Transcriptome Analysis During Cold Acclimation

Wheat CBF gene expression is temporal and upregulated at least two-fold by LT (Kume et al. 2005). The first upregulation occurs within 1–4 h, which might correspond to the rapid response to LT, while the second upregulation occurs between 2 and 3 weeks after the start of cold acclimation. Maintenance of a high CBF transcript level in freezing tolerant cultivars might represent a long-term effect of cold acclimation (Kume et al. 2005). Effects of long-term LT treatment on gene expression profiles could be distinct from rapid changes in response to cold stress. A comprehensive image of transcriptome alteration in cells and tissues of common wheat during cold acclimation and subsequent freezing stress conditions is not yet available. The above-ground tissues of wheat plants become wilted and wither under freezing conditions. However, cold-acclimated seedlings of freezing tolerant wheat cultivars rapidly recover from freezing stress and develop new shoots from surviving meristems of the crown tissues (Ohno et al. 2001). Therefore, biologically important events in the development of freezing tolerance should occur in the crown tissues.

Fig. 27.1 Cold stress signaling pathways in common wheat. Low temperature leads to accumulation of transcription factors (indicated by ovals) through ABA-dependent and -independent pathways. Specific binding of each transcription factor to cis-acting elements (indicated by boxes) activates Cor/Lea gene expression. TaMYB13 activates fructan biosynthesis-related genes

Freezing stress treatment significantly alters gene expression profiles of more than 400 genes in the crown tissues of cold-acclimated wheat plants (Skinner 2009). This transcriptome analysis revealed that 68 genes, including CBF, WRKY and zinc finger transcription factor genes, were more than fivefold upregulated by freezing stress. The upregulated genes also encoded kinases, phosphatases, calcium trafficking-related proteins and glycosyltransferases. This observation implied the presence of genetic variation among wheat cultivars in the ability to alleviate the damage to crowns exposed to freezing stress (Skinner 2009). Thus, many genes besides the CBF and Cor/Lea genes presumably participate in each step to develop freezing tolerance in the crown tissues of wheat.

To identify other LT-responsive genes related with cold acclimation in hexaploid wheat, we compared comprehensive gene expression patterns of a synthetic hexaploid line under normal and LT conditions using a wheat 38k DNA microarray (Yokota et al. 2015). For hybridization, total RNA samples were extracted from 3-week-old seedling leaves exposed to LT for 12 weeks, and from crown tissues exposed to LT for 6 weeks. The microarray analyses showed that TaWRKY45, TaWRKY72, and TaMYB73 transcription factor genes and two fructan synthesisrelated genes, Ta1FFT and Ta6SFT, were highly upregulated by long-term LT treatment, in addition to a number of Cor/Lea genes (Yokota et al. 2015). The transcript accumulation levels of these upregulated genes reflected the freezing tolerance levels of two distinct lines of synthetic hexaploid wheat. Our observations suggest that, in addition to COR/LEA proteins, the WRKY and MYB transcription factors and fructan biosynthesis play important roles in development of freezing tolerance.

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