Transcriptomic analysis of barley plant responses to cold stress

Previous molecular and genomic studies have shown that several group genes in Arabidopsis with various functions are induced by cold stresses, and that various transcription factors are involved in the regulation of stress-inducible genes which contribute to an increase in cold tolerance. Here, we present the results of transcriptome analysis indicating the existence of genes of potential importance to cold stress and multiple low-temperature regulatory pathways in addition to the cold response pathway in barley. To identify cold-responsive genes, global expression profiling was performed on barley plants subjected to stress treatments of 4°C in root. RNA samples were collected separately from leaves and roots after 4 weeks cold stress treatment. The expression profiling was conducted with barley Genome Affymetrix microarray with probe sets for approximately 53,030 "unigenes". A total of 2577 genes with greater than 2-fold change over control were identified as being cold responsive, with transcripts for 185 genes increasing ten-fold or more at one or more time points during 4 weeks experiment. These results suggest that extensive up/down-regulation of gene expression occurs during cold acclimation, and about 7% of the transcriptome is sensitive to regulation by common stress conditions. AGL19 was found to be the most important regulator in the vernaliztion response pathway. FAD7 was found to be very active in many pathways, indicating the gene can protect plant cell from cold damage. FAD7 is under the control of Salicylate and the existing of Propyl Gallate which acted as antioxidant suppressed the expression of FAD7. Other genes, ICE1, LTI30 and RAB18 showed a highly expressed in root cooling treatment and have significant strong links with other cold responsive genes which can enhance the cold and freezing tolerance in Barley. SEX1 was identified to be the main regulator in the starch catabolic process, and was highly expressed in root cooling treatment. This observation suggests that fructan metabolism may also occur during root cooling, offering further potential for the control of sucrose gradients in the leaf