Transcriptome profiling of the chilling response in wheat spikes: I, acclimation response to long-term chilling treatment

Chilling conditions coinciding with the early stage of flowering cause significant yield losses in temperate climate zone wheat crops. Progress in breeding for chilling tolerance has been hampered by a lack in understanding of the physiological basis of the problem. Phenotyping methods have therefore used grain yield related traits, rather than traits that focus directly on the cause of the problem. In this study we used transcriptome profiling to gain a better understanding about the differences in cold acclimation in young microspore (YM) stage wheat spikes of a chilling-tolerant (Young, Yng) and a chilling-sensitive (Wyalkatchem, Wk) wheat variety. Gene expression studies were carried out for a longer-term (4-days) controlled environment cyclic chilling treatment (21 °C day/−3 °C night). The accompanying paper addresses the short-term response to chilling using the same treatment cycle (4 h and 12 h), enabling us to compare the regulatory and cold acclimation responses. We used Gene Ontology (GO) enrichment analysis to objectively identify processes that differ in the chilling response of both wheat lines. The transcriptome analysis reveals significant quantitative and qualitative differences between the two wheat lines. Most notable are differences in the expression of genes involved in lipid metabolism and cuticular wax deposition. Several genes involved in auxin metabolism and signalling were enriched in chilling-tolerant Yng compared to Wk, including genes of the Small Auxin Up-Regulated (SAUR) gene family. The results indicate that the chilling tolerant and sensitive wheat varieties differ significantly in their adaption of lipid metabolism and cuticular wax deposition to chilling temperatures. This suggests that controlling membrane fluidity and permeability of the cell wall play a crucial role in controlling chilling tolerance. The results also indicate that auxin metabolism and signalling differentiate the chilling tolerant and sensitive wheat lines, suggesting that this hormone may play an important role in establishing chilling tolerance.