Transcriptome profiling of the chilling response in wheat spikes: II, Response to short-term cold exposure

In this paper we use transcriptome profiling to compare the 4 h and 12 h chilling response in young microspore stage spikes of two wheat lines with contrasting chilling tolerance: chilling-sensitive Wyalkatchem (Wk) and tolerant Young (Yng). In contrast to the previously published paper (4-days chilling), the shorter overnight chilling treatment allowed us to focus on the diversification of early regulatory and metabolic processes in the two wheat lines. The transcriptome results show significant quantitative and qualitative differences in gene expression at the two time points. After 4 h, Wk shows significantly more differentially expressed genes (DEGs) compared to Yng, but a large proportion of these genes are repressed. In Yng, the 4 h cold response is more restrained and most DEGs are cold-induced. After 12 h, the DEG numbers are more comparable between the two lines. GO enrichment analysis was used to identify and compare cold-affected gene functions. After 4 h chilling treatment, genes involved in lipid, sugar, and cell wall metabolism, as well as hormone signalling (SAUR, PP2C, calcium signalling) were mainly repressed in sensitive line Wk, while changes in regulatory factors (APO1, FAR-1, SKP-1) were most notable in tolerant Yng. At both the 4 h and 12 h time points several transcription factors are affected by chilling (Myb, Zinc-finger, bHLH), but the individual genes differ between both wheat lines. After 12 h chilling, LEA genes were induced in Wk only. After 12 h chilling, several SAUR genes are repressed in both wheat lines. Comparison of the response to chilling of lipid metabolism genes indicates that membrane modification starts earlier in tolerant Yng compared to Wk. In contrast, genes involved in deposition of cuticular wax are activated earlier in Wk compared to Yng, but there are significant differences in the response of both wheat lines. Induction of CBF/DREB factors involved in mounting the cold acclimation response occurs earlier in cold-tolerant Yng. The data presented in this paper provide new insights about dynamic and qualitative differences in chilling responses between chilling sensitive and tolerant wheat lines, as well as differences in the kinetics of establishing chilling acclimation.