated FR (75% survival) and FS (30% survival). Using two winter lines for this comparative analysis removed the influence of differential expression of the vernalization genes and allowed our study to focus on  Cbf  genes located within the  Fr-A2  allele independent of the effect of the closely mapped  Vrn  allele.    Results  Vernalization genes, ( Vrn-A1 ,  B1  and  D1 ), and the transcription factor gene,  TaVrt-2 , were up-regulated to the same extent in FR and FS lines with cold acclimation thus confirming that azide mutagenesis had not modified the winter habitat of the lines. One category of  Cbf  genes, ( Cbf-2 , - A22  and B-22) reflected an increase in level of expression with cold acclimation in both FR and FS lines. Another category of  Cbf  genes ( Cbf-3 , - 5 , - 6 , - 12 , - 14  and - 19 ) were differentially expressed between cold-acclimated FR and FS lines relative to the non-acclimated controls. Comparison of expression patterns of the two categories of  Cbf  genes with the expression patterns of a set of ABA-dependent and -independent  Cor/Lea  genes revealed similar patterns of expression for this sample of  Cor/Lea  genes with that for  Cbf-2  and  -22 . This pattern of expression was also exhibited by the  Vrn  genes.    Conclusion  Some  Cor/Lea  genes may be co-regulated by the  Vrn  genes during cold acclimation and the  Vrn  genes may also control the expression of  Cbf-2, -A22 and -B22 . The increased freeze survival by the FR line and the increase in expression levels of wheat  Cbf  genes,  Cbf-3 , - 5 , - 6 , - 12 , - 14  and - 19  with cold acclimation in the FR line suggests a possible gain of function mutation resulting in higher levels of expression of these  Cbf  genes and increased freeze survival.

bmc plant biology

Cbf genes of the Fr-A2 allele are differentially regulated between long-term cold acclimated crown tissue of freeze-resistant and – susceptible, winter wheat mutant lines